httpcore-4.0.1.jar
httpmime-4.0.3.jar
intervalstore-v1.0.jar
-jabaws-min-client-2.2.0.jar
+jabaws-min-client-NO_LOG4J-2.2.0.jar Apache license
java-json.jar
jaxrpc.jar
jersey-client-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
jswingreader-0.3.jar Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
libquaqua64-8.0.jnilib.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
libquaqua-8.0.jnilib.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
-log4j-1.2.8.jar
+log4j-1.2-api-2.16.0.jar Apache license version 2.0
+log4j-api-2.16.0.jar Apache license version 2.0
+log4j-core-2.16.0.jar Apache license version 2.0
+log4j-slf4j18-impl-2.16.0.jar Apache license version 2.0
mail.jar
miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt
quaqua-filechooser-only-8.0.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
regex.jar
saaj.jar
servlet-api-3.1.jar
-slf4j-api-1.7.7.jar
-slf4j-log4j12-1.7.7.jar
+slf4j-api-1.7.32.jar MIT license - https://opensource.org/licenses/mit-license.php
+slf4j-log4j12-1.7.32.jar MIT license - https://opensource.org/licenses/mit-license.php
vamsas-client.jar
VAqua5-patch.jar This is a patched version of VAqua v5 (latest stable) by Alan Snyder et al. GPLv3 with Classpath exception, also includes contributions from Quaqua: http://violetlib.org/vaqua/overview.html - see doc/patching-vaqua.txt for patch details, and http://issues.jalview.org/browse/JAL-2988 for details of the bug that the patch addresses.
VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
jaxb-api-2.3.1.jar CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1
jaxb-runtime-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
jaxws-api-2.3.1.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
-Jmol-14.6.4_2016.10.26-no_netscape.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
jsr311-api-1.1.1.jar CDDL License - http://www.opensource.org/licenses/cddl1.php
mimepull-1.9.11.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
policy-2.7.6.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
-slf4j-api-1.7.26.jar MIT License - https://opensource.org/licenses/mit-license.php
-slf4j-log4j12-1.7.26.jar MIT License - https://opensource.org/licenses/mit-license.php
stax-ex-1.8.1.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
stax2-api-4.2.jar The BSD License - http://www.opensource.org/licenses/bsd-license.php
streambuffer-1.5.7.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
// Import channel_properties
channelDir = string("${jalviewDir}/${channel_properties_dir}/${propertiesChannelName}")
channelGradleProperties = string("${channelDir}/channel_gradle.properties")
+ channelPropsFile = string("${channelDir}/${resource_dir}/${channel_props}")
overrideProperties(channelGradleProperties, false)
// local build environment properties
// can be "projectDir/local.properties"
'--add-modules', j11modules
]
*/
- } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
- JAVA_INTEGER_VERSION = JAVA_VERSION
- libDir = j11libDir
- libDistDir = j11libDir
- compile_source_compatibility = JAVA_VERSION
- compile_target_compatibility = JAVA_VERSION
+ } else if (JAVA_VERSION.equals("17")) {
+ JAVA_INTEGER_VERSION = string("17")
+ libDir = j17libDir
+ libDistDir = j17libDir
+ compile_source_compatibility = 17
+ compile_target_compatibility = 17
getdownAltJavaMinVersion = string(findProperty("getdown_alt_java11_min_version"))
getdownAltJavaMaxVersion = string(findProperty("getdown_alt_java11_max_version"))
getdownAltMultiJavaLocation = string(findProperty("getdown_alt_java11_txt_multi_java_location"))
- eclipseJavaRuntimeName = string("JavaSE-11")
+ eclipseJavaRuntimeName = string("JavaSE-17")
/* compile without modules -- using classpath libraries
additional_compiler_args += [
'--module-path', modules_compileClasspath.asPath,
}
getdownWebsiteResourceFilenames += "${getdownAppDistDir}/${getdown_build_properties}"
+ copy {
+ from channelPropsFile
+ into getdownWebsiteDir
+ }
+ getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
+
// set some getdown_txt_ properties then go through all properties looking for getdown_txt_...
def props = project.properties.sort { it.key }
if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
from launchJvl
from getdownLauncher
from "${getdownWebsiteDir}/${getdown_build_properties}"
+ from "${getdownWebsiteDir}/${channel_props}"
if (file(getdownLauncher).getName() != getdown_launcher) {
rename(file(getdownLauncher).getName(), getdown_launcher)
}
-1.8.3-1.2.10_FJVL
+1.8.3-1.2.11_FJVL
-1.8.3-1.2.10_JVL
+1.8.3-1.2.11_JVL
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.10_FJVL</version>
+ <version>1.8.3-1.2.11_FJVL</version>
</parent>
<artifactId>getdown-ant</artifactId>
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.10_FJVL</version>
+ <version>1.8.3-1.2.11_FJVL</version>
</parent>
<artifactId>getdown-core</artifactId>
import jalview.bin.HiDPISetting;
import jalview.bin.MemorySetting;
-//import com.install4j.api.launcher.Variables;
+import jalview.util.LaunchUtils;
import com.threerings.getdown.util.*;
// avoid ambiguity with java.util.Base64 which we can't use as it's 1.8+
continue;
}
}
+
+ // use saved preferences if no cmdline args
+ LaunchUtils.loadChannelProps(getAppDir());
+ if (LaunchUtils.getBooleanUserPreference(MemorySetting.CUSTOMISED_SETTINGS)) {
+ if (jvmmempc == null) {
+ jvmmempc = LaunchUtils.getUserPreference(MemorySetting.MEMORY_JVMMEMPC);
+ }
+ if (jvmmemmax == null) {
+ jvmmemmax = LaunchUtils.getUserPreference(MemorySetting.MEMORY_JVMMEMMAX);
+ }
+ }
// add the memory setting from jvmmempc and jvmmemmax
long maxMemLong = -1;
/*
+
+ private static String ADJUSTMENT_MESSAGE = null;
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* @author bsoares
*
*/
+
public class MemorySetting
{
public static final String MAX_HEAPSIZE_PERCENT_PROPERTY_NAME = "jvmmempc";
private static final long NOMEM_MAX_HEAPSIZE_GB_DEFAULT = 8;
+ public static final String NS = "MEMORY";
+
+ public static final String CUSTOMISED_SETTINGS = NS
+ + "_CUSTOMISED_SETTINGS";
+
+ public static final String MEMORY_JVMMEMPC = NS + "_"
+ + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME.toUpperCase();
+
+ public static final String MEMORY_JVMMEMMAX = NS + "_"
+ + MAX_HEAPSIZE_PROPERTY_NAME.toUpperCase();
+
protected static boolean logToClassChecked = false;
+ public static String memorySuffixes = "bkmgt"; // order of the suffixes is
+ // important!
+
public static long getMemorySetting()
{
return getMemorySetting(null, null);
}
+ public static long getMemorySetting(String jvmmemmaxarg,
+ String jvmmempcarg)
+ {
+ return getMemorySetting(jvmmemmaxarg, jvmmempcarg, true, false);
+ }
+
/**
* Decide on appropriate memory setting for Jalview based on the two arguments
* values: jvmmempc - the maximum percentage of total physical memory to
* @param jvmmempcarg
* Max percentage of physical memory to use. Defaults to "90".
*
+ * @param useProps
+ * boolean to decide whether to look at System properties.
+ *
* @return The amount of memory (in bytes) to allocate to Jalview
*/
public static long getMemorySetting(String jvmmemmaxarg,
- String jvmmempcarg)
+ String jvmmempcarg, boolean useProps, boolean quiet)
{
// actual Xmx value-to-be
long maxMemLong = -1;
+ clearAdjustmentMessage();
// (absolute) jvmmaxmem setting, start with default
long memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- if (jvmmemmaxarg == null)
+ if (jvmmemmaxarg == null && useProps)
{
jvmmemmaxarg = System.getProperty(MAX_HEAPSIZE_PROPERTY_NAME);
}
String jvmmemmax = jvmmemmaxarg;
if (jvmmemmax != null && jvmmemmax.length() > 0)
{
- long multiplier = 1;
- switch (jvmmemmax.toLowerCase().substring(jvmmemmax.length() - 1))
- {
- case "t":
- multiplier = 1099511627776L; // 2^40
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "g":
- multiplier = 1073741824; // 2^30
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "m":
- multiplier = 1048576; // 2^20
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "k":
- multiplier = 1024; // 2^10
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "b":
- multiplier = 1; // 2^0
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- default:
- break;
- }
-
// parse the arg
try
{
- memmax = Long.parseLong(jvmmemmax);
+ memmax = memoryStringToLong(jvmmemmax);
+ if (memmax == 0)
+ {
+ throw (new NumberFormatException("Not allowing 0"));
+ }
} catch (NumberFormatException e)
{
memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
- + "') badly formatted, using default ("
- + MAX_HEAPSIZE_GB_DEFAULT + "g).");
- }
-
- // apply multiplier if not too big (i.e. bigger than a long)
- if (Long.MAX_VALUE / memmax < multiplier)
- {
- memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- System.out.println("MemorySetting Property '"
- + MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
- + ") too big, using default (" + MAX_HEAPSIZE_GB_DEFAULT
- + "g).");
- }
- else
- {
- memmax = multiplier * memmax;
+ + "') badly formatted or 0, using default ("
+ + MAX_HEAPSIZE_GB_DEFAULT + "g).", quiet);
}
// check at least minimum value (this accounts for negatives too)
if (memmax < APPLICATION_MIN_MEMORY)
{
memmax = APPLICATION_MIN_MEMORY;
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
+ ") too small, using minimum (" + APPLICATION_MIN_MEMORY
- + ").");
+ + ").", quiet);
}
}
else
{
// no need to warn if no setting
- // System.out.println("MemorySetting Property '" + maxHeapSizeProperty
+ // adjustmentMessage("MemorySetting Property '" + maxHeapSizeProperty
// + "' not
// set.");
}
// get max percent of physical memory, starting with default
float percent = MAX_HEAPSIZE_PERCENT_DEFAULT;
- if (jvmmempcarg == null)
+ if (jvmmempcarg == null && useProps)
{
jvmmempcarg = System.getProperty(MAX_HEAPSIZE_PERCENT_PROPERTY_NAME);
}
{
if (jvmmempc != null)
{
- float trypercent = Float.parseFloat(jvmmempc);
- if (0 < trypercent && trypercent <= 100f)
+ int trypercent = Integer.parseInt(jvmmempc);
+ if (0 <= trypercent && trypercent <= 100)
{
percent = trypercent;
}
else
{
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME
- + "' should be in range 1..100. Using default " + percent
- + "%");
+ + "' should be in range 0..100. Using default " + percent
+ + "%", quiet);
}
}
} catch (NumberFormatException e)
{
- System.out.println("MemorySetting property '"
+ setAdjustmentMessage("MemorySetting property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg
- + ") badly formatted");
+ + ") badly formatted", quiet);
}
// catch everything in case of no com.sun.management.OperatingSystemMXBean
{
mempc = physicalMem - LEAVE_FREE_MIN_MEMORY;
reducedmempc = true;
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg
+ ") too large. Leaving free space for OS and reducing to ("
- + mempc + ").");
+ + mempc + ").", quiet);
}
// check for minimum application memsize
{
if (reducedmempc)
{
- System.out.println("Reduced MemorySetting (" + mempc
+ setAdjustmentMessage("Reduced MemorySetting (" + mempc
+ ") too small. Increasing to application minimum ("
- + APPLICATION_MIN_MEMORY + ").");
+ + APPLICATION_MIN_MEMORY + ").", quiet);
}
else
{
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' ("
+ jvmmempcarg + ") too small. Using minimum ("
- + APPLICATION_MIN_MEMORY + ").");
+ + APPLICATION_MIN_MEMORY + ").", quiet);
}
mempc = APPLICATION_MIN_MEMORY;
}
{
// not enough memory for application, just try and grab what we can!
mempc = physicalMem;
- System.out.println(
+ setAdjustmentMessage(
"Not enough physical memory for application. Ignoring MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' ("
+ jvmmempcarg
+ "). Using maximum memory available ("
- + physicalMem + ").");
+ + physicalMem + ").",
+ quiet);
}
} catch (Throwable t)
{
memoryPercentError = true;
- System.out.println(
- "Problem calling GetMemory.getPhysicalMemory(). Likely to be problem with com.sun.management.OperatingSystemMXBean");
+ setAdjustmentMessage(
+ "Problem calling GetMemory.getPhysicalMemory(). Likely to be problem with com.sun.management.OperatingSystemMXBean",
+ quiet);
t.printStackTrace();
}
// == null))
&& memmax > NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE)
{
- System.out.println(
+ setAdjustmentMessage(
"Capping maximum memory to " + NOMEM_MAX_HEAPSIZE_GB_DEFAULT
- + "g due to failure to read physical memory size.");
+ + "g due to failure to read physical memory size.",
+ quiet);
memmax = NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
}
return maxMemLong;
}
+ public static boolean isValidMemoryString(String text)
+ {
+ if (text.length() > 0)
+ {
+ char lastChar = text.charAt(text.length() - 1);
+ char[] otherChars = text.substring(0, text.length() - 1)
+ .toCharArray();
+ for (char c : otherChars)
+ {
+ if (c < '0' || c > '9')
+ {
+ return false;
+ }
+ }
+ if ((lastChar < '0' || lastChar > '9') && memorySuffixes
+ .indexOf(Character.toLowerCase(lastChar)) == -1)
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ public static long memoryStringToLong(String memString)
+ throws NumberFormatException
+ {
+ if (!isValidMemoryString(memString)) // not valid
+ {
+ throw (new NumberFormatException("Not a valid memory string"));
+ }
+ char suffix = Character
+ .toLowerCase(memString.charAt(memString.length() - 1));
+ if ('0' <= suffix && suffix <= '9') // no suffix
+ {
+ return Long.valueOf(memString);
+ }
+ if (memorySuffixes.indexOf(suffix) == -1) // suffix is unknown
+ {
+ return -1;
+ }
+
+ long multiplier = (long) Math.pow(2,
+ memorySuffixes.indexOf(suffix) * 10); // note order of suffixes in
+ // memorySuffixes important
+ // here!
+ // parse the arg. NumberFormatExceptions passed on to calling method
+ long mem = Long
+ .parseLong(memString.substring(0, memString.length() - 1));
+ if (mem == 0)
+ {
+ return 0;
+ }
+
+ // apply multiplier only if result is not too big (i.e. bigger than a long)
+ if (Long.MAX_VALUE / mem > multiplier)
+ {
+ return multiplier * mem;
+ }
+ else
+ {
+ // number too big for a Long. Limit to Long.MAX_VALUE
+ System.out.println("Memory parsing of '" + memString
+ + "' produces number too big. Limiting to Long.MAX_VALUE="
+ + Long.MAX_VALUE);
+ return Long.MAX_VALUE;
+ }
+ }
+
+ public static String memoryLongToString(long mem)
+ {
+ return memoryLongToString(mem, "%.1f");
+ }
+
+ public static String memoryLongToString(long mem, String format)
+ {
+ int exponent = 0;
+ float num = mem;
+ char suffix = 'b';
+
+ for (int i = 0; i < memorySuffixes.length(); i++)
+ {
+ char s = Character.toUpperCase(memorySuffixes.charAt(i));
+ if (mem < (long) Math.pow(2, exponent + 10)
+ || i == memorySuffixes.length() - 1) // last suffix
+ {
+ suffix = s;
+ num = (float) (mem / Math.pow(2, exponent));
+ break;
+ }
+ exponent += 10;
+ }
+
+ return String.format(format, num) + suffix;
+ }
+
+ private static String ADJUSTMENT_MESSAGE = null;
+
+ private static void setAdjustmentMessage(String reason, boolean quiet)
+ {
+ ADJUSTMENT_MESSAGE = reason;
+ if (!quiet)
+ {
+ System.out.println(reason);
+ }
+ }
+
+ public static void clearAdjustmentMessage()
+ {
+ ADJUSTMENT_MESSAGE = null;
+ }
+
+ public static String getAdjustmentMessage()
+ {
+ return ADJUSTMENT_MESSAGE;
+ }
+
}
\ No newline at end of file
--- /dev/null
+package jalview.util;
+
+import java.awt.Image;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import javax.swing.ImageIcon;
+
+public class ChannelProperties
+{
+
+ public static final String CHANNEL_PROPERTIES_FILENAME = "channel.props";
+
+ private static Properties channelProps;
+
+ private static final Properties defaultProps;
+
+ private static Map<String, Image> imageMap = new HashMap<String, Image>();
+
+ private static Map<String, URL> urlMap = new HashMap<String, URL>();
+
+ private static final ArrayList<Image> iconList;
+
+ static
+ {
+ defaultProps = new Properties();
+ // these should be kept up to date, but in real life they should never
+ // actually be used anyway.
+ defaultProps.put("app_name", "Jalview");
+ defaultProps.put("banner", "/default_images/jalview_banner.png");
+ defaultProps.put("logo.16", "/default_images/jalview_logo-16.png");
+ defaultProps.put("logo.32", "/default_images/jalview_logo-32.png");
+ defaultProps.put("logo.38", "/default_images/jalview_logo-38.png");
+ defaultProps.put("logo.48", "/default_images/jalview_logo-48.png");
+ defaultProps.put("logo.64", "/default_images/jalview_logo-64.png");
+ defaultProps.put("logo.128", "/default_images/jalview_logo-128.png");
+ defaultProps.put("logo.256", "/default_images/jalview_logo-256.png");
+ defaultProps.put("logo.512", "/default_images/jalview_logo-512.png");
+ defaultProps.put("rotatable_logo.48",
+ "/default_images/rotatable_jalview_logo-38.png");
+ defaultProps.put("bg_logo.28", "/default_images/barton_group-28.png");
+ defaultProps.put("bg_logo.30", "/default_images/barton_group-30.png");
+ defaultProps.put("bg_logo.32", "/default_images/barton_group-32.png");
+ defaultProps.put("uod_banner.28", "/default_images/UoD_banner-28.png");
+ defaultProps.put("uod_banner.30", "/default_images/UoD_banner-30.png");
+ defaultProps.put("uod_banner.32", "/default_images/UoD_banner-32.png");
+ defaultProps.put("default_appbase",
+ "https://www.jalview.org/getdown/release/1.8");
+ defaultProps.put("preferences.filename", ".jalview_properties");
+
+ // load channel_properties
+ Properties tryChannelProps = new Properties();
+ URL channelPropsURL = ChannelProperties.class
+ .getResource("/" + CHANNEL_PROPERTIES_FILENAME);
+ if (channelPropsURL == null)
+ {
+ // complete failure of channel_properties, set all properties to defaults
+ System.err.println("Failed to find '/" + CHANNEL_PROPERTIES_FILENAME
+ + "' file at '"
+ + (channelPropsURL == null ? "null"
+ : channelPropsURL.toString())
+ + "'. Using class defaultProps.");
+ tryChannelProps = defaultProps;
+ }
+ else
+ {
+ try
+ {
+ InputStream channelPropsIS = channelPropsURL.openStream();
+ tryChannelProps.load(channelPropsIS);
+ channelPropsIS.close();
+ } catch (IOException e)
+ {
+ System.err.println(e.getMessage());
+ // return false;
+ }
+ }
+ channelProps = tryChannelProps;
+
+ /*
+ * The following slight palava for caching an icon list is so that all sizes of icons
+ * are the same. i.e. if there are /any/ channel_properties icons to use, then _only_
+ * use those channel_properties icons, don't mix in class default icons for missing
+ * sizes. If there are _no_ (usable) channel icons then we can use the class default icons.
+ */
+ iconList = new ArrayList<Image>();
+ List<String> sizes = Arrays.asList("16", "32", "48", "64", "128", "256",
+ "512");
+ for (String size : sizes)
+ {
+ Image logo = null;
+ // not using defaults or class props first time through
+ logo = ChannelProperties.getImage("logo." + size, null, false);
+ if (logo != null)
+ {
+ iconList.add(logo);
+ }
+ }
+ // now add the class defaults if there were no channel icons defined
+ if (iconList.size() == 0)
+ {
+ for (String size : sizes)
+ {
+ Image logo = null;
+ String path = defaultProps.getProperty("logo." + size);
+ URL imageURL = ChannelProperties.class.getResource(path);
+ ImageIcon imgIcon = imageURL == null ? null
+ : new ImageIcon(imageURL);
+ logo = imgIcon == null ? null : imgIcon.getImage();
+ if (logo != null)
+ {
+ iconList.add(logo);
+ }
+ }
+ }
+ }
+
+ protected static void loadProps(File dir)
+ {
+ File channelPropsFile = new File(dir, CHANNEL_PROPERTIES_FILENAME);
+ if (channelPropsFile.exists())
+ {
+ try
+ {
+ InputStream is = new FileInputStream(channelPropsFile);
+ channelProps.load(is);
+ } catch (FileNotFoundException e)
+ {
+ System.err.println(e.getMessage());
+ } catch (IOException e)
+ {
+ System.err.println(e.getMessage());
+ }
+ }
+ }
+
+ private static Properties channelProps()
+ {
+ return channelProps;
+ }
+
+ private static Map<String, Image> imageMap()
+ {
+ return imageMap;
+ }
+
+ private static Map<String, URL> urlMap()
+ {
+ return urlMap;
+ }
+
+ /*
+ * getProperty(key) will get property value from channel_properties for key.
+ * If no property for key is found, it will fall back to using the defaultProps defined for this class.
+ */
+ public static String getProperty(String key)
+ {
+ return getProperty(key, null, true);
+ }
+
+ /*
+ * getProperty(key, defaultVal) will get property value from channel_properties for key.
+ * If no property for key is found, it will return defaultVal and NOT fall back to the class defaultProps.
+ */
+ public static String getProperty(String key, String defaultVal)
+ {
+ return getProperty(key, defaultVal, false);
+ }
+
+ /*
+ * internal method. note that setting useClassDefaultProps=true will ignore the provided defaultVal
+ */
+ private static String getProperty(String key, String defaultVal,
+ boolean useClassDefaultProps)
+ {
+ if (channelProps() != null)
+ {
+ if (channelProps().containsKey(key))
+ {
+ return channelProps().getProperty(key,
+ useClassDefaultProps ? defaultProps.getProperty(key)
+ : defaultVal);
+ }
+ else
+ {
+ System.err.println("Failed to get channel property '" + key + "'");
+ }
+ }
+ return null;
+ }
+
+ /*
+ * getImage(key) returns the channel defined image for property key. If that is null (e.g. due to
+ * no defined channel image or the image file being corrupt/unusable/missing) it uses the image
+ * defined in defaultChannelProps
+ */
+ public static Image getImage(String key)
+ {
+ return getImage(key, null, true);
+ }
+
+ /*
+ * getImage(key, defaultImg) will get image associated with value from channel_properties for key.
+ * If no property or associated image for key is found (or is usable), it will return defaultImg
+ * and NOT fall back to the class defaultProps.
+ */
+ public static Image getImage(String key, Image defaultImg)
+ {
+ return getImage(key, defaultImg, false);
+ }
+
+ /*
+ * internal method. note that setting useClassDefaultImage=true will ignore the provided defaultImg
+ */
+ private static Image getImage(String key, Image defaultImg,
+ boolean useClassDefaultImage)
+ {
+ Image img = null;
+ if (imageMap().containsKey(key))
+ {
+ img = imageMap().get(key);
+ }
+ // Catch a previously untried or failed load
+ if (img == null)
+ {
+ String path = getProperty(key, null, useClassDefaultImage);
+ if (path == null) // no channel property or class default property (if
+ // requested)
+ {
+ return useClassDefaultImage ? null : defaultImg;
+ }
+
+ URL imageURL = ChannelProperties.class.getResource(path);
+ ImageIcon imgIcon = imageURL == null ? null : new ImageIcon(imageURL);
+ img = imgIcon == null ? null : imgIcon.getImage();
+ if (img == null)
+ {
+ System.err.println(
+ "Failed to load channel image " + key + "=" + path);
+ if (!useClassDefaultImage)
+ {
+ return defaultImg;
+ }
+ }
+ else
+ {
+ imageMap().put(key, img);
+ urlMap.put(key, imageURL);
+ }
+ }
+ return img;
+ }
+
+ /*
+ * Public method to get the URL object pointing to a cached image.
+ */
+ public static URL getImageURL(String key)
+ {
+ if (getImage(key) != null)
+ {
+ if (urlMap().containsKey(key))
+ {
+ return urlMap().getOrDefault(key, null);
+ }
+ System.err.println(
+ "Do not use getImageURL(key) before using getImage(key...)");
+ }
+ return null;
+ }
+
+ /*
+ * Get a List of Icon images of different sizes.
+ */
+ public static ArrayList<Image> getIconList()
+ {
+ return iconList;
+ }
+}
--- /dev/null
+package jalview.util;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.Properties;
+
+public class LaunchUtils
+{
+
+ public static void loadChannelProps(File dir)
+ {
+ ChannelProperties.loadProps(dir);
+ }
+
+ private static Properties userPreferences = null;
+
+ public static String getUserPreference(String key)
+ {
+ if (userPreferences == null)
+ {
+ String channelPrefsFilename = ChannelProperties
+ .getProperty("preferences.filename");
+ if (channelPrefsFilename == null)
+ {
+ return null;
+ }
+ File propertiesFile = new File(System.getProperty("user.home"),
+ channelPrefsFilename);
+ if (!propertiesFile.exists())
+ {
+ return null;
+ }
+ try
+ {
+ userPreferences = new Properties();
+ userPreferences.load(new FileInputStream(propertiesFile));
+ } catch (FileNotFoundException e)
+ {
+ // didn't find user preferences file
+ return null;
+ } catch (IOException e)
+ {
+ System.err.println(e.getMessage());
+ return null;
+ }
+ }
+ return userPreferences.getProperty(key);
+ }
+
+ public static boolean getBooleanUserPreference(String key)
+ {
+ return Boolean.parseBoolean(getUserPreference(key));
+ }
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Pattern;
+
+public class StringUtils
+{
+ private static final Pattern DELIMITERS_PATTERN = Pattern
+ .compile(".*='[^']*(?!')");
+
+ private static final char PERCENT = '%';
+
+ private static final boolean DEBUG = false;
+
+ /*
+ * URL encoded characters, indexed by char value
+ * e.g. urlEncodings['='] = urlEncodings[61] = "%3D"
+ */
+ private static String[] urlEncodings = new String[255];
+
+ /**
+ * Returns a new character array, after inserting characters into the given
+ * character array.
+ *
+ * @param in
+ * the character array to insert into
+ * @param position
+ * the 0-based position for insertion
+ * @param count
+ * the number of characters to insert
+ * @param ch
+ * the character to insert
+ */
+ public static final char[] insertCharAt(char[] in, int position,
+ int count, char ch)
+ {
+ char[] tmp = new char[in.length + count];
+
+ if (position >= in.length)
+ {
+ System.arraycopy(in, 0, tmp, 0, in.length);
+ position = in.length;
+ }
+ else
+ {
+ System.arraycopy(in, 0, tmp, 0, position);
+ }
+
+ int index = position;
+ while (count > 0)
+ {
+ tmp[index++] = ch;
+ count--;
+ }
+
+ if (position < in.length)
+ {
+ System.arraycopy(in, position, tmp, index, in.length - position);
+ }
+
+ return tmp;
+ }
+
+ /**
+ * Delete
+ *
+ * @param in
+ * @param from
+ * @param to
+ * @return
+ */
+ public static final char[] deleteChars(char[] in, int from, int to)
+ {
+ if (from >= in.length || from < 0)
+ {
+ return in;
+ }
+
+ char[] tmp;
+
+ if (to >= in.length)
+ {
+ tmp = new char[from];
+ System.arraycopy(in, 0, tmp, 0, from);
+ to = in.length;
+ }
+ else
+ {
+ tmp = new char[in.length - to + from];
+ System.arraycopy(in, 0, tmp, 0, from);
+ System.arraycopy(in, to, tmp, from, in.length - to);
+ }
+ return tmp;
+ }
+
+ /**
+ * Returns the last part of 'input' after the last occurrence of 'token'. For
+ * example to extract only the filename from a full path or URL.
+ *
+ * @param input
+ * @param token
+ * a delimiter which must be in regular expression format
+ * @return
+ */
+ public static String getLastToken(String input, String token)
+ {
+ if (input == null)
+ {
+ return null;
+ }
+ if (token == null)
+ {
+ return input;
+ }
+ String[] st = input.split(token);
+ return st[st.length - 1];
+ }
+
+ /**
+ * Parses the input string into components separated by the delimiter. Unlike
+ * String.split(), this method will ignore occurrences of the delimiter which
+ * are nested within single quotes in name-value pair values, e.g. a='b,c'.
+ *
+ * @param input
+ * @param delimiter
+ * @return elements separated by separator
+ */
+ public static String[] separatorListToArray(String input,
+ String delimiter)
+ {
+ int seplen = delimiter.length();
+ if (input == null || input.equals("") || input.equals(delimiter))
+ {
+ return null;
+ }
+ List<String> jv = new ArrayList<>();
+ int cp = 0, pos, escape;
+ boolean wasescaped = false, wasquoted = false;
+ String lstitem = null;
+ while ((pos = input.indexOf(delimiter, cp)) >= cp)
+ {
+ escape = (pos > 0 && input.charAt(pos - 1) == '\\') ? -1 : 0;
+ if (wasescaped || wasquoted)
+ {
+ // append to previous pos
+ jv.set(jv.size() - 1, lstitem = lstitem + delimiter
+ + input.substring(cp, pos + escape));
+ }
+ else
+ {
+ jv.add(lstitem = input.substring(cp, pos + escape));
+ }
+ cp = pos + seplen;
+ wasescaped = escape == -1;
+ // last separator may be in an unmatched quote
+ wasquoted = DELIMITERS_PATTERN.matcher(lstitem).matches();
+ }
+ if (cp < input.length())
+ {
+ String c = input.substring(cp);
+ if (wasescaped || wasquoted)
+ {
+ // append final separator
+ jv.set(jv.size() - 1, lstitem + delimiter + c);
+ }
+ else
+ {
+ if (!c.equals(delimiter))
+ {
+ jv.add(c);
+ }
+ }
+ }
+ if (jv.size() > 0)
+ {
+ String[] v = jv.toArray(new String[jv.size()]);
+ jv.clear();
+ if (DEBUG)
+ {
+ System.err.println("Array from '" + delimiter
+ + "' separated List:\n" + v.length);
+ for (int i = 0; i < v.length; i++)
+ {
+ System.err.println("item " + i + " '" + v[i] + "'");
+ }
+ }
+ return v;
+ }
+ if (DEBUG)
+ {
+ System.err.println(
+ "Empty Array from '" + delimiter + "' separated List");
+ }
+ return null;
+ }
+
+ /**
+ * Returns a string which contains the list elements delimited by the
+ * separator. Null items are ignored. If the input is null or has length zero,
+ * a single delimiter is returned.
+ *
+ * @param list
+ * @param separator
+ * @return concatenated string
+ */
+ public static String arrayToSeparatorList(String[] list, String separator)
+ {
+ StringBuffer v = new StringBuffer();
+ if (list != null && list.length > 0)
+ {
+ for (int i = 0, iSize = list.length; i < iSize; i++)
+ {
+ if (list[i] != null)
+ {
+ if (v.length() > 0)
+ {
+ v.append(separator);
+ }
+ // TODO - escape any separator values in list[i]
+ v.append(list[i]);
+ }
+ }
+ if (DEBUG)
+ {
+ System.err
+ .println("Returning '" + separator + "' separated List:\n");
+ System.err.println(v);
+ }
+ return v.toString();
+ }
+ if (DEBUG)
+ {
+ System.err.println(
+ "Returning empty '" + separator + "' separated List\n");
+ }
+ return "" + separator;
+ }
+
+ /**
+ * Converts a list to a string with a delimiter before each term except the
+ * first. Returns an empty string given a null or zero-length argument. This
+ * can be replaced with StringJoiner in Java 8.
+ *
+ * @param terms
+ * @param delim
+ * @return
+ */
+ public static String listToDelimitedString(List<String> terms,
+ String delim)
+ {
+ StringBuilder sb = new StringBuilder(32);
+ if (terms != null && !terms.isEmpty())
+ {
+ boolean appended = false;
+ for (String term : terms)
+ {
+ if (appended)
+ {
+ sb.append(delim);
+ }
+ appended = true;
+ sb.append(term);
+ }
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Convenience method to parse a string to an integer, returning 0 if the
+ * input is null or not a valid integer
+ *
+ * @param s
+ * @return
+ */
+ public static int parseInt(String s)
+ {
+ int result = 0;
+ if (s != null && s.length() > 0)
+ {
+ try
+ {
+ result = Integer.parseInt(s);
+ } catch (NumberFormatException ex)
+ {
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Compares two versions formatted as e.g. "3.4.5" and returns -1, 0 or 1 as
+ * the first version precedes, is equal to, or follows the second
+ *
+ * @param v1
+ * @param v2
+ * @return
+ */
+ public static int compareVersions(String v1, String v2)
+ {
+ return compareVersions(v1, v2, null);
+ }
+
+ /**
+ * Compares two versions formatted as e.g. "3.4.5b1" and returns -1, 0 or 1 as
+ * the first version precedes, is equal to, or follows the second
+ *
+ * @param v1
+ * @param v2
+ * @param pointSeparator
+ * a string used to delimit point increments in sub-tokens of the
+ * version
+ * @return
+ */
+ public static int compareVersions(String v1, String v2,
+ String pointSeparator)
+ {
+ if (v1 == null || v2 == null)
+ {
+ return 0;
+ }
+ String[] toks1 = v1.split("\\.");
+ String[] toks2 = v2.split("\\.");
+ int i = 0;
+ for (; i < toks1.length; i++)
+ {
+ if (i >= toks2.length)
+ {
+ /*
+ * extra tokens in v1
+ */
+ return 1;
+ }
+ String tok1 = toks1[i];
+ String tok2 = toks2[i];
+ if (pointSeparator != null)
+ {
+ /*
+ * convert e.g. 5b2 into decimal 5.2 for comparison purposes
+ */
+ tok1 = tok1.replace(pointSeparator, ".");
+ tok2 = tok2.replace(pointSeparator, ".");
+ }
+ try
+ {
+ float f1 = Float.valueOf(tok1);
+ float f2 = Float.valueOf(tok2);
+ int comp = Float.compare(f1, f2);
+ if (comp != 0)
+ {
+ return comp;
+ }
+ } catch (NumberFormatException e)
+ {
+ System.err
+ .println("Invalid version format found: " + e.getMessage());
+ return 0;
+ }
+ }
+
+ if (i < toks2.length)
+ {
+ /*
+ * extra tokens in v2
+ */
+ return -1;
+ }
+
+ /*
+ * same length, all tokens match
+ */
+ return 0;
+ }
+
+ /**
+ * Converts the string to all lower-case except the first character which is
+ * upper-cased
+ *
+ * @param s
+ * @return
+ */
+ public static String toSentenceCase(String s)
+ {
+ if (s == null)
+ {
+ return s;
+ }
+ if (s.length() <= 1)
+ {
+ return s.toUpperCase();
+ }
+ return s.substring(0, 1).toUpperCase() + s.substring(1).toLowerCase();
+ }
+
+ /**
+ * A helper method that strips off any leading or trailing html and body tags.
+ * If no html tag is found, then also html-encodes angle bracket characters.
+ *
+ * @param text
+ * @return
+ */
+ public static String stripHtmlTags(String text)
+ {
+ if (text == null)
+ {
+ return null;
+ }
+ String tmp2up = text.toUpperCase();
+ int startTag = tmp2up.indexOf("<HTML>");
+ if (startTag > -1)
+ {
+ text = text.substring(startTag + 6);
+ tmp2up = tmp2up.substring(startTag + 6);
+ }
+ // is omission of "<BODY>" intentional here??
+ int endTag = tmp2up.indexOf("</BODY>");
+ if (endTag > -1)
+ {
+ text = text.substring(0, endTag);
+ tmp2up = tmp2up.substring(0, endTag);
+ }
+ endTag = tmp2up.indexOf("</HTML>");
+ if (endTag > -1)
+ {
+ text = text.substring(0, endTag);
+ }
+
+ if (startTag == -1 && (text.contains("<") || text.contains(">")))
+ {
+ text = text.replaceAll("<", "<");
+ text = text.replaceAll(">", ">");
+ }
+ return text;
+ }
+
+ /**
+ * Answers the input string with any occurrences of the 'encodeable'
+ * characters replaced by their URL encoding
+ *
+ * @param s
+ * @param encodable
+ * @return
+ */
+ public static String urlEncode(String s, String encodable)
+ {
+ if (s == null || s.isEmpty())
+ {
+ return s;
+ }
+
+ /*
+ * do % encoding first, as otherwise it may double-encode!
+ */
+ if (encodable.indexOf(PERCENT) != -1)
+ {
+ s = urlEncode(s, PERCENT);
+ }
+
+ for (char c : encodable.toCharArray())
+ {
+ if (c != PERCENT)
+ {
+ s = urlEncode(s, c);
+ }
+ }
+ return s;
+ }
+
+ /**
+ * Answers the input string with any occurrences of {@code c} replaced with
+ * their url encoding. Answers the input string if it is unchanged.
+ *
+ * @param s
+ * @param c
+ * @return
+ */
+ static String urlEncode(String s, char c)
+ {
+ String decoded = String.valueOf(c);
+ if (s.indexOf(decoded) != -1)
+ {
+ String encoded = getUrlEncoding(c);
+ if (!encoded.equals(decoded))
+ {
+ s = s.replace(decoded, encoded);
+ }
+ }
+ return s;
+ }
+
+ /**
+ * Answers the input string with any occurrences of the specified (unencoded)
+ * characters replaced by their URL decoding.
+ * <p>
+ * Example: {@code urlDecode("a%3Db%3Bc", "-;=,")} should answer
+ * {@code "a=b;c"}.
+ *
+ * @param s
+ * @param encodable
+ * @return
+ */
+ public static String urlDecode(String s, String encodable)
+ {
+ if (s == null || s.isEmpty())
+ {
+ return s;
+ }
+
+ for (char c : encodable.toCharArray())
+ {
+ String encoded = getUrlEncoding(c);
+ if (s.indexOf(encoded) != -1)
+ {
+ String decoded = String.valueOf(c);
+ s = s.replace(encoded, decoded);
+ }
+ }
+ return s;
+ }
+
+ /**
+ * Does a lazy lookup of the url encoding of the given character, saving the
+ * value for repeat lookups
+ *
+ * @param c
+ * @return
+ */
+ private static String getUrlEncoding(char c)
+ {
+ if (c < 0 || c >= urlEncodings.length)
+ {
+ return String.valueOf(c);
+ }
+
+ String enc = urlEncodings[c];
+ if (enc == null)
+ {
+ try
+ {
+ enc = urlEncodings[c] = URLEncoder.encode(String.valueOf(c),
+ "UTF-8");
+ } catch (UnsupportedEncodingException e)
+ {
+ enc = urlEncodings[c] = String.valueOf(c);
+ }
+ }
+ return enc;
+ }
+
+ public static int firstCharPosIgnoreCase(String text, String chars)
+ {
+ int min = text.length() + 1;
+ for (char c : chars.toLowerCase().toCharArray())
+ {
+ int i = text.toLowerCase().indexOf(c);
+ if (0 <= i && i < min)
+ {
+ min = i;
+ }
+ }
+ return min < text.length() + 1 ? min : -1;
+ }
+}
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.10_FJVL</version>
+ <version>1.8.3-1.2.11_FJVL</version>
</parent>
<artifactId>getdown-launcher</artifactId>
_getdown = getdown;
_msgs = msgs;
+ String[] hostPortAuthUser = ProxyUtil.jalviewProxyProperties(getdown._app);
+ String host = hostPortAuthUser[0];
+ String port = hostPortAuthUser[1];
+ boolean proxyAuth = Boolean.parseBoolean(hostPortAuthUser[2]);
+ String username = hostPortAuthUser[3];
+
setLayout(new VGroupLayout());
setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
add(new SaneLabelField(get("m.configure_proxy")));
JPanel row = new JPanel(new GridLayout());
row.add(new SaneLabelField(get("m.proxy_host")), BorderLayout.WEST);
row.add(_host = new SaneTextField());
+ _host.setText(host);
add(row);
row = new JPanel(new GridLayout());
row.add(new SaneLabelField(get("m.proxy_port")), BorderLayout.WEST);
row.add(_port = new SaneTextField());
+ _port.setText(port);
add(row);
add(new Spacer(5, 5));
row = new JPanel(new GridLayout());
row.add(new SaneLabelField(get("m.proxy_auth_required")), BorderLayout.WEST);
_useAuth = new JCheckBox();
+ _useAuth.setSelected(proxyAuth);
row.add(_useAuth);
add(row);
row = new JPanel(new GridLayout());
row.add(new SaneLabelField(get("m.proxy_username")), BorderLayout.WEST);
_username = new SaneTextField();
- _username.setEnabled(false);
+ _username.setText(username);
+ _username.setEnabled(_useAuth.isSelected());
row.add(_username);
add(row);
row = new JPanel(new GridLayout());
row.add(new SaneLabelField(get("m.proxy_password")), BorderLayout.WEST);
_password = new SanePasswordField();
- _password.setEnabled(false);
+ _password.setEnabled(_useAuth.isSelected());
row.add(_password);
add(row);
package com.threerings.getdown.launcher;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
+import java.io.InputStream;
import java.io.PrintStream;
import java.net.Authenticator;
import java.net.HttpURLConnection;
import java.util.Iterator;
import java.util.ServiceLoader;
+import jalview.util.LaunchUtils;
+
import ca.beq.util.win32.registry.RegistryKey;
import ca.beq.util.win32.registry.RegistryValue;
import ca.beq.util.win32.registry.RootKey;
port = hostPort[1];
}
+ // look in jalview_properties
+ String[] hostPortAuthUser = jalviewProxyProperties(app);
+ host = hostPortAuthUser[0];
+ port = hostPortAuthUser[1];
+ boolean proxyAuth = Boolean.parseBoolean(hostPortAuthUser[2]);
+ String username = hostPortAuthUser[3];
+
if (StringUtil.isBlank(host)) {
return false;
}
// yay, we found a proxy configuration, configure it in the app
- initProxy(app, host, port, null, null);
+ initProxy(app, host, port, username, null);
return true;
}
+ public static String[] jalviewProxyProperties(Application app) {
+ String host = null;
+ String port = null;
+ boolean proxyAuth = false;
+ String username = null;
+ LaunchUtils.loadChannelProps(app.getAppDir());
+ if (LaunchUtils.getBooleanUserPreference("USE_PROXY")) {
+ host = LaunchUtils.getUserPreference("PROXY_SERVER_HTTPS");
+ port = LaunchUtils.getUserPreference("PROXY_PORT_HTTPS");
+ if (StringUtil.isBlank(host)) {
+ host = LaunchUtils.getUserPreference("PROXY_SERVER");
+ port = LaunchUtils.getUserPreference("PROXY_PORT");
+ }
+ proxyAuth = LaunchUtils.getBooleanUserPreference("PROXY_AUTH");
+ if (proxyAuth) {
+ username = LaunchUtils.getUserPreference("PROXY_AUTH_USERNAME");
+ }
+ }
+ return new String[]{ host, port, String.valueOf(proxyAuth), username };
+ }
+
public static boolean canLoadWithoutProxy (URL rurl)
{
log.info("Testing whether proxy is needed, via: " + rurl);
public static void initProxy (Application app, String host, String port,
String username, String password)
{
+System.out.println("**** initProxy(app, '"+host+"', "+port+", '"+username+"', "+(password==null?"null":"*x"+password.length())+")");
// check whether we have saved proxy credentials
String appDir = app.getAppDir().getAbsolutePath();
ServiceLoader<ProxyAuth> loader = ServiceLoader.load(ProxyAuth.class);
if [ x$JVLVERSION != x ]; then
export VERSION=$JVLVERSION
else
- export VERSION=1.8.3-1.2.10_JVL
+ export VERSION=1.8.3-1.2.11_JVL
fi
if [ x${VERSION%_JVL} = x$VERSION ]; then
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
<packaging>pom</packaging>
- <version>1.8.3-1.2.10_FJVL</version>
+ <version>1.8.3-1.2.11_FJVL</version>
<name>getdown</name>
<description>An application installer and updater.</description>
getdown_alt_java8_max_version = 01089999
getdown_alt_java11_min_version = 11000000
getdown_alt_java11_max_version =
-#getdown_alt_java11_txt_multi_java_location = [windows-amd64] /getdown/jre/windows-jre11.jar,[linux-amd64] /getdown/jre/linux-jre11.tgz,[mac os x] /getdown/jre/macos-jre11.tgz
-#getdown_alt_java8_txt_multi_java_location = [windows-amd64] /getdown/jre/windows-jre1.8.tgz,[linux-amd64] /getdown/jre/linux-jre1.8.tgz,[mac os x] /getdown/jre/macos-jre1.8.tgz
+#getdown_alt_java11_txt_multi_java_location = [windows-amd64] /getdown/jre/jre-11-windows-x64.zip,[linux-amd64] /getdown/jre/jre-11-linux-x64.zip,[mac os x] /getdown/jre/jre-11-mac-x64.zip
+#getdown_alt_java8_txt_multi_java_location = [windows-amd64] /getdown/jre/jre-8-windows-x64.zip,[linux-amd64] /getdown/jre/jre-8-linux-x64.zip,[mac os x] /getdown/jre/jre-8-mac-x64.zip
jre_installs_dir = ~/buildtools/jre
j8libDir = j8lib
flexmark_css = utils/doc/github.css
channel_properties_dir = utils/channels
+channel_props = channel.props
install4j_home_dir = ~/buildtools/install4j8
install4j_copyright_message = ...
<mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
<mapID target="pdbjmol" url="html/features/jmol.html"/>
<mapID target="chimera" url="html/features/chimera.html"/>
+ <mapID target="pymol" url="html/features/pymol.html"/>
<mapID target="chimera.annotxfer" url="html/features/chimera.html#annotxfer"/>
<mapID target="varna" url="html/features/varna.html"/>
<mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
</tocitem>
<tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
- <tocitem text="PDB Structure Chooser" target="pdbchooser" />
+ <tocitem text="PDB & 3D-Beacons Structure Chooser" target="pdbchooser" />
<tocitem text="Jmol Viewer" target="pdbjmol" />
- <tocitem text="Chimera Viewer" target="chimera" />
+ <tocitem text="Chimera Viewer" target="chimera" />
+ <tocitem text="Pymol Viewer" target="pymol" />
</tocitem>
<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
</head>
<body>
<p>
- <strong>The Chimera Viewer</strong>
+ <strong>The Chimera and ChimeraX Viewers</strong>
</p>
<p>
Since Jalview 2.8.2, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a>
(http://www.cgl.ucsf.edu/chimera/) can be used for viewing
structures opened via the <a href="structurechooser.html"><strong>"View
- Structure Data.."</strong> dialog</a>.
+ Structure Data.."</strong> dialog</a>. In Jalview 2.11.2, support
+ was also added for ChimeraX.
</p>
<p>
You can set a default choice of Jmol or Chimera structure viewer in
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>The Pymol PDB Viewer</title>
+</head>
+<body>
+ <p>
+ <strong>The Pymol Viewer</strong>
+ </p>
+ <p>
+ In Jalview 2.11.2, support was added for <a href="https://pymol.org/2/">Pymol</a>
+ (https://pymol.org/2/) to be used for viewing
+ structures opened via the <a href="structurechooser.html"><strong>"View
+ Structure Data.."</strong> dialog</a>.
+ </p>
+ <p>
+ You can configure Pymol as your preferred structure viewer in
+ <a href="preferences.html#structure"> Preferences</a>. You can also
+ optionally specify the path to the Pymol program here (if it differs
+ from the standard paths searched by Jalview).<br /> <strong>Jalview
+ requires Pymol's RPC interface, which is not available in older
+ versions of the Pymol community edition.<br />Please make sure your
+ version of Pymol is up to date.
+ </strong>
+ </p>
+ <p>
+ If you save your Jalview session as a project file, the state of any
+ open Pymol windows will also be saved, and can be reopened by
+ loading the project file on any machine with Pymol installed.
+ </p>
+ <p>
+ <strong>Known Limitations</strong><br /> Jalview provides an easy way
+ to employ Pymol for linked analysis of sequences and structures in the
+ same way as <a href="chimera.html">Chimera and ChimeraX</a>. There are
+ some limitations, however:
+ </p>
+ <ul>
+ <li>Pymol does not support some forms of legacy structural data
+ (e.g. the 1A70 C-alpha only PDB file included in the Jalview example
+ project).</li>
+ <li>Pymol to Jalview communication does not support transfer of
+ properties or highlighting sequence regions corresponding to
+ structure selections or mouse-overs in Pymol.</li>
+ </ul>
+ <p>
+ Basic screen operations (see <a
+ href="https://pymol.org/dokuwiki/doku.php?id=mouse">Pymol Wiki</a> at
+ https://pymol.org/dokuwiki/doku.php?id=mouse
+ for full details).
+ <table border="1">
+ <tr>
+ <td><strong>Action</strong></td>
+ <td><strong>Windows</strong></td>
+ <td><strong>Unix</strong></td>
+ <td><strong>Mac/OSX</strong></td>
+ </tr>
+ <tr>
+ <td>Rotate View</td>
+ <td>Left Click and Drag</td>
+ <td>Left Click and Drag</td>
+ <td>Left Click and Drag</td>
+ </tr>
+ <tr>
+ <td>Zoom</td>
+ <td>Right Click<br> drag mouse up or down
+ </td>
+ <td>Right Click<br>drag mouse up or down
+ </td>
+ <td>cmd or Right + Click and drag mouse up or down, <br>or
+ use mouse scroll button
+ </td>
+ </tr>
+ <tr>
+ <td>Move Origin</td>
+ <td>Middle Button + Drag</td>
+ <td>Middle Button and drag</td>
+ <td>alt + Click<br> and drag
+ </td>
+ </tr>
+ <tr>
+ <td>Select Residues</td>
+ <td>Ctrl + Click (and drag to select a region)</td>
+ <td>Ctrl + Click (and drag)</td>
+ <td>Ctrl + Click (and drag)</td>
+ </tr>
+ </table>
+ </p>
+ <p>
+ <strong>Jalview Controls</strong>
+ <p>The Jalview Pymol View window has up to five menus:</p>
+ <ul>
+ <li><Strong>File<br>
+ </strong>
+ <ul>
+ <li><strong>View Mapping<br>
+ </strong><em> Opens a text window showing the alignment between the
+ residues corresponding to alpha-carbon atoms in the PDB
+ structure and the residues in the associated sequence.</em></li>
+ </ul></li>
+ <li><strong>View</strong>
+ <ul>
+ <li><strong>Show Chains<br>
+ </strong><em>Select which of the PDB file's chains (if more than
+ one) are to be displayed.</em></li>
+ <li><strong>Colour by ..<br></strong><em>Submenu
+ allowing specific alignment views to be selected for
+ colouring associated chains in the structure display. This
+ menu contains all the alignment views associated with the
+ structure view, with those used to colour the view indicated
+ by ticks. Addditionally, it contains the following menu
+ entries:</em>
+ <ul>
+ <li><strong>Select many views<br></strong><em>When
+ this option is enabled, selecting an alignment view adds
+ it to the set used to colour the structures. Use this
+ when colouring structures related to a number of
+ alignments involving different domains or chains which
+ are shown in the same structure view.</em></li>
+ <li><strong>Select all views<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will add all associated views to
+ the set used to colour the structure display.</em></li>
+ <li><strong>Invert selection<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will replace the current set of
+ views with any remaining views not currently used to
+ colour the structure display.</em></li>
+ </ul></li>
+ </ul>
+ <li><strong>Colours<br>
+ </strong>
+ <ul>
+ <li><strong>By Sequence<br>
+ </strong><em> Colours each residue in the structure with the colour
+ of its corresponding residue in the associated sequence as
+ rendered in the associated alignment views, including any
+ UniProt sequence features or region colourings.<br />Pick
+ which of the associated alignment views are used to colour
+ the structures using the <strong>View→Colour
+ by ..</strong> sub menu.
+ </em><br> Residues which only exist in the PDB structure are
+ coloured white if they are insertions (relative to the
+ associated sequence in the alignment) and grey if they are N
+ or C terminal flanks outside the region mapped to the
+ alignment window's sequence.</em></li>
+ <li><strong>By Chain<br>
+ </strong><em>Uses Pymol's 'spectrum(chain)' command to apply a
+ different colour to each chain.</em></li>
+ <li><strong>Charge & Cysteine<br>
+ </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid
+ or Glutamic Acid) residues in red, and cationic (Lysine or
+ Arginine) residues in blue.</em></li>
+ <li><strong>Colour with Pymol<br></strong><em>Defers
+ any colouring operations to Pymol. Select this if you want
+ to use the Pymol scripting interface or menu to modify the
+ view directly.</em></li>
+ <li><strong>Standard and User Defined Jalview
+ colourschemes.<br>
+ </strong><em>The remaining entries apply the colourschemes available
+ from the standard and user defined <a
+ href="../colourSchemes/index.html">amino acid
+ colours</a>.
+ </em></li>
+ </ul></li>
+ <li><strong>Pymol<br>
+ </strong><em>This pulldown menu provides access to Pymol's capabilities from Jalview.</em>
+ <ul>
+ <li><strong><a name="sAlign">Align</a> <br> </strong><em>
+ When selected, the associated alignment will be used to
+ superimpose all the structures in the view onto the first
+ structure in the alignment. The regions used to calculate
+ the superposition will be highlighted using the 'Cartoon'
+ rendering style, and the remaining data shown as a chain
+ trace.<br />
+ <br />
+ </em></li>
+ <li><a name="annotxfer"><strong>Write Jalview
+ features</strong></a><br /> <em>Selecting this option will create
+ new atom properties for any features currently visible in
+ the associated alignment views. This allows those atoms to
+ be selected and analysed in Pymol directly.
+ </em><br>
+ <ul><li>Feature transfer in Pymol is experimental.</li><li>To select by a particular feature use the string matching syntax:<br>
+ select foo,p.jv_helix in helix
+ </li>
+ <li>To view transferred properties use Pymol's Properties Inspector</li><li>
+ For more information see <a href="https://pymol.org/dokuwiki/doku.php?id=properties#selection_language">Property based selection in Pymol's Documentation</a>.
+ </li>
+ </ul>
+ </li>
+ </ul></li>
+ <li><strong>Help<br>
+ </strong>
+ <ul>
+ <li><strong>Pymol Help<br>
+ </strong><em>Access the Pymol Help documentation in a new browser window.
+ window.</em></li>
+ </ul></li>
+ </ul>
+ <p>
+ <strong>Pymol and Windows Firewall</strong>
+ </p>
+ Jalview and Pymol communicate using the <a href="https://pymolwiki.org/index.php/RPC">Pymol's XML-RPC over HTTP interface</a>(https://pymolwiki.org/index.php/RPC).
+
+<br> Technically this requires both Pymol and Jalview to open
+ ports on the local network, and this may be blocked by Windows
+ Firewall with a warning message such as
+ <br /> "Windows Firewall has blocked some features of this program"
+ (where the program may be java.exe or javaw.exe).
+ <br /> To allow Jalview and Pymol to interact, you may need to add
+ permission for the program to communicate over the network. This can
+ be done from the warning dialogue, or in Control Panel, Firewall
+ settings.
+</body>
+</html>
the database you want to retrieve sequences</strong> from the database
chooser.
</p>
- <img src="selectfetchdb.gif" align="left" width="480" height="204"
+ <img src="selectfetchdb.gif" align="left"
alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
<p>
The databases are shown as a tree, and ordered alphabetically;
accession ids</strong> (as a semi-colon separated list), or press the
"Example" button to paste the example accession for the
currently selected database into the retrieval box. Finally, press
- "OK" to initiate the retrieval.</li>
+ "OK" to initiate the retrieval.
+ <br />
+ For the PDB and UniProt sequence fetchers, choose the "Retrieve IDs" tab
+ to search for accession ids.</li>
</ol>
<p>If you use the Sequence Fetcher, please remember to cite the
The Structure Chooser allows you to select
3D structures to view for the currently selected set of
sequences. It is opened by selecting the <strong>"3D
- Structure Data..."</strong> option from the Sequence ID panel's <a
- href="../menus/popupMenu.html">pop-up menu</a>. The dialog
+ Structure Data..."</strong> option from the Sequence ID panel's
+ <a href="../menus/popupMenu.html">pop-up menu</a>. <br/>
+ <img src="3dstructuredata_popupmenu.png" alt="pop-up menu"/>
+ <br/>
+ The dialog
provides:
</p>
<ul>
associated with the sequence. It does this based on the sequence's
ID string, and any other associated database IDs. <br />
<br />
+ Since Jalview 2.11.2, you can also <a href="#3dbeaconssearch">initiate a search
+ of the 3D-Beacons Network</a>.
+ </p>
<p>
<strong><a name="cachedstructview">Viewing existing
structures for your sequences</a></strong>
</p>
<p>Jalview can automatically select the best structures according
to meta-data provided by the PDB. For alignments with no existing
- structure data, the 'Best Quality' structure for each sequence will
+ structure data, the 'PDBe Best Quality' structure for each sequence will
by default be selected, but clicking on the drop down menu allows
other criteria to be chosen, including Resolution (only defined for
X-Ray structures), Highest Protein Chain etc. When 'Invert' is
<br>The screenshot above shows the Structure Chooser displayed after
selecting all the sequences in the Jalview example project. If no
structures were auto-discovered, options for manually associating
- PDB records will be shown (see below).<p>
+ PDB records will be shown (see below).
+
+ <p>
+ <strong><a name="3dbeaconssearch">3D-Beacons Network Search</a></strong>
+ </p>
+ <p>
+ To initiate a search of the 3D-Beacons Network—which searches
+ across experimentally determined and predicted structure models from
+ several resources including PDBe, AlphaFold DB, SWISS-MODEL, PED, SASDB, Genome3D and
+ PDBe-KB—click on the <strong>3D-Beacons Search</strong> button at the top of the
+ Structure Chooser window.
+ <br/>
+ <img src="3dbeacons_button.png"/>
+ <br/>
+ The 3D-Beacons Network search requires UniProt references and Jalview will ask
+ to attempt to fetch these references for the selected sequences.
+ UniProt references might not always be found in which case you can revert to the PDB
+ search.
+ <br/>
+ <img src="3dbeacons_structurechooser.png"/>
+ <br/>
+ If structures are found through the 3D-Beacons network you can filter which structures
+ are shown using the drop-down filter at the top of the Structure Chooser window.
+ <br/>
+ You can view information about each related model, such as the resource providing
+ each model, in the columns displayed. You can sort the list of models by clicking on
+ column headings.
+ <br/>
+ Select and view the structures in the usual way using the <a href="viewingpdbs.html#afterviewbutton">open structure options</a> at
+ the bottom of the Structure Chooser window.
+ </p>
+
+ <p>
<strong>Exploration of meta-data for available structures</strong>
</p>
<p>Information on each structure available is displayed in columns
2.9. </em>
</p>
</body>
-</html>
\ No newline at end of file
+</html>
</head>
<body>
<p>
- <strong>Discovering and Viewing PDB Structures</strong>
+ <strong>Discovering and Viewing PDB and 3D-Beacons structures</strong>
</p>
Jalview can be used to explore the 3D structures of sequences in an
alignment by following the steps below:
menu</a> to open the <a href="structurechooser.html">Structure
Chooser</a> dialog box.
<ul>
- <li>If one or more structures exists for the given
+ <li>If one or more structures exist in the PDB for the given
sequence, the <a href="structurechooser.html">Structure
Chooser</a> dialog will open with them listed in the results
pane.
href="structurechooser.html">Structure Chooser</a> interface
will present options for manual association of PDB structures.
</li>
+ <li>
+ Since Jalview 2.11.2 you can also search the 3D-Beacons Network
+ for structures. The 3D-Beacons Network acts as a one-stop shop for protein
+ structures by combining and standardising data from several providers.
+ See <a href="structurechooser.html#3dbeaconssearch">3D-Beacons Search</a> for
+ instructions.
+ </li>
</ul>
</li>
- <li><strong>Selecting Structures</strong><br />You can select
+ <li><strong>Selecting PDB Structures</strong><br />
+ If one or more structures have been found from the PDB, you can select
the structures that you want to open and view by selecting them
with the mouse and keyboard.<br />By default, if structures were
discovered, then some will already be selected according to the
<strong>Structure Viewers in the Jalview Desktop</strong><br /> The
<a href="jmol.html">Jmol viewer</a> has been included since Jalview
2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>,
- provided it is installed and can be launched by Jalview. The default
+ provided it is installed and can be launched by Jalview. ChimeraX and PyMOL
+ support is included from Jalview 2.11.2. The default
viewer can be configured in the <a href="preferences.html#structure">Structure
tab</a> in the <strong>Tools→Preferences</strong> dialog box.
for more information.
</p>
<p>
- <img src="schooser_viewbutton.png"
- style="width: 465px; height: 81px" /><br/> <strong><a
+ <strong><a
name="afterviewbutton">Controlling where the new structures
will be shown</a></strong>
+ <br/>
+ <img src="schooser_viewbutton.png" />
<br />The Structure Chooser offers several options
- for viewing a structure. <br/><strong>New View</strong> will open a new
+ for viewing a structure. <br/>
+ The <strong>Open new structure view</strong> button will open a new
structure viewer for the selected structures, but if there are views
already open, you can select which one to use, and press the <strong>Add</strong>
button. Jalview can automatically superimpose new structures based
<tr>
<td width="60" align="center" nowrap><strong><a
id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
- <em>29/09/2021</em></strong></td>
+ <em>01/02/2022</em></strong></td>
<td align="left" valign="top">
- <ul>
- <li><!-- --></li>
- </ul>
- <em>Development</em>
+ <ul>
+ <li>
+ <!-- -->
+ </li>
+ </ul> <!-- <em>Development</em>
+ <ul>
+ <li>Updated building instructions</li>
+ </ul> -->
+
+ </td>
+ <td>
+ <ul>
+ <li>
+ TO DOCUMENT: JAL-3700,JAL-3751,JAL-3763
+ </li>
+ <li>
+ <!-- JAL-3915 -->Removed RNAview checkbox and logic from
+ Structure Preferences
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>Fixed non-fatal gradle errors during build</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
+ <em>18/01/2022</em></strong></td>
+ <td></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
+ updated by Jalview or other applications (Windows, other non
+ Unix/BSD OSs)
+ </li>
+ </ul> <em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
+ certificates.
+ </li>
+ </ul>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
+ <em>6/01/2022</em></strong></td>
+
+ <td align="left" valign="top"><em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
+ </li>
+ </ul></td>
+ <td>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
+ <em>20/12/2021</em></strong></td>
+
+ <td align="left" valign="top"><em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
+ (was log4j 1.2.x).
+ </ul> <em>Development</em>
<ul>
<li>Updated building instructions</li>
</ul></td>
Created Date;created;string;g3;80;150;85;true;false
UniProt Accession;uniprot_accession;String;g1;50;400;95;false;true
Url;model_url;String;g3;100;150;105;true;false
+Model Format;model_format;String;g3;20;60;20;true;false
Page URL;model_page_url;String;g3;100;150;105;true;false
Ensemble Sample Url;ensembl_sample_url;String;g3;100;150;105;false;false
label.web_services = Web Services
label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter.
label.let_jmol_manage_structure_colours = Let Jmol manage structure colours
-label.fetch_chimera_attributes = Fetch Chimera attributes
-label.fetch_chimera_attributes_tip = Copy Chimera attribute to Jalview feature
+label.fetch_viewer_attributes = Fetch {0} attributes
+label.fetch_viewer_attributes_tip = Copy {0} attribute to Jalview feature
label.marks_leaves_tree_not_associated_with_sequence = Marks leaves of tree not associated with a sequence
label.index_web_services_menu_by_host_site = Index web services in menu by the host site
label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up = Check this option if you want to be informed<br>when a web service URL cannot be accessed by Jalview<br>when it starts up
label.insufficient_residues = Not enough aligned residues ({0}) to perform superposition
label.create_viewer_attributes = Write Jalview features
label.create_viewer_attributes_tip = Set structure residue attributes for Jalview features
-label.attributes_set = {0} attribute values set on Chimera
+label.attributes_set = {0} attribute values set on {1}
label.sort_alignment_by_tree = Sort Alignment By Tree
label.mark_unlinked_leaves = Mark Unlinked Leaves
label.associate_leaves_with = Associate Leaves With
label.log_level_tooltip = Temporarily set the log level for this console. The log level will revert to {0} when this Java console is closed.
label.copy_to_clipboard = Copy to clipboard
label.copy_to_clipboard_tooltip = Copy all of the log text in this console to the system clipboard
+label.startup = Startup
+label.memory = Memory
+label.customise_memory_settings = Customise maximum memory settings
+label.memory_setting_text = New memory settings will only come into effect the next time you start Jalview
+label.maximum_memory_used = Maximum memory limited to both
+label.percent_of_physical_memory = Maximum percent of physical memory
+label.maximum_memory = Maximum absolute memory
+label.maximum_memory_tooltip = Enter memory as an integer number optionally followed by 'b', 'k', 'm', 'g' or 't'
+label.adjustments_for_this_computer = Adjustments for this computer
+label.memory_example_text = Maximum memory that would be used with these settings on this computer
+label.memory_example_tooltip = The memory allocated to Jalview is the smaller of the percentage of physical memory (default 90%) and the maximum absolute memory (default 32GB). If your computer's memory cannot be ascertained then the maximum absolute memory defaults to 8GB (if not customised).<br>Jalview will always try and reserve 512MB for the OS and at least 512MB for itself.
label.log_level_tooltip = Establezca temporalmente el nivel de registro para esta consola. El nivel de registro volverá a {0} cuando se cierre esta consola de Java.
label.copy_to_clipboard = Copiar en el portapapeles
label.copy_to_clipboard_tooltip = Copie todo el texto de registro en esta consola al portapapeles del sistema
+label.startup = Inicio
+label.memory = Memoria
+label.customise_memory_settings = Personalizar la configuración de memoria máxima
+label.memory_setting_text = La nueva configuración de memoria solo entrará en vigor la próxima vez que inicie Jalview
+label.maximum_memory_used = Memoria máxima limitada a ambos
+label.percent_of_physical_memory = Porcentaje máximo de memoria fÃsica
+label.maximum_memory = Memoria absoluta máxima
+label.maximum_memory_tooltip = Ingrese la memoria como un número entero seguido opcionalmente por 'b', 'k', 'm', 'g' o 't'
+label.adjustments_for_this_computer = Ajustes para esta computadora
+label.memory_example_text = Memoria máxima que se usarÃa con esta configuración en esta computadora
+label.memory_example_tooltip = La memoria asignada a Jalview es el menor entre el porcentaje de memoria fÃsica (predeterminado 90%) y la memoria absoluta máxima (predeterminado 32 GB). Si no se puede determinar la memoria de su computadora, la memoria absoluta máxima predeterminada es de 8 GB (si no está personalizada).<br>Jalview siempre intentará reservar 512 MB para el sistema operativo y al menos 512 MB para sà mismo.
import java.util.Locale;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.NoSuchElementException;
+import java.util.Set;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import jalview.bin.Cache;
import jalview.commands.RemoveGapColCommand;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.util.MapList;
import jalview.util.MappingUtils;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.NoSuchElementException;
-import java.util.Set;
-import java.util.SortedMap;
-import java.util.TreeMap;
-
/**
* grab bag of useful alignment manipulation operations Expect these to be
* refactored elsewhere at some point.
SequenceI newSeq = null;
- final MapList maplist = mapping.getMap();
- if (maplist.isContiguous() && maplist.isFromForwardStrand())
- {
- /*
- * just a subsequence, keep same dataset sequence
- */
- int start = maplist.getFromLowest();
- int end = maplist.getFromHighest();
- newSeq = seq.getSubSequence(start - 1, end);
- newSeq.setName(seqId);
- }
- else
- {
- /*
- * construct by splicing mapped from ranges
- */
- char[] seqChars = seq.getSequence();
- List<int[]> fromRanges = maplist.getFromRanges();
- int cdsWidth = MappingUtils.getLength(fromRanges);
- char[] newSeqChars = new char[cdsWidth];
+ /*
+ * construct CDS sequence by splicing mapped from ranges
+ */
+ char[] seqChars = seq.getSequence();
+ List<int[]> fromRanges = mapping.getMap().getFromRanges();
+ int cdsWidth = MappingUtils.getLength(fromRanges);
+ char[] newSeqChars = new char[cdsWidth];
- int newPos = 0;
- for (int[] range : fromRanges)
+ int newPos = 0;
+ for (int[] range : fromRanges)
+ {
+ if (range[0] <= range[1])
{
- if (range[0] <= range[1])
- {
- // forward strand mapping - just copy the range
- int length = range[1] - range[0] + 1;
- System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos,
- length);
- newPos += length;
- }
- else
+ // forward strand mapping - just copy the range
+ int length = range[1] - range[0] + 1;
+ System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos,
+ length);
+ newPos += length;
+ }
+ else
+ {
+ // reverse strand mapping - copy and complement one by one
+ for (int i = range[0]; i >= range[1]; i--)
{
- // reverse strand mapping - copy and complement one by one
- for (int i = range[0]; i >= range[1]; i--)
- {
- newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]);
- }
+ newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]);
}
}
}
else
{
- System.err.println(
- "JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):"
- + mtch.toString());
+ Cache.log.error(
+ "JAL-2154 regression: warning - found (and ignored) a duplicate CDS sequence:" + mtch.toString());
}
}
}
*/
void stopProgressBar(String msg, long handle);
+ /**
+ *
+ * @return true if the actions menu is shown for this viewer
+ */
+ boolean hasViewerActionsMenu();
+
}
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
+import org.apache.log4j.builders.appender.ConsoleAppenderBuilder;
+import org.apache.logging.log4j.core.config.Configurator;
+import org.apache.logging.log4j.core.config.builder.api.AppenderComponentBuilder;
+import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilder;
+import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilderFactory;
+import org.apache.logging.log4j.core.config.builder.impl.BuiltConfiguration;
import jalview.datamodel.PDBEntry;
import jalview.gui.Preferences;
}
try
{
- // TODO: redirect stdout and stderr here in order to grab the output of
- // the log
-
- ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
- "System.err");
- ap.setName("JalviewLogger");
- org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
+ // configure the root logger to stderr
+ ConfigurationBuilder<BuiltConfiguration> builder = ConfigurationBuilderFactory.newConfigurationBuilder();
+ AppenderComponentBuilder consoleApp = builder.newAppender("stderr", "Console");
+ builder.add(consoleApp);
+ Configurator.initialize(builder.build());
// log output
Logger laxis = Logger.getLogger("org.apache.axis");
- Logger lcastor = Logger.getLogger("org.exolab.castor");
jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
laxis.setLevel(Level.toLevel(
Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
- lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- Level.INFO.toString())));
- lcastor = Logger.getLogger("org.exolab.castor.xml");
- lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- Level.INFO.toString())));
// lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
// lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
// Level.INFO.toString())));
}
// anything else!
+ // allow https handshakes to download intermediate certs if necessary
+ System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
+
final String jabawsUrl = aparser.getValue("jabaws");
if (jabawsUrl != null)
{
import java.util.List;
import jalview.util.ChannelProperties;
+import jalview.util.LaunchUtils;
/**
* A Launcher class for Jalview. This class is used to launch Jalview from the
}
}
+ // use saved preferences if no cmdline args
+ boolean useCustomisedSettings = LaunchUtils
+ .getBooleanUserPreference(MemorySetting.CUSTOMISED_SETTINGS);
+ if (useCustomisedSettings)
+ {
+ if (jvmmempc == null)
+ {
+ jvmmempc = LaunchUtils
+ .getUserPreference(MemorySetting.MEMORY_JVMMEMPC);
+ }
+ if (jvmmemmax == null)
+ {
+ jvmmemmax = LaunchUtils
+ .getUserPreference(MemorySetting.MEMORY_JVMMEMMAX);
+ }
+ }
+
// add memory setting if not specified
boolean memSet = false;
boolean dockIcon = false;
e.printStackTrace();
}
// System.exit(0);
-
}
}
/*
+
+ private static String ADJUSTMENT_MESSAGE = null;
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* @author bsoares
*
*/
-import java.util.Locale;
-
public class MemorySetting
{
public static final String MAX_HEAPSIZE_PERCENT_PROPERTY_NAME = "jvmmempc";
private static final long NOMEM_MAX_HEAPSIZE_GB_DEFAULT = 8;
+ public static final String NS = "MEMORY";
+
+ public static final String CUSTOMISED_SETTINGS = NS
+ + "_CUSTOMISED_SETTINGS";
+
+ public static final String MEMORY_JVMMEMPC = NS + "_"
+ + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME.toUpperCase();
+
+ public static final String MEMORY_JVMMEMMAX = NS + "_"
+ + MAX_HEAPSIZE_PROPERTY_NAME.toUpperCase();
+
protected static boolean logToClassChecked = false;
+ public static String memorySuffixes = "bkmgt"; // order of the suffixes is
+ // important!
+
public static long getMemorySetting()
{
return getMemorySetting(null, null);
}
+ public static long getMemorySetting(String jvmmemmaxarg,
+ String jvmmempcarg)
+ {
+ return getMemorySetting(jvmmemmaxarg, jvmmempcarg, true, false);
+ }
+
/**
* Decide on appropriate memory setting for Jalview based on the two arguments
* values: jvmmempc - the maximum percentage of total physical memory to
* @param jvmmempcarg
* Max percentage of physical memory to use. Defaults to "90".
*
+ * @param useProps
+ * boolean to decide whether to look at System properties.
+ *
* @return The amount of memory (in bytes) to allocate to Jalview
*/
public static long getMemorySetting(String jvmmemmaxarg,
- String jvmmempcarg)
+ String jvmmempcarg, boolean useProps, boolean quiet)
{
// actual Xmx value-to-be
long maxMemLong = -1;
+ clearAdjustmentMessage();
// (absolute) jvmmaxmem setting, start with default
long memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- if (jvmmemmaxarg == null)
+ if (jvmmemmaxarg == null && useProps)
{
jvmmemmaxarg = System.getProperty(MAX_HEAPSIZE_PROPERTY_NAME);
}
String jvmmemmax = jvmmemmaxarg;
if (jvmmemmax != null && jvmmemmax.length() > 0)
{
- long multiplier = 1;
- switch (jvmmemmax.toLowerCase(Locale.ROOT).substring(jvmmemmax.length() - 1))
- {
- case "t":
- multiplier = 1099511627776L; // 2^40
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "g":
- multiplier = 1073741824; // 2^30
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "m":
- multiplier = 1048576; // 2^20
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "k":
- multiplier = 1024; // 2^10
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- case "b":
- multiplier = 1; // 2^0
- jvmmemmax = jvmmemmax.substring(0, jvmmemmax.length() - 1);
- break;
- default:
- break;
- }
-
// parse the arg
try
{
- memmax = Long.parseLong(jvmmemmax);
+ memmax = memoryStringToLong(jvmmemmax);
+ if (memmax == 0)
+ {
+ throw (new NumberFormatException("Not allowing 0"));
+ }
} catch (NumberFormatException e)
{
memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
- + "') badly formatted, using default ("
- + MAX_HEAPSIZE_GB_DEFAULT + "g).");
- }
-
- // apply multiplier if not too big (i.e. bigger than a long)
- if (Long.MAX_VALUE / memmax < multiplier)
- {
- memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- System.out.println("MemorySetting Property '"
- + MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
- + ") too big, using default (" + MAX_HEAPSIZE_GB_DEFAULT
- + "g).");
- }
- else
- {
- memmax = multiplier * memmax;
+ + "') badly formatted or 0, using default ("
+ + MAX_HEAPSIZE_GB_DEFAULT + "g).", quiet);
}
// check at least minimum value (this accounts for negatives too)
if (memmax < APPLICATION_MIN_MEMORY)
{
memmax = APPLICATION_MIN_MEMORY;
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
+ ") too small, using minimum (" + APPLICATION_MIN_MEMORY
- + ").");
+ + ").", quiet);
}
}
else
{
// no need to warn if no setting
- // System.out.println("MemorySetting Property '" + maxHeapSizeProperty
+ // adjustmentMessage("MemorySetting Property '" + maxHeapSizeProperty
// + "' not
// set.");
}
// get max percent of physical memory, starting with default
float percent = MAX_HEAPSIZE_PERCENT_DEFAULT;
- if (jvmmempcarg == null)
+ if (jvmmempcarg == null && useProps)
{
jvmmempcarg = System.getProperty(MAX_HEAPSIZE_PERCENT_PROPERTY_NAME);
}
{
if (jvmmempc != null)
{
- float trypercent = Float.parseFloat(jvmmempc);
- if (0 < trypercent && trypercent <= 100f)
+ int trypercent = Integer.parseInt(jvmmempc);
+ if (0 <= trypercent && trypercent <= 100)
{
percent = trypercent;
}
else
{
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME
- + "' should be in range 1..100. Using default " + percent
- + "%");
+ + "' should be in range 0..100. Using default " + percent
+ + "%", quiet);
}
}
} catch (NumberFormatException e)
{
- System.out.println("MemorySetting property '"
+ setAdjustmentMessage("MemorySetting property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg
- + ") badly formatted");
+ + ") badly formatted", quiet);
}
// catch everything in case of no com.sun.management.OperatingSystemMXBean
{
mempc = physicalMem - LEAVE_FREE_MIN_MEMORY;
reducedmempc = true;
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg
+ ") too large. Leaving free space for OS and reducing to ("
- + mempc + ").");
+ + mempc + ").", quiet);
}
// check for minimum application memsize
{
if (reducedmempc)
{
- System.out.println("Reduced MemorySetting (" + mempc
+ setAdjustmentMessage("Reduced MemorySetting (" + mempc
+ ") too small. Increasing to application minimum ("
- + APPLICATION_MIN_MEMORY + ").");
+ + APPLICATION_MIN_MEMORY + ").", quiet);
}
else
{
- System.out.println("MemorySetting Property '"
+ setAdjustmentMessage("MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' ("
+ jvmmempcarg + ") too small. Using minimum ("
- + APPLICATION_MIN_MEMORY + ").");
+ + APPLICATION_MIN_MEMORY + ").", quiet);
}
mempc = APPLICATION_MIN_MEMORY;
}
{
// not enough memory for application, just try and grab what we can!
mempc = physicalMem;
- System.out.println(
+ setAdjustmentMessage(
"Not enough physical memory for application. Ignoring MemorySetting Property '"
+ MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' ("
+ jvmmempcarg
+ "). Using maximum memory available ("
- + physicalMem + ").");
+ + physicalMem + ").",
+ quiet);
}
} catch (Throwable t)
{
memoryPercentError = true;
- System.out.println(
- "Problem calling GetMemory.getPhysicalMemory(). Likely to be problem with com.sun.management.OperatingSystemMXBean");
+ setAdjustmentMessage(
+ "Problem calling GetMemory.getPhysicalMemory(). Likely to be problem with com.sun.management.OperatingSystemMXBean",
+ quiet);
t.printStackTrace();
}
// == null))
&& memmax > NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE)
{
- System.out.println(
+ setAdjustmentMessage(
"Capping maximum memory to " + NOMEM_MAX_HEAPSIZE_GB_DEFAULT
- + "g due to failure to read physical memory size.");
+ + "g due to failure to read physical memory size.",
+ quiet);
memmax = NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
}
return maxMemLong;
}
-}
\ No newline at end of file
+ public static boolean isValidMemoryString(String text)
+ {
+ if (text.length() > 0)
+ {
+ char lastChar = text.charAt(text.length() - 1);
+ char[] otherChars = text.substring(0, text.length() - 1)
+ .toCharArray();
+ for (char c : otherChars)
+ {
+ if (c < '0' || c > '9')
+ {
+ return false;
+ }
+ }
+ if ((lastChar < '0' || lastChar > '9') && memorySuffixes
+ .indexOf(Character.toLowerCase(lastChar)) == -1)
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ public static long memoryStringToLong(String memString)
+ throws NumberFormatException
+ {
+ if (!isValidMemoryString(memString)) // not valid
+ {
+ throw (new NumberFormatException("Not a valid memory string"));
+ }
+ char suffix = Character
+ .toLowerCase(memString.charAt(memString.length() - 1));
+ if ('0' <= suffix && suffix <= '9') // no suffix
+ {
+ return Long.valueOf(memString);
+ }
+ if (memorySuffixes.indexOf(suffix) == -1) // suffix is unknown
+ {
+ return -1;
+ }
+
+ long multiplier = (long) Math.pow(2,
+ memorySuffixes.indexOf(suffix) * 10); // note order of suffixes in
+ // memorySuffixes important
+ // here!
+ // parse the arg. NumberFormatExceptions passed on to calling method
+ long mem = Long
+ .parseLong(memString.substring(0, memString.length() - 1));
+ if (mem == 0)
+ {
+ return 0;
+ }
+
+ // apply multiplier only if result is not too big (i.e. bigger than a long)
+ if (Long.MAX_VALUE / mem > multiplier)
+ {
+ return multiplier * mem;
+ }
+ else
+ {
+ // number too big for a Long. Limit to Long.MAX_VALUE
+ System.out.println("Memory parsing of '" + memString
+ + "' produces number too big. Limiting to Long.MAX_VALUE="
+ + Long.MAX_VALUE);
+ return Long.MAX_VALUE;
+ }
+ }
+
+ public static String memoryLongToString(long mem)
+ {
+ return memoryLongToString(mem, "%.3f");
+ }
+
+ public static String memoryLongToString(long mem, String format)
+ {
+ int exponent = 0;
+ float num = mem;
+ char suffix = 'b';
+
+ for (int i = 0; i < memorySuffixes.length(); i++)
+ {
+ char s = Character.toUpperCase(memorySuffixes.charAt(i));
+ if (mem < (long) Math.pow(2, exponent + 10)
+ || i == memorySuffixes.length() - 1) // last suffix
+ {
+ suffix = s;
+ num = (float) (mem / Math.pow(2, exponent));
+ break;
+ }
+ exponent += 10;
+ }
+
+ return String.format(format, num) + suffix;
+ }
+
+ private static String ADJUSTMENT_MESSAGE = null;
+
+ private static void setAdjustmentMessage(String reason, boolean quiet)
+ {
+ ADJUSTMENT_MESSAGE = reason;
+ if (!quiet)
+ {
+ System.out.println(reason);
+ }
+ }
+
+ public static void clearAdjustmentMessage()
+ {
+ ADJUSTMENT_MESSAGE = null;
+ }
+
+ public static String getAdjustmentMessage()
+ {
+ return ADJUSTMENT_MESSAGE;
+ }
+
+}
*/
package jalview.datamodel;
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
-
import java.util.AbstractList;
import java.util.ArrayList;
import java.util.List;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+
/**
* Stores mapping between the columns of a protein alignment and a DNA alignment
* and a list of individual codon to amino acid mappings between sequences.
{
return mapping;
}
+
+ /**
+ * Returns true if the mapping covers the full length of the given sequence.
+ * This allows us to distinguish the CDS that codes for a protein from
+ * another overlapping CDS in the parent dna sequence.
+ *
+ * @param seq
+ * @return
+ */
+ public boolean covers(SequenceI seq)
+ {
+ List<int[]> mappedRanges = null;
+ MapList mapList = mapping.getMap();
+ if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
+ {
+ mappedRanges = mapList.getFromRanges();
+ }
+ else if (mapping.to == seq || mapping.to == seq.getDatasetSequence())
+ {
+ mappedRanges = mapList.getToRanges();
+ }
+ else
+ {
+ return false;
+ }
+
+ /*
+ * check that each mapped range lies within the sequence range
+ * (necessary for circular CDS - example EMBL:J03321:AAA91567)
+ * and mapped length covers (at least) sequence length
+ */
+ int length = 0;
+ for (int[] range : mappedRanges)
+ {
+ int from = Math.min(range[0], range[1]);
+ int to = Math.max(range[0], range[1]);
+ if (from < seq.getStart() || to > seq.getEnd())
+ {
+ return false;
+ }
+ length += (to - from + 1);
+ }
+ // add 1 to mapped length to allow for a mapped stop codon
+ if (length + 1 < (seq.getEnd() - seq.getStart() + 1))
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Adds any regions mapped to or from position {@code pos} in sequence
+ * {@code seq} to the given search results
+ *
+ * @param seq
+ * @param pos
+ * @param sr
+ */
+ public void markMappedRegion(SequenceI seq, int pos, SearchResultsI sr)
+ {
+ int[] codon = null;
+ SequenceI mappedSeq = null;
+ SequenceI ds = seq.getDatasetSequence();
+ if (ds == null)
+ {
+ ds = seq;
+ }
+
+ if (this.fromSeq == seq || this.fromSeq == ds)
+ {
+ codon = this.mapping.map.locateInTo(pos, pos);
+ mappedSeq = this.mapping.to;
+ }
+ else if (this.mapping.to == seq || this.mapping.to == ds)
+ {
+ codon = this.mapping.map.locateInFrom(pos, pos);
+ mappedSeq = this.fromSeq;
+ }
+
+ if (codon != null)
+ {
+ for (int i = 0; i < codon.length; i += 2)
+ {
+ sr.addResult(mappedSeq, codon[i], codon[i + 1]);
+ }
+ }
+ }
}
private List<SequenceToSequenceMapping> mappings;
}
/**
+ * Return the corresponding aligned or dataset dna sequence for given amino
+ * acid sequence, or null if not found. returns the sequence from the first
+ * mapping found that involves the protein sequence.
*
- * @param sequenceRef
- * @return null or corresponding aaSeq entry for dnaSeq entry
+ * @param aaSeqRef
+ * @return
*/
public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)
{
/**
* Add search results for regions in other sequences that translate or are
- * translated from a particular position in seq
+ * translated from a particular position in seq (which may be an aligned or
+ * dataset sequence)
*
* @param seq
* @param index
public void markMappedRegion(SequenceI seq, int index,
SearchResultsI results)
{
- int[] codon;
SequenceI ds = seq.getDatasetSequence();
- for (SequenceToSequenceMapping ssm : mappings)
+ if (ds == null)
{
- if (ssm.fromSeq == seq || ssm.fromSeq == ds)
- {
- codon = ssm.mapping.map.locateInTo(index, index);
- if (codon != null)
- {
- for (int i = 0; i < codon.length; i += 2)
- {
- results.addResult(ssm.mapping.to, codon[i], codon[i + 1]);
- }
- }
- }
- else if (ssm.mapping.to == seq || ssm.mapping.to == ds)
- {
- {
- codon = ssm.mapping.map.locateInFrom(index, index);
- if (codon != null)
- {
- for (int i = 0; i < codon.length; i += 2)
- {
- results.addResult(ssm.fromSeq, codon[i], codon[i + 1]);
- }
- }
- }
- }
+ ds = seq;
}
- }
-
- /**
- * Returns the DNA codon positions (base 1) for the given position (base 1) in
- * a mapped protein sequence, or null if no mapping is found.
- *
- * Intended for use in aligning cDNA to match aligned protein. Only the first
- * mapping found is returned, so not suitable for use if multiple protein
- * sequences are mapped to the same cDNA (but aligning cDNA as protein is
- * ill-defined for this case anyway).
- *
- * @param seq
- * the DNA dataset sequence
- * @param aaPos
- * residue position (base 1) in a protein sequence
- * @return
- */
- public int[] getDnaPosition(SequenceI seq, int aaPos)
- {
- /*
- * Adapted from markMappedRegion().
- */
- MapList ml = null;
- int i = 0;
for (SequenceToSequenceMapping ssm : mappings)
{
- if (ssm.fromSeq == seq)
- {
- ml = getdnaToProt()[i];
- break;
- }
- i++;
+ ssm.markMappedRegion(ds, index, results);
}
- return ml == null ? null : ml.locateInFrom(aaPos, aaPos);
}
/**
* Two AlignedCodonFrame objects are equal if they hold the same ordered list
* of mappings
*
- * @see SequenceToSequenceMapping#
+ * @see SequenceToSequenceMapping#equals
*/
@Override
public boolean equals(Object obj)
{
return mappings;
}
+
+ /**
+ * Returns the first mapping found which is between the two given sequences,
+ * and covers the full extent of both.
+ *
+ * @param seq1
+ * @param seq2
+ * @return
+ */
+ public SequenceToSequenceMapping getCoveringMapping(SequenceI seq1,
+ SequenceI seq2)
+ {
+ for (SequenceToSequenceMapping mapping : mappings)
+ {
+ if (mapping.covers(seq2) && mapping.covers(seq1))
+ {
+ return mapping;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Returns the first mapping found which is between the given dataset sequence
+ * and another, is a triplet mapping (3:1 or 1:3), and covers the full extent
+ * of both sequences involved
+ *
+ * @param seq
+ * @return
+ */
+ public SequenceToSequenceMapping getCoveringCodonMapping(SequenceI seq)
+ {
+ for (SequenceToSequenceMapping mapping : mappings)
+ {
+ if (mapping.getMapping().getMap().isTripletMap()
+ && mapping.covers(seq))
+ {
+ if (mapping.fromSeq == seq
+ && mapping.covers(mapping.getMapping().getTo()))
+ {
+ return mapping;
+ }
+ else if (mapping.getMapping().getTo() == seq
+ && mapping.covers(mapping.fromSeq))
+ {
+ return mapping;
+ }
+ }
+ }
+ return null;
+ }
}
String canonicalSourceName;
- boolean isCanonicalAccession;
+ boolean isCanonicalAccession=false;
/*
* maps from associated sequence to the database sequence's coordinate system
{
// TODO is FILE needed; if not is this enum needed, or can we
// use FileFormatI for PDB, MMCIF?
- PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), FILE("?", "?");
+ PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), BCIF("bcif","bcif"),FILE("?", "?");
/*
* file extension for cached structure file; must be one that
}
/**
- * Two SearchResults are considered equal if they contain the same matches in
- * the same order.
+ * Two SearchResults are considered equal if they contain the same matches
+ * (Sequence, start position, end position) in the same order
+ *
+ * @see Match#equals(Object)
*/
@Override
public boolean equals(Object obj)
{
out.close();
}
+ if (Cache.log.isTraceEnabled())
+ {
+ Cache.log.trace("Sent: " + command.toString());
+ if (result != null)
+ {
+ Cache.log.trace("Received: " + result);
+ }
+ }
}
return result;
}
"Response from command ('" + cmd + "') was:\n" + lastReply);
}
}
+ else
+ {
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Command executed: " + cmd);
+ }
+ }
return reply;
}
{
return;
}
-
+ if (!found)
+ {
+ // not a valid residue label command, so clear
+ cmd.setLength(0);
+ }
/*
- * unshow the label for the previous residue
+ * prepend with command
+ * to unshow the label for the previous residue
*/
if (lastHighlightCommand != null)
{
- executeCommand(false, null, new StructureCommand("~" + lastHighlightCommand));
+ cmd.insert(0, ";");
+ cmd.insert(0,lastHighlightCommand);
+ cmd.insert(0,"~");
+
}
- if (found)
- {
- executeCommand(false, null, new StructureCommand(command));
+ if (cmd.length()>0) {
+ executeCommand(true, null, new StructureCommand(cmd.toString()));
+ }
+
+ if (found) {
+ this.lastHighlightCommand = command;
}
- this.lastHighlightCommand = command;
}
/**
btn_autosearch.setText(MessageManager.getString("option.autosearch"));
btn_autosearch.setToolTipText(
MessageManager.getString("option.enable_disable_autosearch"));
+ // disable autosearch by default
btn_autosearch.setSelected(!Platform.isJS()
- && Cache.getDefault(getAutosearchPreference(), true));
+ && Cache.getDefault(getAutosearchPreference(), false));
btn_autosearch.addActionListener(new java.awt.event.ActionListener()
{
@Override
} catch (Exception ex)
{
}
-
if (b)
{
- alignFrame.setDisplayedView(this);
+ setAlignFrameView();
}
}
-
+ public void setAlignFrameView()
+ {
+ alignFrame.setDisplayedView(this);
+ }
+
@Override
public StructureSelectionManager getStructureSelectionManager()
{
String[] filesInViewer = getStructureFiles();
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
- Pdb pdbclient = new Pdb();
- EBIAlfaFold afclient = new EBIAlfaFold();
for (int pi = 0; pi < getPdbCount(); pi++)
{
- String file = getPdbEntry(pi).getFile();
+ PDBEntry strucEntry = getPdbEntry(pi);
+
+ String file = strucEntry.getFile();
if (file == null)
{
- // todo: extract block as method and pull up (also ChimeraViewFrame)
- // retrieve the pdb and store it locally
- AlignmentI pdbseq = null;
- PDBEntry strucEntry = getPdbEntry(pi);
pdbid = strucEntry.getId();
- long hdl = pdbid.hashCode() - System.currentTimeMillis();
- structureViewer.setProgressMessage(MessageManager
- .formatMessage("status.fetching_pdb", new String[]
- { pdbid }), hdl);
- try
- {
- if (afclient.isValidReference(pdbid))
- {
- pdbseq = afclient.getSequenceRecords(pdbid);
- } else {
- if (strucEntry.hasRetrievalUrl())
- {
- File tmpFile = File.createTempFile(pdbid, ".cif");
- String fromUrl = strucEntry.getRetrievalUrl();
- UrlDownloadClient.download(fromUrl, tmpFile);
-
- // may not need this check ?
- file = tmpFile.getAbsolutePath();
- if (file != null)
- {
- pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,tmpFile,pdbid,null,null,null);
- }
- } else {
- pdbseq = pdbclient.getSequenceRecords(pdbid);
- }
- }
+ try{
+ file = structureViewer.fetchPdbFile(strucEntry);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
{
ex.printStackTrace();
errormsgs.append("'").append(pdbid).append("'");
- } finally
- {
- structureViewer.setProgressMessage(
- MessageManager.getString("label.state_completed"), hdl);
}
- if (pdbseq != null)
+ if (file!=null)
{
- // just transfer the file name from the first sequence's first
- // PDBEntry
- file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
- .elementAt(0).getFile()).getAbsolutePath();
- getPdbEntry(pi).setFile(file);
+ // success
files.add(file);
}
else
private int myHeight = 150;
- /**
+ private JMenuItem writeFeatures=null;
+
+ private JMenu fetchAttributes=null;
+/**
* Initialise menu options.
*/
@Override
savemenu.setVisible(false); // not yet implemented
viewMenu.add(fitToWindow);
- JMenuItem writeFeatures = new JMenuItem(
+ writeFeatures = new JMenuItem(
MessageManager.getString("label.create_viewer_attributes"));
writeFeatures.setToolTipText(MessageManager
.getString("label.create_viewer_attributes_tip"));
});
viewerActionMenu.add(writeFeatures);
- final JMenu fetchAttributes = new JMenu(
- MessageManager.getString("label.fetch_chimera_attributes"));
+ fetchAttributes = new JMenu(
+ MessageManager.formatMessage("label.fetch_viewer_attributes",getViewerName()));
fetchAttributes.setToolTipText(
- MessageManager.getString("label.fetch_chimera_attributes_tip"));
+ MessageManager.formatMessage("label.fetch_viewer_attributes_tip",getViewerName()));
fetchAttributes.addMouseListener(new MouseAdapter()
{
});
viewerActionMenu.add(fetchAttributes);
}
-
+ @Override
+ protected void buildActionMenu()
+ {
+ super.buildActionMenu();
+ // add these back in after menu is refreshed
+ viewerActionMenu.add(writeFeatures);
+ viewerActionMenu.add(fetchAttributes);
+
+ };
/**
* Query the structure viewer for its residue attribute names and add them as
* items off the attributes menu
// todo pull up?
int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
statusBar.setText(
- MessageManager.formatMessage("label.attributes_set", count));
+ MessageManager.formatMessage("label.attributes_set", count, getViewerName()));
}
/**
if (Cache.getDefault(Preferences.ADD_SS_ANN, true)) {
ssm.setAddTempFacAnnot(Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
ssm.setProcessSecondaryStructure(Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
- ssm.setSecStructServices(Cache.getDefault(Preferences.USE_RNAVIEW, true));
+ // JAL-3915 - RNAView is no longer an option so this has no effect
+ ssm.setSecStructServices(Cache.getDefault(Preferences.USE_RNAVIEW, false));
} else {
ssm.setAddTempFacAnnot(false);
ssm.setProcessSecondaryStructure(false);
int[] localRange = mf.getMappedPositions(start, end);
if (localRange == null)
{
+ // e.g. variant extending to stop codon so not mappable
return;
}
start = localRange[0];
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
+import jalview.bin.MemorySetting;
import jalview.ext.pymol.PymolManager;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
/*
* Set Structure tab defaults
*/
- final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true);
structFromPdb.setSelected(structSelected);
- useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
- useRnaView.setEnabled(structSelected);
- addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true));
addSecondaryStructure.setEnabled(structSelected);
- addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+ addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true));
addTempFactor.setEnabled(structSelected);
/*
* Set Backups tab defaults
*/
loadLastSavedBackupsOptions();
+
+ /*
+ * Set Startup tab defaults
+ */
+
}
/**
Boolean.toString(addTempFactor.isSelected()));
Cache.applicationProperties.setProperty(ADD_SS_ANN,
Boolean.toString(addSecondaryStructure.isSelected()));
- Cache.applicationProperties.setProperty(USE_RNAVIEW,
- Boolean.toString(useRnaView.isSelected()));
Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
Boolean.toString(structFromPdb.isSelected()));
String viewer = structViewer.getSelectedItem().toString();
Cache.applicationProperties.setProperty(
BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
+ /*
+ * Save Memory Settings
+ */
+ Cache.applicationProperties.setProperty(
+ MemorySetting.CUSTOMISED_SETTINGS,
+ Boolean.toString(customiseMemorySetting.isSelected()));
+ Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMPC,
+ Integer.toString(jvmMemoryPercentSlider.getValue()));
+ Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMMAX,
+ jvmMemoryMaxTextField.getText());
+
+ /*
+ * save and close Preferences
+ */
+
Cache.saveProperties();
Desktop.instance.doConfigureStructurePrefs();
try
* a second parameter sets the pdbid as the loaded PyMOL object name
*/
String pdbId = pe.getId();
+ try {
+ String safePDBId = java.net.URLEncoder.encode(pdbId,"UTF-8");
+ pdbId = safePDBId.replace('%', '_');
+ pdbId = pdbId.replace("-", "__");
+ char fc = pdbId.charAt(0);
+ // put an 's' before any numerics
+ if (fc>='0' && fc<='9')
+ {
+ pdbId = 's'+pdbId;
+ }
+// pdbId.replace('-', 0)
+ } catch (Exception x)
+ {
+ Cache.log.error("Unxpected encoding exception for '"+pdbId+"'",x);
+ }
cmd.addParameter(pdbId);
executeCommand(cmd, false);
{
return "PyMOL";
}
-
+ JMenuItem writeFeatures = null;
@Override
protected void initMenus()
{
savemenu.setVisible(false); // not yet implemented
viewMenu.add(fitToWindow);
- JMenuItem writeFeatures = new JMenuItem(
+ writeFeatures = new JMenuItem(
MessageManager.getString("label.create_viewer_attributes"));
writeFeatures.setToolTipText(MessageManager
.getString("label.create_viewer_attributes_tip"));
});
viewerActionMenu.add(writeFeatures);
}
+
+ @Override
+ protected void buildActionMenu()
+ {
+ super.buildActionMenu();
+ viewerActionMenu.add(writeFeatures);
+ }
protected void sendFeaturesToPymol()
{
int count = binding.sendFeaturesToViewer(getAlignmentPanel());
statusBar.setText(
- MessageManager.formatMessage("label.attributes_set", count));
+ MessageManager.formatMessage("label.attributes_set", count, getViewerName()));
}
}
canQueryTDB = true;
if (needCanonical)
{
- notQueriedTDBYet = false;
+ // triggers display of the 'Query TDB' button
+ notQueriedTDBYet = true;
}
}
};
@Override
public void actionPerformed(ActionEvent e)
{
- promptForTDBFetch();
+ promptForTDBFetch(false);
}
});
updateCurrentView();
}
- private void promptForTDBFetch()
+ /**
+ * raises dialog for Uniprot fetch followed by 3D beacons search
+ * @param ignoreGui - when true, don't ask, just fetch
+ */
+ public void promptForTDBFetch(boolean ignoreGui)
{
final long progressId = System.currentTimeMillis();
// redo initial discovery - this time with 3d beacons
// Executors.
previousWantedFields=null;
+ lastSelected=(FilterOption) cmb_filterOption.getSelectedItem();
+ cmb_filterOption.setSelectedItem(null);
+ cachedPDBExists=false; // reset to initial
initialStructureDiscovery();
if (!isStructuresDiscovered())
{
btn_queryTDB.setToolTipText(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"));
btn_queryTDB.setEnabled(false);
} else {
+ cmb_filterOption.setSelectedIndex(0); // select 'best'
btn_queryTDB.setVisible(false);
progressBar.setProgressBar(null, progressId);
}
}
};
};
+ if (ignoreGui)
+ {
+ Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs).start();
+ return;
+ }
// need cancel and no to result in the discoverPDB action - mocked is
- // 'cancel'
+ // 'cancel' TODO: mock should be OK
JvOptionPane.newOptionDialog(this)
.setResponseHandler(JvOptionPane.OK_OPTION,
discoverCanonicalDBrefs)
&& mainFrame.isVisible()
&& cmb_filterOption.getSelectedItem() != null;
}
+ /**
+ *
+ * @return true if the 3D-Beacons query button will/has been displayed
+ */
+ public boolean isCanQueryTDB() {
+ return canQueryTDB;
+ }
+
+ public boolean isNotQueriedTDBYet()
+ {
+ return notQueriedTDBYet;
+ }
}
_alignwith.add(ap);
}
;
+ // TODO: refactor to allow concrete classes to register buttons for adding
+ // here
+ // currently have to override to add buttons back in after they are cleared
+ // in this loop
for (Component c : viewerActionMenu.getMenuComponents())
{
if (c != alignStructs)
{
if (afclient.isValidReference(pdbid))
{
- pdbseq = afclient.getSequenceRecords(pdbid);
+ pdbseq = afclient.getSequenceRecords(pdbid,processingEntry.getRetrievalUrl());
} else {
if (processingEntry.hasRetrievalUrl())
{
+ String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8");
+
// retrieve from URL to new local tmpfile
- File tmpFile = File.createTempFile(pdbid,
+ File tmpFile = File.createTempFile(safePDBId,
"." + (PDBEntry.Type.MMCIF.toString().equals(
processingEntry.getType().toString()) ? "cif"
: "pdb"));
*/
public File saveSession()
{
- // TODO: a wait loop to ensure the file is written fully before returning?
- return getBinding() == null ? null : getBinding().saveSession();
+ if (getBinding() == null) { return null;}
+ File session = getBinding().saveSession();
+ long l = session.length();
+ int wait=50;
+ do {
+ try {
+ Thread.sleep(5);
+ } catch (InterruptedException e) {
+ }
+ long nextl = session.length();
+ if (nextl!=l)
+ {
+ wait = 50;
+ l=nextl;
+ }
+ } while (--wait>0);
+ return session;
}
/**
+ ex.getMessage());
}
}
-
+ @Override
+ public boolean hasViewerActionsMenu()
+ {
+ return viewerActionMenu != null && viewerActionMenu.isEnabled()
+ && viewerActionMenu.getItemCount() > 0
+ && viewerActionMenu.isVisible();
+ }
}
import jalview.api.AlignmentViewPanel;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.Component;
import java.awt.event.ActionEvent;
}
}
});
+ final ViewSelectionMenu us=this;
checkBox.addMouseListener(new MouseAdapter()
{
@Override
{
try
{
- ap.setSelected(false);
} catch (Exception ex)
{
}
{
try
{
- ap.setSelected(true);
+ ap.setAlignFrameView();
} catch (Exception ex)
{
}
BitSet cover = new BitSet();
cover.set(seq.getStart(), seq.getEnd());
// walk down the list of structures, selecting some to add to selected
+ // TODO: could do simple DP - double loop to select largest number of
+ // structures covering largest number of sites
for (FTSData structure : filteredStructures)
{
Object[] odata = structure.getSummaryData();
import javax.swing.JTable;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
private static final String FILTER_SOURCE_PREFIX = "only_";
- private static int MAX_QLENGTH = 7820;
-
protected FTSRestRequest lastTdbRequest;
protected FTSRestClientI tdbRestClient;
public String buildQuery(SequenceI seq)
{
- boolean isPDBRefsFound = false;
- boolean isUniProtRefsFound = false;
- StringBuilder queryBuilder = new StringBuilder();
- Set<String> seqRefs = new LinkedHashSet<>();
-
- /*
- * note PDBs as DBRefEntry so they are not duplicated in query
- */
- Set<String> pdbids = new HashSet<>();
-
List<DBRefEntry> refs = seq.getDBRefs();
int ib = checkUniprotRefs(refs);
- if (ib>-1)
+ if (ib > -1)
{
return getDBRefId(refs.get(ib));
}
/**
* Searches DBRefEntry for uniprot refs
+ *
* @param seq
- * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of Uniprot canonical DBRefEntry
+ * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of
+ * Uniprot canonical DBRefEntry
*/
public static int checkUniprotRefs(List<DBRefEntry> refs)
{
*/
static boolean isValidSeqName(String seqName)
{
- // System.out.println("seqName : " + seqName);
String ignoreList = "pdb,uniprot,swiss-prot";
if (seqName.length() < 3)
{
{
FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
resultList = tdbRestClient.executeRequest(tdbRequest);
-
+
lastTdbRequest = tdbRequest;
- if (resultList!=null)
+ if (resultList != null)
{ // Query the PDB and add additional metadata
FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
getPDBQuerySource(), resultList);
- FTSRestResponse joinedResp = joinResponses(resultList, pdbResponse);
+
+ resultList = joinResponses(resultList, pdbResponse);
}
return resultList;
}
{
if (tdbEntries != null && lastTdbRequest != null)
{
- int prov_idx = lastTdbRequest.getFieldIndex("Provider");
- boolean hasPDBe=false;
+ boolean hasPDBe = false;
for (FTSData _row : tdbEntries)
{
// tdb returns custom object
tdBeaconsFilters.add(FILTER_SOURCE_PREFIX + provider);
if ("PDBe".equalsIgnoreCase(provider))
{
- hasPDBe=true;
+ hasPDBe = true;
}
}
}
if (!hasPDBe)
{
// remove the PDBe options from the available filters
- int op=0;
- while (op<xtantOptions.size())
+ int op = 0;
+ while (op < xtantOptions.size())
{
FilterOption filter = xtantOptions.get(op);
- if (filter.getQuerySource() instanceof PDBStructureChooserQuerySource)
+ if (filter
+ .getQuerySource() instanceof PDBStructureChooserQuerySource)
{
xtantOptions.remove(op);
- } else {
+ }
+ else
+ {
op++;
}
}
int urlColumnIndex = restable.getColumn("Url").getModelIndex();
int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
int humanUrl = restable.getColumn("Page URL").getModelIndex();
- int categoryColumnIndex = restable.getColumn("Model Category")
- .getModelIndex();
+ int modelformat = restable.getColumn("Model Format").getModelIndex();
final int up_start_idx = restable.getColumn("Uniprot Start")
.getModelIndex();
final int up_end_idx = restable.getColumn("Uniprot End")
.toString();
String modelPage = humanUrl < 1 ? null
: (String) restable.getValueAt(row, humanUrl);
+ String strucFormat = restable.getValueAt(row, modelformat).toString();
+
SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
{
pdbEntry = new PDBEntry();
pdbEntry.setId(pdbIdStr);
- boolean hasCif = urlStr.toLowerCase(Locale.ENGLISH).endsWith("cif");
- boolean probablyPdb = urlStr.toLowerCase(Locale.ENGLISH)
- .contains("pdb");
- pdbEntry.setType(hasCif ? PDBEntry.Type.MMCIF
- : probablyPdb ? PDBEntry.Type.PDB : PDBEntry.Type.FILE);
+ try
+ {
+ pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
+ } catch (Exception q)
+ {
+ Cache.log.warn("Unknown filetype for 3D Beacons Model from: "
+ + strucFormat + " - " + pdbIdStr + " - " + modelPage);
+ }
+
if (!"PDBe".equalsIgnoreCase(typeColumn))
{
pdbEntry.setRetrievalUrl(urlStr);
public String buildPDBFTSQueryFor(FTSRestResponse upResponse)
{
- List<String> pdbIds = new ArrayList<String>();
+ Set<String> pdbIds = new HashSet<String>();
int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
for (FTSData row : upResponse.getSearchSummary())
: -1;
int tdbTitle_idx = getLastFTSRequest().getFieldIndex("Title");
- List<FTSData> joinedRows = new ArrayList<FTSData>();
for (final FTSData row : upResponse.getSearchSummary())
{
String id = (String) row.getSummaryData()[idx_modelId];
Collection<FTSData> discoveredStructuresSet)
{
int idColumnIndex = restable.getColumn("Model id").getModelIndex();
-
- String modelId = (String) restable.getValueAt(selectedRow, idColumnIndex);
- for (FTSData row:discoveredStructuresSet)
+
+ String modelId = (String) restable.getValueAt(selectedRow,
+ idColumnIndex);
+ for (FTSData row : discoveredStructuresSet)
{
- if (row instanceof TDB_FTSData && ((TDB_FTSData)row).getModelId().equals(modelId))
+ if (row instanceof TDB_FTSData
+ && ((TDB_FTSData) row).getModelId().equals(modelId))
{
- return ((TDB_FTSData)row);
+ return ((TDB_FTSData) row);
}
}
return null;
*/
package jalview.io;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-
import java.io.IOException;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
/**
* DOCUMENT ME!
*
private boolean parseImmediately = true;
+ private boolean dataClosed = false;
+
/**
* @return if doParse() was called at construction time
*/
public AlignFile(boolean parseImmediately, FileParse source)
throws IOException
{
+ this(parseImmediately, source, true);
+ }
+
+ public AlignFile(boolean parseImmediately, FileParse source,
+ boolean closeData) throws IOException
+ {
super(source);
initData();
if (parseImmediately)
{
- doParse();
+ doParse(closeData);
}
}
*/
public void doParse() throws IOException
{
+ doParse(true);
+ }
+
+ public void doParse(boolean closeData) throws IOException
+ {
if (parseCalled)
{
throw new IOException(
}
parseCalled = true;
parse();
+ if (closeData && !dataClosed)
+ {
+ dataIn.close();
+ dataClosed = true;
+ }
}
/**
*/
package jalview.io;
+import java.io.IOException;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import java.io.IOException;
-
/**
* DOCUMENT ME!
*
public FastaFile(FileParse source) throws IOException
{
- super(source);
+ this(source, true);
+ }
+
+ public FastaFile(FileParse source, boolean closeData) throws IOException
+ {
+ super(true, source, closeData);
}
public FastaFile(SequenceI[] seqs)
} catch (IOException q)
{
}
- FastaFile parser = new FastaFile(this);
+ // Opening a FastaFile object with the remainder of this object's dataIn.
+ // Tell the constructor to NOT close the dataIn when finished.
+ FastaFile parser = new FastaFile(this, false);
List<SequenceI> includedseqs = parser.getSeqs();
SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs);
return false;
}
input.mark(4);
-
+
// get first 2 bytes or return false
byte[] bytes = new byte[2];
int read = input.read(bytes);
{
return false;
}
-
+
int header = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
return (GZIPInputStream.GZIP_MAGIC == header);
}
import jalview.javascript.log4j.spi.OptionHandler;
import org.apache.log4j.PatternLayout;
-import org.apache.log4j.TTCCLayout;
+//import org.apache.log4j.TTCCLayout;
public abstract class Layout implements OptionHandler
{
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.DefaultListCellRenderer;
import javax.swing.JButton;
import javax.swing.JPasswordField;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
+import javax.swing.JSlider;
import javax.swing.JSpinner;
import javax.swing.JTabbedPane;
import javax.swing.JTable;
import javax.swing.table.TableCellRenderer;
import jalview.bin.Cache;
+import jalview.bin.MemorySetting;
import jalview.fts.core.FTSDataColumnPreferences;
import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.io.IntKeyStringValueEntry;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.StringUtils;
/**
* Base class for the Preferences panel.
protected JCheckBox structFromPdb = new JCheckBox();
- protected JCheckBox useRnaView = new JCheckBox();
-
protected JCheckBox addSecondaryStructure = new JCheckBox();
protected JCheckBox addTempFactor = new JCheckBox();
private JLabel messageLabel = new JLabel("", JLabel.CENTER);
+ /*
+ * Startup tab components
+ */
+
+ protected JCheckBox customiseMemorySetting = new JCheckBox();
+
+ protected JLabel exampleMemoryLabel = new JLabel();
+
+ protected JTextArea exampleMemoryMessageTextArea = new JTextArea();
+
+ protected JLabel maxMemoryLabel = new JLabel();
+
+ protected JLabel jvmMemoryPercentLabel = new JLabel();
+
+ protected JSlider jvmMemoryPercentSlider = new JSlider();
+
+ protected JLabel jvmMemoryPercentDisplay = new JLabel();
+
+ protected JLabel jvmMemoryMaxLabel = new JLabel();
+
+ protected JTextField jvmMemoryMaxTextField = new JTextField(null, 8);
+
+ protected JComboBox<Object> lafCombo = new JComboBox<>();
+
/**
* Creates a new GPreferences object.
*/
tabbedPane.add(initEditingTab(),
MessageManager.getString("label.editing"));
+ tabbedPane.add(initStartupTab(),
+ MessageManager.getString("label.startup"));
+
/*
* See WsPreferences for the real work of configuring this tab.
*/
{
boolean selected = structFromPdb.isSelected();
// enable other options only when the first is checked
- useRnaView.setEnabled(selected);
addSecondaryStructure.setEnabled(selected);
addTempFactor.setEnabled(selected);
}
// indent checkboxes that are conditional on the first one
ypos += lineSpacing;
- useRnaView.setFont(LABEL_FONT);
- useRnaView.setText(MessageManager.getString("label.use_rnaview"));
- useRnaView.setBounds(new Rectangle(25, ypos, width, height));
- structureTab.add(useRnaView);
-
- ypos += lineSpacing;
addSecondaryStructure.setFont(LABEL_FONT);
addSecondaryStructure
.setText(MessageManager.getString("label.autoadd_secstr"));
updateBackupFilesExampleLabel();
}
+ /*
+ * Load the saved Memory settings
+ */
+ protected void loadLastSavedMemorySettings()
+ {
+ customiseMemorySetting.setSelected(
+ Cache.getDefault(MemorySetting.CUSTOMISED_SETTINGS, false));
+ jvmMemoryPercentSlider
+ .setValue(Cache.getDefault(MemorySetting.MEMORY_JVMMEMPC, 90));
+ jvmMemoryMaxTextField.setText(
+ Cache.getDefault(MemorySetting.MEMORY_JVMMEMMAX, "32g"));
+ }
+
private boolean warnAboutSuffixReverseChange()
{
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
&& nowSuffixTemplate.equals(savedSuffixTemplate);
}
+ /* Initialises the Startup tabbed panel.
+ *
+ * @return
+ * */
+
+ private JPanel initStartupTab()
+ {
+ JPanel startupTab = new JPanel();
+ startupTab.setBorder(
+ new TitledBorder(MessageManager.getString("label.memory")));
+ startupTab.setLayout(new GridBagLayout());
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.weightx = 0.0;
+ gbc.weighty = 0.0;
+ gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+ gbc.fill = GridBagConstraints.NONE;
+
+ initMemoryPanel();
+
+ gbc.gridheight = 1;
+ gbc.gridwidth = 3;
+
+ gbc.gridy = 0; // row 1
+ gbc.gridx = 0;
+ JLabel memoryText = new JLabel();
+ memoryText.setFont(LABEL_FONT_ITALIC);
+ memoryText
+ .setText(MessageManager.getString("label.memory_setting_text"));
+ startupTab.add(memoryText, gbc);
+
+ gbc.gridy++; // row 2
+ gbc.gridx = 0;
+ JPanel exampleMemoryPanel = new JPanel();
+ exampleMemoryPanel
+ .setLayout(new BoxLayout(exampleMemoryPanel, BoxLayout.Y_AXIS));
+ exampleMemoryPanel.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.memory_example_tooltip")));
+ JLabel exampleTextLabel = new JLabel();
+ exampleTextLabel
+ .setText(MessageManager.getString("label.memory_example_text"));
+ exampleTextLabel.setForeground(Color.GRAY);
+ exampleTextLabel.setFont(LABEL_FONT);
+ exampleMemoryPanel.add(exampleTextLabel);
+ exampleMemoryPanel.add(exampleMemoryLabel);
+ exampleMemoryPanel.setBackground(Color.WHITE);
+ exampleMemoryPanel.setBorder(BorderFactory.createEtchedBorder());
+ startupTab.add(exampleMemoryPanel, gbc);
+
+ gbc.gridy++; // row 3
+ gbc.gridx = 0;
+ startupTab.add(customiseMemorySetting, gbc);
+
+ gbc.gridy += 2; // row 4 with a gap
+ gbc.gridx = 0;
+ startupTab.add(maxMemoryLabel, gbc);
+
+ gbc.gridy += 2; // row 5
+ gbc.gridx = 0;
+ gbc.gridwidth = 1;
+ startupTab.add(jvmMemoryPercentLabel, gbc);
+ gbc.gridx++;
+ startupTab.add(jvmMemoryPercentSlider, gbc);
+ gbc.gridx++;
+ // gbc.weightx = 0.1;
+ startupTab.add(jvmMemoryPercentDisplay, gbc);
+ // gbc.weightx = 1.0;
+ gbc.gridwidth = 3;
+
+ gbc.gridy++; // row 6
+ gbc.gridx = 0;
+ startupTab.add(jvmMemoryMaxLabel, gbc);
+ gbc.gridx++;
+ startupTab.add(jvmMemoryMaxTextField, gbc);
+
+ gbc.gridy++; // row 7
+ gbc.gridx = 0;
+ gbc.gridwidth = 4;
+ exampleMemoryMessageTextArea.setBackground(startupTab.getBackground());
+ JScrollPane sp = new JScrollPane(exampleMemoryMessageTextArea);
+ sp.setBorder(BorderFactory.createEmptyBorder());
+ sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
+ startupTab.add(sp, gbc);
+
+ // fill empty space to push widget to top left
+ gbc.gridy++;
+ gbc.weighty = 1.0;
+ gbc.gridx = 100;
+ gbc.gridwidth = 1;
+ gbc.weightx = 1.0;
+ startupTab.add(new JPanel(), gbc);
+
+ setMemoryPercentDisplay();
+ memoryOptionsSetEnabled();
+ return startupTab;
+ }
+
+ private void initMemoryPanel()
+ {
+ // Enable memory settings checkbox
+ customiseMemorySetting.setFont(LABEL_FONT_BOLD);
+ customiseMemorySetting.setText(
+ MessageManager.getString("label.customise_memory_settings"));
+ customiseMemorySetting.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ memoryOptionsSetEnabled();
+ }
+ });
+
+ loadLastSavedMemorySettings();
+
+ exampleMemoryLabel.setFont(LABEL_FONT_BOLD);
+ exampleMemoryLabel.setBackground(Color.WHITE);
+
+ maxMemoryLabel = new JLabel(
+ MessageManager.getString("label.maximum_memory_used"));
+ maxMemoryLabel.setFont(LABEL_FONT_BOLD);
+
+ // Maximum memory percentage slider
+ jvmMemoryPercentLabel.setFont(LABEL_FONT);
+ jvmMemoryPercentLabel.setText(
+ MessageManager.getString("label.percent_of_physical_memory"));
+ jvmMemoryPercentSlider.setPaintLabels(true);
+ jvmMemoryPercentSlider.setPaintTicks(true);
+ jvmMemoryPercentSlider.setPaintTrack(true);
+ jvmMemoryPercentSlider.setMajorTickSpacing(50);
+ jvmMemoryPercentSlider.setMinorTickSpacing(10);
+ jvmMemoryPercentSlider.addChangeListener(new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent e)
+ {
+ setMemoryPercentDisplay();
+ }
+ });
+ jvmMemoryPercentDisplay.setFont(LABEL_FONT);
+ setMemoryPercentDisplay();
+
+ // Maximum memory cap textbox
+ jvmMemoryMaxLabel.setFont(LABEL_FONT);
+ jvmMemoryMaxLabel
+ .setText(MessageManager.getString("label.maximum_memory"));
+ initMemoryMaxTextField();
+
+ exampleMemoryMessageTextArea.setFont(LABEL_FONT_ITALIC);
+ exampleMemoryMessageTextArea.setForeground(Color.GRAY);
+ exampleMemoryMessageTextArea.setEditable(false);
+ exampleMemoryMessageTextArea.setLineWrap(true);
+ exampleMemoryMessageTextArea.setWrapStyleWord(true);
+ exampleMemoryMessageTextArea.setText(" ");
+ exampleMemoryMessageTextArea.setRows(2);
+ exampleMemoryMessageTextArea.setColumns(40);
+
+ setExampleMemoryLabel();
+ }
+
+ private void initMemoryMaxTextField()
+ {
+ jvmMemoryMaxTextField.setToolTipText(
+ MessageManager.getString("label.maximum_memory_tooltip"));
+ jvmMemoryMaxTextField.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ validateMemoryMaxTextField();
+ setExampleMemoryLabel();
+ }
+ });
+
+ jvmMemoryMaxTextField.addKeyListener(new KeyListener()
+ {
+ @Override
+ public void keyReleased(KeyEvent e)
+ {
+ validateMemoryMaxTextField();
+ setExampleMemoryLabel();
+ }
+
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ }
+
+ // try and stop invalid typing
+ @Override
+ public void keyTyped(KeyEvent e)
+ {
+ char c = Character.toLowerCase(e.getKeyChar());
+ String text = jvmMemoryMaxTextField.getText();
+ String suffixes = "tgmkb";
+ int pos = jvmMemoryMaxTextField.getCaretPosition();
+ int suffixPos = StringUtils.firstCharPosIgnoreCase(text, suffixes);
+ if (!((('0' <= c && c <= '9')
+ && (suffixPos == -1 || pos <= suffixPos)) // digits only allowed
+ // before suffix
+ || (suffixes.indexOf(Character.toLowerCase(c)) >= 0 // valid
+ // suffix
+ && pos == text.length() // at end of text and
+ && suffixPos == -1) // there isn't already one
+ ))
+ {
+ // don't process
+ e.consume();
+ }
+ }
+ });
+ }
+
+ private boolean isMemoryMaxTextFieldValid()
+ {
+ return MemorySetting
+ .isValidMemoryString(jvmMemoryMaxTextField.getText());
+ }
+
+ private void validateMemoryMaxTextField()
+ {
+ if (isMemoryMaxTextFieldValid())
+ {
+ jvmMemoryMaxTextField.setBackground(Color.WHITE);
+ }
+ else
+ {
+ jvmMemoryMaxTextField.setBackground(Color.PINK);
+ }
+ }
+
+ private void setMemoryPercentDisplay()
+ {
+ jvmMemoryPercentDisplay
+ .setText(jvmMemoryPercentSlider.getValue() + "%");
+ setExampleMemoryLabel();
+ }
+
+ private void setExampleMemoryLabel()
+ {
+ boolean selected = customiseMemorySetting.isSelected();
+ int jvmmempc = jvmMemoryPercentSlider.getValue();
+ String jvmmemmax = jvmMemoryMaxTextField.getText();
+
+ long mem;
+ if (selected && (0 <= jvmmempc && jvmmempc <= 100)
+ && MemorySetting.isValidMemoryString(jvmmemmax))
+ {
+ mem = MemorySetting.getMemorySetting(jvmmemmax,
+ String.valueOf(jvmmempc), false, true);
+ }
+ else
+ {
+ mem = MemorySetting.getMemorySetting(null, null, false, true);
+ }
+ exampleMemoryLabel.setText(MemorySetting.memoryLongToString(mem));
+ String message = MemorySetting.getAdjustmentMessage();
+ exampleMemoryMessageTextArea.setText(
+ MessageManager.getString("label.adjustments_for_this_computer")
+ + ": "
+ + (message == null
+ ? MessageManager.getString("label.none")
+ : message));
+ }
+
+ private void memoryOptionsSetEnabled()
+ {
+ boolean enabled = customiseMemorySetting.isSelected();
+ // leave exampleMemoryLabel enabled always
+ maxMemoryLabel.setEnabled(enabled);
+ jvmMemoryPercentLabel.setEnabled(enabled);
+ jvmMemoryPercentSlider.setEnabled(enabled);
+ jvmMemoryPercentDisplay.setEnabled(enabled);
+ jvmMemoryMaxLabel.setEnabled(enabled);
+ jvmMemoryMaxTextField.setEnabled(enabled);
+ exampleMemoryMessageTextArea.setEnabled(enabled);
+ setExampleMemoryLabel();
+ }
+
/**
* Initialises the Backups tabbed panel.
*
*/
package jalview.project;
-import java.util.Locale;
-
import static jalview.math.RotatableMatrix.Axis.X;
import static jalview.math.RotatableMatrix.Axis.Y;
import static jalview.math.RotatableMatrix.Axis.Z;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
{
final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
final String pdbId = pdbentry.getId();
- if (!pdbId.equals(entry.getId())
- && !(entry.getId().length() > 4 && entry.getId().toLowerCase(Locale.ROOT)
+ if (!pdbId.equals(entry.getId()) && !(entry.getId().length() > 4
+ && entry.getId().toLowerCase(Locale.ROOT)
.startsWith(pdbId.toLowerCase(Locale.ROOT))))
{
/*
entryCount++;
}
} while (jarentry != null);
+ jin.close();
resolveFrefedSequences();
} catch (IOException ex)
{
import java.util.HashMap;
import java.util.IdentityHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
// TODO: JAL-3868 need to know if structure is actually from
// PDB (has valid PDB ID and has provenance suggesting it
// actually came from PDB)
- isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-");
+ boolean isProtein = false;
+ for (SequenceI s:sequenceArray) {
+ if (s.isProtein()) {
+ isProtein = true;
+ break;
+ }
+ }
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-") && isProtein;
} catch (Exception ex)
{
pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(siftsMapping, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");
+ maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));
maxChain.transferResidueAnnotation(siftsMapping, null);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA:Jalview"); // FIXME: is
+ maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
// this
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
siftsClient);
foundSiftsMappings.add(siftsMapping);
chain.makeExactMapping(siftsMapping, seq);
- chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
+ chain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this
// "IEA:SIFTS" ?
chain.transferResidueAnnotation(siftsMapping, null);
} catch (SiftsException e)
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
- maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ maxChain.transferRESNUMFeatures(seq, null,pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
- maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferRESNUMFeatures(seq, null, pdb.getId().toLowerCase(Locale.ROOT));
HashMap<Integer, int[]> mapping = new HashMap<>();
int resNum = -10000;
* executed.
* <p>
* If a reply is wanted, the execution is done synchronously (waits),
- * otherwise it is done in a separate thread (doesn't wait).
+ * otherwise it is done in a separate thread (doesn't wait). WARNING: if you
+ * are sending commands that need to execute before later calls to
+ * executeCommand (e.g. mouseovers, which clean up after previous ones) then
+ * set getReply true to ensure that commands are not executed out of order.
*
* @param getReply
* @param msg
package jalview.util;
import java.awt.Image;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import javax.swing.ImageIcon;
-import jalview.bin.Cache;
-
public class ChannelProperties
{
- private static final String CHANNEL_PROPERTIES_FILENAME = "/channel.props";
+ public static final String CHANNEL_PROPERTIES_FILENAME = "channel.props";
- private static final Properties channelProps;
+ private static Properties channelProps;
private static final Properties defaultProps;
// load channel_properties
Properties tryChannelProps = new Properties();
URL channelPropsURL = ChannelProperties.class
- .getResource(CHANNEL_PROPERTIES_FILENAME);
+ .getResource("/" + CHANNEL_PROPERTIES_FILENAME);
if (channelPropsURL == null)
{
// complete failure of channel_properties, set all properties to defaults
- System.err.println("Failed to find '" + CHANNEL_PROPERTIES_FILENAME
+ System.err.println("Failed to find '/" + CHANNEL_PROPERTIES_FILENAME
+ "' file at '"
+ (channelPropsURL == null ? "null"
: channelPropsURL.toString())
channelPropsIS.close();
} catch (IOException e)
{
- Cache.log.warn(e.getMessage());
+ System.err.println(e.getMessage());
// return false;
}
}
Image logo = null;
String path = defaultProps.getProperty("logo." + size);
URL imageURL = ChannelProperties.class.getResource(path);
- logo = new ImageIcon(imageURL).getImage();
+ ImageIcon imgIcon = imageURL == null ? null
+ : new ImageIcon(imageURL);
+ logo = imgIcon == null ? null : imgIcon.getImage();
if (logo != null)
{
iconList.add(logo);
}
}
+ protected static void loadProps(File dir)
+ {
+ File channelPropsFile = new File(dir, CHANNEL_PROPERTIES_FILENAME);
+ if (channelPropsFile.exists())
+ {
+ try
+ {
+ InputStream is = new FileInputStream(channelPropsFile);
+ channelProps.load(is);
+ } catch (FileNotFoundException e)
+ {
+ System.err.println(e.getMessage());
+ } catch (IOException e)
+ {
+ System.err.println(e.getMessage());
+ }
+ }
+ }
+
private static Properties channelProps()
{
return channelProps;
}
URL imageURL = ChannelProperties.class.getResource(path);
- img = new ImageIcon(imageURL).getImage();
+ ImageIcon imgIcon = imageURL == null ? null : new ImageIcon(imageURL);
+ img = imgIcon == null ? null : imgIcon.getImage();
if (img == null)
{
System.err.println(
--- /dev/null
+package jalview.util;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.Properties;
+
+public class LaunchUtils
+{
+
+ public static void loadChannelProps(File dir)
+ {
+ ChannelProperties.loadProps(dir);
+ }
+
+ private static Properties userPreferences = null;
+
+ public static String getUserPreference(String key)
+ {
+ if (userPreferences == null)
+ {
+ String channelPrefsFilename = ChannelProperties
+ .getProperty("preferences.filename");
+ if (channelPrefsFilename == null)
+ {
+ return null;
+ }
+ File propertiesFile = new File(System.getProperty("user.home"),
+ channelPrefsFilename);
+ if (!propertiesFile.exists())
+ {
+ return null;
+ }
+ try
+ {
+ userPreferences = new Properties();
+ userPreferences.load(new FileInputStream(propertiesFile));
+ } catch (FileNotFoundException e)
+ {
+ // didn't find user preferences file
+ return null;
+ } catch (IOException e)
+ {
+ System.err.println(e.getMessage());
+ return null;
+ }
+ }
+ return userPreferences.getProperty(key);
+ }
+
+ public static boolean getBooleanUserPreference(String key)
+ {
+ return Boolean.parseBoolean(getUserPreference(key));
+ }
+}
import jalview.commands.EditCommand.Edit;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
for (AlignedCodonFrame acf : codonFrames)
{
- SequenceI mappedSequence = targetIsNucleotide
- ? acf.getDnaForAaSeq(selected)
- : acf.getAaForDnaSeq(selected);
- if (mappedSequence != null)
+ for (SequenceI seq : mapTo.getAlignment().getSequences())
{
- for (SequenceI seq : mapTo.getAlignment().getSequences())
+ SequenceI peptide = targetIsNucleotide ? selected : seq;
+ SequenceI cds = targetIsNucleotide ? seq : selected;
+ SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds,
+ peptide);
+ if (s2s == null)
{
- int mappedStartResidue = 0;
- int mappedEndResidue = 0;
- if (seq.getDatasetSequence() == mappedSequence)
- {
- /*
- * Found a sequence mapping. Locate the start/end mapped residues.
- */
- List<AlignedCodonFrame> mapping = Arrays
- .asList(new AlignedCodonFrame[]
- { acf });
- SearchResultsI sr = buildSearchResults(selected,
- startResiduePos, mapping);
- for (SearchResultMatchI m : sr.getResults())
- {
- mappedStartResidue = m.getStart();
- mappedEndResidue = m.getEnd();
- }
- sr = buildSearchResults(selected, endResiduePos, mapping);
- for (SearchResultMatchI m : sr.getResults())
- {
- mappedStartResidue = Math.min(mappedStartResidue,
- m.getStart());
- mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
- }
-
- /*
- * Find the mapped aligned columns, save the range. Note findIndex
- * returns a base 1 position, SequenceGroup uses base 0
- */
- int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
- minStartCol = minStartCol == -1 ? mappedStartCol
- : Math.min(minStartCol, mappedStartCol);
- int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
- maxEndCol = maxEndCol == -1 ? mappedEndCol
- : Math.max(maxEndCol, mappedEndCol);
- mappedGroup.addSequence(seq, false);
- break;
- }
+ continue;
+ }
+ int mappedStartResidue = 0;
+ int mappedEndResidue = 0;
+ List<AlignedCodonFrame> mapping = Arrays.asList(acf);
+ SearchResultsI sr = buildSearchResults(selected, startResiduePos,
+ mapping);
+ for (SearchResultMatchI m : sr.getResults())
+ {
+ mappedStartResidue = m.getStart();
+ mappedEndResidue = m.getEnd();
+ }
+ sr = buildSearchResults(selected, endResiduePos, mapping);
+ for (SearchResultMatchI m : sr.getResults())
+ {
+ mappedStartResidue = Math.min(mappedStartResidue, m.getStart());
+ mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
}
+
+ /*
+ * Find the mapped aligned columns, save the range. Note findIndex
+ * returns a base 1 position, SequenceGroup uses base 0
+ */
+ int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
+ minStartCol = minStartCol == -1 ? mappedStartCol
+ : Math.min(minStartCol, mappedStartCol);
+ int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
+ maxEndCol = maxEndCol == -1 ? mappedEndCol
+ : Math.max(maxEndCol, mappedEndCol);
+ mappedGroup.addSequence(seq, false);
+ break;
}
}
}
{
for (AlignedCodonFrame acf : mappings)
{
- SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
- : acf.getAaForDnaSeq(seq);
- if (mappedSeq != null)
- {
for (SequenceI seq2 : mapTo.getSequences())
{
- if (seq2.getDatasetSequence() == mappedSeq)
+ /*
+ * the corresponding peptide / CDS is the one for which there is
+ * a complete ('covering') mapping to 'seq'
+ */
+ SequenceI peptide = mappingToNucleotide ? seq2 : seq;
+ SequenceI cds = mappingToNucleotide ? seq : seq2;
+ SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds,
+ peptide);
+ if (s2s != null)
{
mappedOrder.add(seq2);
j++;
break;
}
}
- }
}
}
if (colsel == null)
{
- return; // mappedColumns;
+ return;
}
char fromGapChar = mapFrom.getAlignment().getGapCharacter();
mapHiddenColumns(regions.next(), codonFrames, newHidden,
fromSequences, toSequences, fromGapChar);
}
- return; // mappedColumns;
+ return;
}
/**
*/
for (SequenceI toSeq : toSequences)
{
- if (toSeq.getDatasetSequence() == mappedSeq)
+ if (toSeq.getDatasetSequence() == mappedSeq
+ && mappedStartResidue >= toSeq.getStart()
+ && mappedEndResidue <= toSeq.getEnd())
{
int mappedStartCol = toSeq.findIndex(mappedStartResidue);
int mappedEndCol = toSeq.findIndex(mappedEndResidue);
{
text = text.substring(0, endTag);
}
-
+
if (startTag == -1 && (text.contains("<") || text.contains(">")))
{
text = text.replaceAll("<", "<");
}
/**
- * Answers the input string with any occurrences of the 'encodeable' characters
- * replaced by their URL encoding
+ * Answers the input string with any occurrences of the 'encodeable'
+ * characters replaced by their URL encoding
*
* @param s
* @param encodable
}
return enc;
}
+
+ public static int firstCharPosIgnoreCase(String text, String chars)
+ {
+ int min = text.length() + 1;
+ for (char c : chars.toLowerCase().toCharArray())
+ {
+ int i = text.toLowerCase().indexOf(c);
+ if (0 <= i && i < min)
+ {
+ min = i;
+ }
+ }
+ return min < text.length() + 1 ? min : -1;
+ }
}
import jalview.api.FeatureColourI;
import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.MappedFeatures;
-import jalview.datamodel.Mapping;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
* todo: direct lookup of CDS for peptide and vice-versa; for now,
* have to search through an unordered list of mappings for a candidate
*/
- Mapping mapping = null;
+ SequenceToSequenceMapping mapping = null;
SequenceI mapFrom = null;
for (AlignedCodonFrame acf : mappings)
{
- mapping = acf.getMappingForSequence(sequence);
- if (mapping == null || !mapping.getMap().isTripletMap())
+ mapping = acf.getCoveringCodonMapping(ds);
+ if (mapping == null)
{
- continue; // we are only looking for 3:1 or 1:3 mappings
+ continue;
}
SearchResultsI sr = new SearchResults();
- acf.markMappedRegion(ds, pos, sr);
+ mapping.markMappedRegion(ds, pos, sr);
for (SearchResultMatchI match : sr.getResults())
{
int fromRes = match.getStart();
}
}
- return new MappedFeatures(mapping, mapFrom, pos, residue, result);
+ return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue, result);
}
@Override
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
@Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
+ return getSequenceRecords(queries, null);
+ }
+ public AlignmentI getSequenceRecords(String queries, String retrievalUrl) throws Exception
+ {
AlignmentI pdbAlignment = null;
String chain = null;
String id = null;
return null;
}
String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
+ if (retrievalUrl != null)
+ {
+ alphaFoldCif = retrievalUrl;
+ }
try
{
dbVersion, (chid == null ? id : id + chid));
// dbentry.setMap()
pdbcs.addDBRef(dbentry);
+ // update any feature groups
+ List<SequenceFeature> allsf = pdbcs.getFeatures().getAllFeatures();
+ List<SequenceFeature> newsf = new ArrayList<SequenceFeature>();
+ if (allsf!=null && allsf.size()>0)
+ {
+ for (SequenceFeature f:allsf)
+ {
+ if (file.equals(f.getFeatureGroup()))
+ {
+ f = new SequenceFeature(f, f.type, f.begin, f.end, id, f.score);
+ }
+ newsf.add(f);
+ }
+ pdbcs.setSequenceFeatures(newsf);
+ }
}
}
else
{
return new PDBFeatureSettings();
}
+
}
* @param seq
* @param status
* The Status of the transferred annotation
+ *
+ * @param altPDBID the group id for the features on the destination sequence (e.g. the official accession ID)
*/
public void transferRESNUMFeatures(SequenceI seq,
- String status)
+ String status, String altPDBID)
{
+ if (altPDBID==null)
+ {
+ altPDBID = pdbid;
+ }
SequenceI sq = seq;
while (sq != null && sq.getDatasetSequence() != null)
{
int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
.elementAt(0).alignmentMapping;
SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
- feature.getFeatureGroup(), feature.getScore());
+ altPDBID, feature.getScore());
tx.setStatus(status
+ ((tx.getStatus() == null || tx.getStatus().length() == 0)
? ""
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed
+ private static final int TEST_TIMEOUT = 10500; // Note longer timeout needed
// on
// full test run than on
// individual tests
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
-import jalview.gui.JvOptionPane;
-import jalview.util.MapList;
-
import java.util.Arrays;
import java.util.List;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
+
public class AlignedCodonFrameTest
{
public void testGetMappedRegion()
{
// introns lower case, exons upper case
- final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
- seq1.createDatasetSequence();
- final Sequence seq2 = new Sequence("Seq2", "-TA-gG-Gg-CG-a");
- seq2.createDatasetSequence();
+ final Sequence dna1 = new Sequence("Seq1/10-18", "c-G-TA-gC-gT-T");
+ dna1.createDatasetSequence();
+ final Sequence dna2 = new Sequence("Seq2/20-28", "-TA-gG-Gg-CG-a");
+ dna2.createDatasetSequence();
- final Sequence aseq1 = new Sequence("Seq1", "-P-R");
- aseq1.createDatasetSequence();
- final Sequence aseq2 = new Sequence("Seq2", "-LY-Q");
- aseq2.createDatasetSequence();
+ final Sequence pep1 = new Sequence("Seq1/3-4", "-P-R");
+ pep1.createDatasetSequence();
+ final Sequence pep2 = new Sequence("Seq2/7-9", "-LY-Q");
+ pep2.createDatasetSequence();
/*
* First with no mappings
*/
AlignedCodonFrame acf = new AlignedCodonFrame();
- assertNull(acf.getMappedRegion(seq1, aseq1, 1));
+ assertNull(acf.getMappedRegion(dna1, pep1, 3));
/*
* Set up the mappings for the exons (upper-case bases)
* Note residue Q is unmapped
*/
- MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
- 1, 2 }, 3, 1);
- acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- map = new MapList(new int[] { 1, 2, 4, 5, 7, 8 }, new int[] { 1, 2 },
+ MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 }, new int[] {
+ 3, 4 }, 3, 1);
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
+ MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 }, new int[] { 7, 9 },
3, 1);
- acf.addMap(seq2.getDatasetSequence(), aseq2.getDatasetSequence(), map);
+ acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
- assertArrayEquals(new int[] { 2, 4 },
- acf.getMappedRegion(seq1, aseq1, 1));
- assertArrayEquals(new int[] { 6, 6, 8, 9 },
- acf.getMappedRegion(seq1, aseq1, 2));
- assertArrayEquals(new int[] { 1, 2, 4, 4 },
- acf.getMappedRegion(seq2, aseq2, 1));
- assertArrayEquals(new int[] { 5, 5, 7, 8 },
- acf.getMappedRegion(seq2, aseq2, 2));
+ /*
+ * get codon positions for peptide position
+ */
+ assertArrayEquals(new int[] { 11, 13 },
+ acf.getMappedRegion(dna1, pep1, 3));
+ assertArrayEquals(new int[] { 15, 15, 17, 18 },
+ acf.getMappedRegion(dna1, pep1, 4));
+ assertArrayEquals(new int[] { 20, 21, 23, 23 },
+ acf.getMappedRegion(dna2, pep2, 7));
+ assertArrayEquals(new int[] { 24, 24, 26, 27 },
+ acf.getMappedRegion(dna2, pep2, 8));
/*
- * No mapping from seq2 to Q
+ * No mapping from dna2 to Q
*/
- assertNull(acf.getMappedRegion(seq2, aseq2, 3));
+ assertNull(acf.getMappedRegion(dna2, pep2, 9));
/*
- * No mapping from sequence 1 to sequence 2
+ * No mapping from dna1 to pep2
*/
- assertNull(acf.getMappedRegion(seq1, aseq2, 1));
+ assertNull(acf.getMappedRegion(dna1, pep2, 7));
+
+ /*
+ * get peptide position for codon position
+ */
+ assertArrayEquals(new int[] { 3, 3 },
+ acf.getMappedRegion(pep1, dna1, 11));
+ assertArrayEquals(new int[] { 3, 3 },
+ acf.getMappedRegion(pep1, dna1, 12));
+ assertArrayEquals(new int[] { 3, 3 },
+ acf.getMappedRegion(pep1, dna1, 13));
+ assertNull(acf.getMappedRegion(pep1, dna1, 14)); // intron base, not mapped
+
}
@Test(groups = { "Functional" })
assertEquals(1, acf.getMappingsFromSequence(seq1).size());
assertSame(before, acf.getMappingsFromSequence(seq1).get(0));
}
+
+ @Test(groups = { "Functional" })
+ public void testGetCoveringMapping()
+ {
+ SequenceI dna = new Sequence("dna", "acttcaATGGCGGACtaattt");
+ SequenceI cds = new Sequence("cds/7-15", "ATGGCGGAC");
+ cds.setDatasetSequence(dna);
+ SequenceI pep = new Sequence("pep", "MAD");
+
+ /*
+ * with null argument or no mappings
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ assertNull(acf.getCoveringMapping(null, null));
+ assertNull(acf.getCoveringMapping(dna, null));
+ assertNull(acf.getCoveringMapping(null, pep));
+ assertNull(acf.getCoveringMapping(dna, pep));
+
+ /*
+ * with a non-covering mapping e.g. overlapping exon
+ */
+ MapList map = new MapList(new int[] { 7, 9 }, new int[] {
+ 1, 1 }, 3, 1);
+ acf.addMap(dna, pep, map);
+ assertNull(acf.getCoveringMapping(dna, pep));
+
+ acf = new AlignedCodonFrame();
+ MapList map2 = new MapList(new int[] { 13, 18 }, new int[] {
+ 2, 2 }, 3, 1);
+ acf.addMap(dna, pep, map2);
+ assertNull(acf.getCoveringMapping(dna, pep));
+
+ /*
+ * with a covering mapping from CDS (dataset) to protein
+ */
+ acf = new AlignedCodonFrame();
+ MapList map3 = new MapList(new int[] { 7, 15 }, new int[] {
+ 1, 3 }, 3, 1);
+ acf.addMap(dna, pep, map3);
+ assertNull(acf.getCoveringMapping(dna, pep));
+ SequenceToSequenceMapping mapping = acf.getCoveringMapping(cds, pep);
+ assertNotNull(mapping);
+
+ /*
+ * with a mapping that extends to stop codon
+ */
+ acf = new AlignedCodonFrame();
+ MapList map4 = new MapList(new int[] { 7, 18 }, new int[] {
+ 1, 3 }, 3, 1);
+ acf.addMap(dna, pep, map4);
+ assertNull(acf.getCoveringMapping(dna, pep));
+ assertNull(acf.getCoveringMapping(cds, pep));
+ SequenceI cds2 = new Sequence("cds/7-18", "ATGGCGGACtaa");
+ cds2.setDatasetSequence(dna);
+ mapping = acf.getCoveringMapping(cds2, pep);
+ assertNotNull(mapping);
+ }
+
+ /**
+ * Test the method that adds mapped positions to SearchResults
+ */
+ @Test(groups = { "Functional" })
+ public void testMarkMappedRegion()
+ {
+ // introns lower case, exons upper case
+ final Sequence dna1 = new Sequence("Seq1/10-18", "c-G-TA-gC-gT-T");
+ dna1.createDatasetSequence();
+ final Sequence dna2 = new Sequence("Seq2/20-28", "-TA-gG-Gg-CG-a");
+ dna2.createDatasetSequence();
+
+ final Sequence pep1 = new Sequence("Seq1/3-4", "-P-R");
+ pep1.createDatasetSequence();
+ final Sequence pep2 = new Sequence("Seq2/7-9", "-LY-Q");
+ pep2.createDatasetSequence();
+
+ /*
+ * First with no mappings
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ SearchResults sr = new SearchResults();
+ acf.markMappedRegion(dna1, 12, sr);
+ assertTrue(sr.isEmpty());
+
+ /*
+ * Set up the mappings for the exons (upper-case bases)
+ * Note residue Q is unmapped
+ */
+ MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 }, new int[] {
+ 3, 4 }, 3, 1);
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
+ MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 }, new int[] { 7, 8 },
+ 3, 1);
+ acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
+
+ /*
+ * intron bases are not mapped
+ */
+ acf.markMappedRegion(dna1, 10, sr);
+ assertTrue(sr.isEmpty());
+
+ /*
+ * Q is not mapped
+ */
+ acf.markMappedRegion(pep2, 9, sr);
+ assertTrue(sr.isEmpty());
+
+ /*
+ * mark peptide position for exon position (of aligned sequence)
+ */
+ acf.markMappedRegion(dna1, 11, sr);
+ SearchResults expected = new SearchResults();
+ expected.addResult(pep1.getDatasetSequence(), 3, 3);
+ assertEquals(sr, expected);
+
+ /*
+ * mark peptide position for exon position of dataset sequence - same result
+ */
+ sr = new SearchResults();
+ acf.markMappedRegion(dna1.getDatasetSequence(), 11, sr);
+ assertEquals(sr, expected);
+
+ /*
+ * marking the same position a second time should not create a duplicate match
+ */
+ acf.markMappedRegion(dna1.getDatasetSequence(), 12, sr);
+ assertEquals(sr, expected);
+
+ /*
+ * mark exon positions for peptide position (of aligned sequence)
+ */
+ sr = new SearchResults();
+ acf.markMappedRegion(pep2, 7, sr); // codon positions 20, 21, 23
+ expected = new SearchResults();
+ expected.addResult(dna2.getDatasetSequence(), 20, 21);
+ expected.addResult(dna2.getDatasetSequence(), 23, 23);
+ assertEquals(sr, expected);
+
+ /*
+ * add another codon to the same SearchResults
+ */
+ acf.markMappedRegion(pep1.getDatasetSequence(), 4, sr); // codon positions 15, 17, 18
+ expected.addResult(dna1.getDatasetSequence(), 15, 15);
+ expected.addResult(dna1.getDatasetSequence(), 17, 18);
+ assertEquals(sr, expected);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetCoveringCodonMapping()
+ {
+ SequenceI dna = new Sequence("dna/10-30", "acttcaATGGCGGACtaattt");
+ // CDS sequence with its own dataset sequence (JAL-3763)
+ SequenceI cds = new Sequence("cds/1-9", "-A--TGGC-GGAC");
+ cds.createDatasetSequence();
+ SequenceI pep = new Sequence("pep/1-3", "MAD");
+
+ /*
+ * with null argument or no mappings
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ assertNull(acf.getCoveringCodonMapping(null));
+ assertNull(acf.getCoveringCodonMapping(dna));
+ assertNull(acf.getCoveringCodonMapping(pep));
+
+ /*
+ * with a non-covering mapping e.g. overlapping exon
+ */
+ MapList map = new MapList(new int[] { 16, 18 }, new int[] {
+ 1, 1 }, 3, 1);
+ acf.addMap(dna, pep, map);
+ assertNull(acf.getCoveringCodonMapping(dna));
+ assertNull(acf.getCoveringCodonMapping(pep));
+
+ acf = new AlignedCodonFrame();
+ MapList map2 = new MapList(new int[] { 13, 18 }, new int[] {
+ 2, 2 }, 3, 1);
+ acf.addMap(dna, pep, map2);
+ assertNull(acf.getCoveringCodonMapping(dna));
+ assertNull(acf.getCoveringCodonMapping(pep));
+
+ /*
+ * with a covering mapping from CDS (dataset) to protein
+ */
+ acf = new AlignedCodonFrame();
+ MapList map3 = new MapList(new int[] { 1, 9 }, new int[] {
+ 1, 3 }, 3, 1);
+ acf.addMap(cds.getDatasetSequence(), pep, map3);
+ assertNull(acf.getCoveringCodonMapping(dna));
+ SequenceToSequenceMapping mapping = acf.getCoveringCodonMapping(pep);
+ assertNotNull(mapping);
+ SequenceToSequenceMapping mapping2 = acf.getCoveringCodonMapping(cds.getDatasetSequence());
+ assertSame(mapping, mapping2);
+
+ /*
+ * with a mapping that extends to stop codon
+ * (EMBL CDS location often includes the stop codon)
+ * - getCoveringCodonMapping is lenient (doesn't require exact length match)
+ */
+ SequenceI cds2 = new Sequence("cds/1-12", "-A--TGGC-GGACTAA");
+ cds2.createDatasetSequence();
+ acf = new AlignedCodonFrame();
+ MapList map4 = new MapList(new int[] { 1, 12 }, new int[] {
+ 1, 3 }, 3, 1);
+ acf.addMap(cds2, pep, map4);
+ mapping = acf.getCoveringCodonMapping(cds2.getDatasetSequence());
+ assertNotNull(mapping);
+ mapping2 = acf.getCoveringCodonMapping(pep);
+ assertSame(mapping, mapping2);
+ }
}
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
@Test(groups = { "External" })
public void testSingleSeqViewChimera()
{
+
String inFile = "examples/1gaq.txt";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
DataSourceType.FILE);
/*
* Wait for viewer load thread to complete
*/
- while (!binding.isFinishedInit())
+ do
{
try
{
} catch (InterruptedException e)
{
}
- }
+ } while (!binding.isFinishedInit() || !chimeraViewer.isVisible());
assertTrue(binding.isViewerRunning(), "Failed to start Chimera");
assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
+ assertTrue(chimeraViewer.hasViewerActionsMenu());
+
+ // now add another sequence and bind to view
+ //
+ AlignmentI al = af.getViewport().getAlignment();
+ PDBEntry xpdb = al.getSequenceAt(0).getPDBEntry("1GAQ");
+ sq = new Sequence("1GAQ", al.getSequenceAt(0).getSequence(25, 95).toString());
+ al.addSequence(sq);
+ structureViewer.viewStructures(new PDBEntry[] { xpdb }, new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+
+ /*
+ * Wait for viewer load thread to complete
+ */
+ do
+ {
+ try {
+ Thread.sleep(1500);
+ } catch (InterruptedException q) {};
+ } while (!binding.isLoadingFinished());
+
+ // still just one PDB structure shown
+ assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
+ // and the viewer action menu should still be visible
+ assertTrue(chimeraViewer.hasViewerActionsMenu());
+
chimeraViewer.closeViewer(true);
chimeraViewer = null;
return;
assertEquals(expectedErrorMsg, parsedErrorResponse);
}
- @Test(groups = { "External" }, expectedExceptions = Exception.class)
+ @Test(groups = { "External" }, enabled = false, expectedExceptions = Exception.class)
public void testForExpectedRuntimeException() throws Exception
{
- // JBPNote: looks like this test fails for no good reason - what exception was supposed to be raised ?
+ // FIXME JBPNote: looks like this test fails for no good reason - what exception was supposed to be raised ?
List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
wantedFields.add(PDBFTSRestClient.getInstance()
.getDataColumnByNameOrCode("pdb_id"));
public static void setMock()
{
String[][] mocks = new String[2][];
- mocks[0] = new String[] {
- "https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(4igk+OR+1t15+OR+4ifi+OR+1t29+OR+3pxb+OR+4y2g+OR+1y98+OR+1jnx+OR+3pxa+OR+3k0h+OR+3k0k+OR+1n5o+OR+3pxc+OR+3pxd+OR+1t2u+OR+3k15+OR+3pxe+OR+3k16+OR+4ofb+OR+3coj+OR+7lyb+OR+1t2v+OR+4y18+OR+4jlu+OR+4u4a+OR+2ing+OR+7jzv+OR+6g2i+OR+1jm7+OR+1oqa)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=",
- "{\n" + " \"responseHeader\":{\n" + " \"status\":0,\n"
- + " \"QTime\":0,\n" + " \"params\":{\n"
- + " \"q\":\"(4igk OR 1t15 OR 4ifi OR 1t29 OR 3pxb OR 4y2g OR 1y98 OR 1jnx OR 3pxa OR 3k0h OR 3k0k OR 1n5o OR 3pxc OR 3pxd OR 1t2u OR 3k15 OR 3pxe OR 3k16 OR 4ofb OR 3coj OR 7lyb OR 1t2v OR 4y18 OR 4jlu OR 4u4a OR 2ing OR 7jzv OR 6g2i OR 1jm7 OR 1oqa) AND molecule_sequence:['' TO *] AND status:REL\",\n"
- + " \"fl\":\"pdb_id,title,experimental_method,resolution\",\n"
- + " \"start\":\"0\",\n" + " \"sort\":\"\",\n"
- + " \"rows\":\"500\",\n" + " \"wt\":\"json\"}},\n"
- + " \"response\":{\"numFound\":64,\"start\":0,\"docs\":[\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4ofb\",\n"
- + " \"resolution\":3.05,\n"
- + " \"title\":\"Crystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3pxe\",\n"
- + " \"resolution\":2.85,\n"
- + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4jlu\",\n"
- + " \"resolution\":3.5,\n"
- + " \"title\":\"Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4y2g\",\n"
- + " \"resolution\":2.5,\n"
- + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Solution NMR\"],\n"
- + " \"pdb_id\":\"1oqa\",\n"
- + " \"title\":\"Solution structure of the BRCT-c domain from human BRCA1\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4u4a\",\n"
- + " \"resolution\":3.51,\n"
- + " \"title\":\"Complex Structure of BRCA1 BRCT with singly phospho Abraxas\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t2v\",\n"
- + " \"resolution\":3.3,\n"
- + " \"title\":\"Structural basis of phospho-peptide recognition by the BRCT domain of BRCA1, structure with phosphopeptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k15\",\n"
- + " \"resolution\":2.8,\n"
- + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t15\",\n"
- + " \"resolution\":1.85,\n"
- + " \"title\":\"Crystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k16\",\n"
- + " \"resolution\":3.0,\n"
- + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t29\",\n"
- + " \"resolution\":2.3,\n"
- + " \"title\":\"Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1y98\",\n"
- + " \"resolution\":2.5,\n"
- + " \"title\":\"Structure of the BRCT repeats of BRCA1 bound to a CtIP phosphopeptide.\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4ifi\",\n"
- + " \"resolution\":2.2,\n"
- + " \"title\":\"Structure of human BRCA1 BRCT in complex with BAAT peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k0k\",\n"
- + " \"resolution\":2.7,\n"
- + " \"title\":\"Crystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus.\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k0h\",\n"
- + " \"resolution\":2.7,\n"
- + " \"title\":\"The crystal structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3pxd\",\n"
- + " \"resolution\":2.8,\n"
- + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1835P\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3pxc\",\n"
- + " \"resolution\":2.8,\n"
- + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1699Q\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3pxa\",\n"
- + " \"resolution\":2.55,\n"
- + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: G1656D\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1jnx\",\n"
- + " \"resolution\":2.5,\n"
- + " \"title\":\"Crystal structure of the BRCT repeat region from the breast cancer associated protein, BRCA1\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4igk\",\n"
- + " \"resolution\":1.75,\n"
- + " \"title\":\"Structure of human BRCA1 BRCT in complex with ATRIP peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Solution NMR\"],\n"
- + " \"pdb_id\":\"1jm7\",\n"
- + " \"title\":\"Solution structure of the BRCA1/BARD1 RING-domain heterodimer\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4jlu\",\n"
- + " \"resolution\":3.5,\n"
- + " \"title\":\"Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"6g2i\",\n"
- + " \"resolution\":5.9,\n"
- + " \"title\":\"Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) at 5.9 A resolution\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3coj\",\n"
- + " \"resolution\":3.21,\n"
- + " \"title\":\"Crystal Structure of the BRCT Domains of Human BRCA1 in Complex with a Phosphorylated Peptide from Human Acetyl-CoA Carboxylase 1\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3pxb\",\n"
- + " \"resolution\":2.5,\n"
- + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: T1700A\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t2u\",\n"
- + " \"resolution\":2.8,\n"
- + " \"title\":\"Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1: structure of BRCA1 missense variant V1809F\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1n5o\",\n"
- + " \"resolution\":2.8,\n"
- + " \"title\":\"Structural consequences of a cancer-causing BRCA1-BRCT missense mutation\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4u4a\",\n"
- + " \"resolution\":3.51,\n"
- + " \"title\":\"Complex Structure of BRCA1 BRCT with singly phospho Abraxas\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4y2g\",\n"
- + " \"resolution\":2.5,\n"
- + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3pxe\",\n"
- + " \"resolution\":2.85,\n"
- + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4ofb\",\n"
- + " \"resolution\":3.05,\n"
- + " \"title\":\"Crystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4y18\",\n"
- + " \"resolution\":3.5,\n"
- + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"2ing\",\n"
- + " \"resolution\":3.6,\n"
- + " \"title\":\"X-ray Structure of the BRCA1 BRCT mutant M1775K\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t29\",\n"
- + " \"resolution\":2.3,\n"
- + " \"title\":\"Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t2v\",\n"
- + " \"resolution\":3.3,\n"
- + " \"title\":\"Structural basis of phospho-peptide recognition by the BRCT domain of BRCA1, structure with phosphopeptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t15\",\n"
- + " \"resolution\":1.85,\n"
- + " \"title\":\"Crystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Solution NMR\"],\n"
- + " \"pdb_id\":\"1jm7\",\n"
- + " \"title\":\"Solution structure of the BRCA1/BARD1 RING-domain heterodimer\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4ifi\",\n"
- + " \"resolution\":2.2,\n"
- + " \"title\":\"Structure of human BRCA1 BRCT in complex with BAAT peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4igk\",\n"
- + " \"resolution\":1.75,\n"
- + " \"title\":\"Structure of human BRCA1 BRCT in complex with ATRIP peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1y98\",\n"
- + " \"resolution\":2.5,\n"
- + " \"title\":\"Structure of the BRCT repeats of BRCA1 bound to a CtIP phosphopeptide.\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k15\",\n"
- + " \"resolution\":2.8,\n"
- + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k0k\",\n"
- + " \"resolution\":2.7,\n"
- + " \"title\":\"Crystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus.\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k16\",\n"
- + " \"resolution\":3.0,\n"
- + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k0h\",\n"
- + " \"resolution\":2.7,\n"
- + " \"title\":\"The crystal structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4y18\",\n"
- + " \"resolution\":3.5,\n"
- + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3coj\",\n"
- + " \"resolution\":3.21,\n"
- + " \"title\":\"Crystal Structure of the BRCT Domains of Human BRCA1 in Complex with a Phosphorylated Peptide from Human Acetyl-CoA Carboxylase 1\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"6g2i\",\n"
- + " \"resolution\":5.9,\n"
- + " \"title\":\"Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) at 5.9 A resolution\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"}]\n"
- + " }}" };
+ mocks[0] = new String[] {"https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(4igk+OR+7lyb+OR+3k0h+OR+3k0k+OR+1t15+OR+3pxc+OR+3pxd+OR+3pxe+OR+1jm7+OR+7jzv+OR+3pxa+OR+3pxb+OR+1y98+OR+1n5o+OR+4ifi+OR+4y2g+OR+3k15+OR+3k16+OR+4jlu+OR+2ing+OR+4ofb+OR+6g2i+OR+3coj+OR+1jnx+OR+4y18+OR+4u4a+OR+1oqa+OR+1t29+OR+1t2u+OR+1t2v)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=",
+ "{\n"
+ + " \"responseHeader\":{\n"
+ + " \"status\":0,\n"
+ + " \"QTime\":0,\n"
+ + " \"params\":{\n"
+ + " \"q\":\"(4igk OR 7lyb OR 3k0h OR 3k0k OR 1t15 OR 3pxc OR 3pxd OR 3pxe OR 1jm7 OR 7jzv OR 3pxa OR 3pxb OR 1y98 OR 1n5o OR 4ifi OR 4y2g OR 3k15 OR 3k16 OR 4jlu OR 2ing OR 4ofb OR 6g2i OR 3coj OR 1jnx OR 4y18 OR 4u4a OR 1oqa OR 1t29 OR 1t2u OR 1t2v) AND molecule_sequence:['' TO *] AND status:REL\",\n"
+ + " \"fl\":\"pdb_id,title,experimental_method,resolution\",\n"
+ + " \"start\":\"0\",\n"
+ + " \"sort\":\"\",\n"
+ + " \"rows\":\"500\",\n"
+ + " \"wt\":\"json\"}},\n"
+ + " \"response\":{\"numFound\":64,\"start\":0,\"docs\":[\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4ofb\",\n"
+ + " \"resolution\":3.05,\n"
+ + " \"title\":\"Crystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxe\",\n"
+ + " \"resolution\":2.85,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4jlu\",\n"
+ + " \"resolution\":3.5,\n"
+ + " \"title\":\"Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4y2g\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Solution NMR\"],\n"
+ + " \"pdb_id\":\"1oqa\",\n"
+ + " \"title\":\"Solution structure of the BRCT-c domain from human BRCA1\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4u4a\",\n"
+ + " \"resolution\":3.51,\n"
+ + " \"title\":\"Complex Structure of BRCA1 BRCT with singly phospho Abraxas\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k16\",\n"
+ + " \"resolution\":3.0,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t15\",\n"
+ + " \"resolution\":1.85,\n"
+ + " \"title\":\"Crystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k15\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t2v\",\n"
+ + " \"resolution\":3.3,\n"
+ + " \"title\":\"Structural basis of phospho-peptide recognition by the BRCT domain of BRCA1, structure with phosphopeptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1y98\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Structure of the BRCT repeats of BRCA1 bound to a CtIP phosphopeptide.\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t29\",\n"
+ + " \"resolution\":2.3,\n"
+ + " \"title\":\"Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k0k\",\n"
+ + " \"resolution\":2.7,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus.\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k0h\",\n"
+ + " \"resolution\":2.7,\n"
+ + " \"title\":\"The crystal structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4ifi\",\n"
+ + " \"resolution\":2.2,\n"
+ + " \"title\":\"Structure of human BRCA1 BRCT in complex with BAAT peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxd\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1835P\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxc\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1699Q\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1jnx\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Crystal structure of the BRCT repeat region from the breast cancer associated protein, BRCA1\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxa\",\n"
+ + " \"resolution\":2.55,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: G1656D\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Solution NMR\"],\n"
+ + " \"pdb_id\":\"1jm7\",\n"
+ + " \"title\":\"Solution structure of the BRCA1/BARD1 RING-domain heterodimer\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4igk\",\n"
+ + " \"resolution\":1.75,\n"
+ + " \"title\":\"Structure of human BRCA1 BRCT in complex with ATRIP peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t2u\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1: structure of BRCA1 missense variant V1809F\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxb\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: T1700A\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1n5o\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Structural consequences of a cancer-causing BRCA1-BRCT missense mutation\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3coj\",\n"
+ + " \"resolution\":3.21,\n"
+ + " \"title\":\"Crystal Structure of the BRCT Domains of Human BRCA1 in Complex with a Phosphorylated Peptide from Human Acetyl-CoA Carboxylase 1\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"6g2i\",\n"
+ + " \"resolution\":5.9,\n"
+ + " \"title\":\"Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) at 5.9 A resolution\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4jlu\",\n"
+ + " \"resolution\":3.5,\n"
+ + " \"title\":\"Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4ofb\",\n"
+ + " \"resolution\":3.05,\n"
+ + " \"title\":\"Crystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxe\",\n"
+ + " \"resolution\":2.85,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4u4a\",\n"
+ + " \"resolution\":3.51,\n"
+ + " \"title\":\"Complex Structure of BRCA1 BRCT with singly phospho Abraxas\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4y2g\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4y18\",\n"
+ + " \"resolution\":3.5,\n"
+ + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"2ing\",\n"
+ + " \"resolution\":3.6,\n"
+ + " \"title\":\"X-ray Structure of the BRCA1 BRCT mutant M1775K\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t15\",\n"
+ + " \"resolution\":1.85,\n"
+ + " \"title\":\"Crystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t29\",\n"
+ + " \"resolution\":2.3,\n"
+ + " \"title\":\"Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Solution NMR\"],\n"
+ + " \"pdb_id\":\"1jm7\",\n"
+ + " \"title\":\"Solution structure of the BRCA1/BARD1 RING-domain heterodimer\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t2v\",\n"
+ + " \"resolution\":3.3,\n"
+ + " \"title\":\"Structural basis of phospho-peptide recognition by the BRCT domain of BRCA1, structure with phosphopeptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4ifi\",\n"
+ + " \"resolution\":2.2,\n"
+ + " \"title\":\"Structure of human BRCA1 BRCT in complex with BAAT peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4igk\",\n"
+ + " \"resolution\":1.75,\n"
+ + " \"title\":\"Structure of human BRCA1 BRCT in complex with ATRIP peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k0k\",\n"
+ + " \"resolution\":2.7,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus.\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k16\",\n"
+ + " \"resolution\":3.0,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k15\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k0h\",\n"
+ + " \"resolution\":2.7,\n"
+ + " \"title\":\"The crystal structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1y98\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Structure of the BRCT repeats of BRCA1 bound to a CtIP phosphopeptide.\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3coj\",\n"
+ + " \"resolution\":3.21,\n"
+ + " \"title\":\"Crystal Structure of the BRCT Domains of Human BRCA1 in Complex with a Phosphorylated Peptide from Human Acetyl-CoA Carboxylase 1\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4y18\",\n"
+ + " \"resolution\":3.5,\n"
+ + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"6g2i\",\n"
+ + " \"resolution\":5.9,\n"
+ + " \"title\":\"Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) at 5.9 A resolution\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"}]\n"
+ + " }}" };
mocks[1] = new String[2];
try {
.isEmpty());
Assert.assertEquals(
ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
- 14);
+ 15);
}
@Test(groups = { "Functional" })
String actual = ftsRestClient
.getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
Assert.assertEquals(actual,
- "uniprot_start,uniprot_end,provider,model_identifier,model_category,model_title,resolution,confidence_avg_local_score,confidence_type,confidence_version,coverage,created,model_url,model_page_url");
+ "uniprot_start,uniprot_end,provider,model_identifier,model_category,model_title,resolution,confidence_avg_local_score,confidence_type,confidence_version,coverage,created,model_url,model_format,model_page_url");
}
@Test(groups = { "Functional" })
.getAllFTSDataColumns();
Assert.assertNotNull(allFields);
// System.out.println(allFields.size());
- Assert.assertEquals(allFields.size(), 19);
+ Assert.assertEquals(allFields.size(), 20);
}
@Test(groups = { "Functional" })
}
private static String[][] mocks = { { "P38398.json",
- "{\"uniprot_entry\":{\"sequence_length\":1863,\"ac\":\"P38398\",\"id\":\"BRCA1_HUMAN\"},\"structures\":[{\"model_identifier\":\"4igk\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2012-12-17\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.75,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4igk_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4igk\"},{\"model_identifier\":\"1t15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-15\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t15_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t15\"},{\"model_identifier\":\"4ifi\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2012-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.2,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ifi_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ifi\"},{\"model_identifier\":\"1t29\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-20\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t29_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t29\"},{\"model_identifier\":\"3pxb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxb\"},{\"model_identifier\":\"4y2g\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2015-02-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y2g_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y2g\"},{\"model_identifier\":\"1y98\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1y98_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1y98\"},{\"model_identifier\":\"1jnx\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2001-07-26\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jnx_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jnx\"},{\"model_identifier\":\"3pxa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.55,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxa_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxa\"},{\"model_identifier\":\"3k0h\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0h_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY 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DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k16\"},{\"model_identifier\":\"4ofb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2014-01-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.05,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ofb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ofb\"},{\"model_identifier\":\"3coj\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2008-03-28\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.21,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3coj_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3coj\"},{\"model_identifier\":\"7lyb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2021-03-06\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":100,\"resolution\":3.28,\"coverage\":5.37,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7lyb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/7lyb\"},{\"model_identifier\":\"1t2v\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2v_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t2v\"},{\"model_identifier\":\"4y18\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2015-02-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y18_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y18\"},{\"model_identifier\":\"4jlu\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2013-03-13\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4jlu_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4jlu\"},{\"model_identifier\":\"4u4a\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2014-07-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.51,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4u4a_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4u4a\"},{\"model_identifier\":\"2ing\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2006-10-07\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.6,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/2ing_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/2ing\"},{\"model_identifier\":\"7jzv\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2020-09-02\",\"sequence_identity\":99.0,\"uniprot_start\":2,\"uniprot_end\":104,\"resolution\":3.9,\"coverage\":5.53,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7jzv_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/7jzv\"},{\"model_identifier\":\"6g2i\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2018-03-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":5.9,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/6g2i_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/6g2i\"},{\"model_identifier\":\"1jm7\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2001-07-17\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":110,\"resolution\":null,\"coverage\":5.9,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jm7_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jm7\"},{\"model_identifier\":\"1oqa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2003-03-07\",\"sequence_identity\":100.0,\"uniprot_start\":1755,\"uniprot_end\":1863,\"resolution\":null,\"coverage\":5.85,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1oqa_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1oqa\"},{\"model_identifier\":\"P38398_1646-1859:6g2i.1.K\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-11-05\",\"sequence_identity\":1.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"coverage\":0.115,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.776,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1646-1859&template=6g2i.1.K&provider=swissmodel\",\"model_format\":\"PDB\",\"model_page_url\":\"https://swissmodel.expasy.org/repository/uniprot/P38398?range=1646-1859&template=6g2i.1.K\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"P38398_1-103:1jm7.1.A\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-11-05\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":103,\"coverage\":0.055,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.655,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1-103&template=1jm7.1.A&provider=swissmodel\",\"model_format\":\"PDB\",\"model_page_url\":\"https://swissmodel.expasy.org/repository/uniprot/P38398?range=1-103&template=1jm7.1.A\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"AF-P38398-F1\",\"model_category\":\"DEEP-LEARNING\",\"provider\":\"AlphaFold DB\",\"created\":\"2021-07-01\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":1863,\"coverage\":100.0,\"model_url\":\"https://alphafold.ebi.ac.uk/files/AF-P38398-F1-model_v1.cif\",\"model_format\":\"MMCIF\",\"model_page_url\":\"https://alphafold.ebi.ac.uk/entry/P38398\"}]}" },
{ "P01308.json",null}};
private static void setMockData()
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+ "q":"(5hpu OR 2jmn OR 4iuz OR 6s34 OR 1efe OR 6ce7 OR 1w8p OR 1evr OR 1hls OR 5hpr OR 7jp3 OR 3v19 OR 5bts OR 3q6e OR 2m1d OR 2m1e OR 2n2v OR 2n2w OR 2n2x OR 1t1p OR 1t1q OR 2rn5 OR 2m2o OR 4une OR 3v1g OR 2m2p OR 4unh OR 5t7r OR 4ung OR 4gbi OR 4rxw OR 4gbl OR 4gbk OR 4gbn OR 3aiy OR 1ioh OR 1iog OR 5wob OR 4gbc OR 2m2m OR 2m2n OR 5hqi OR 2hiu OR 6ce9 OR 4z76 OR 4z78 OR 4z77 OR 2kqp OR 2kqq OR 5en9 OR 6k59 OR 1mhj OR 1mhi OR 5hrq OR 6ceb OR 1jca OR 4p65 OR 1k3m OR 3kq6 OR 6s4i OR 4f0o OR 6s4j OR 4f0n OR 6gnq OR 5ems OR 2mvc OR 2mvd OR 1sf1 OR 3hyd OR 2l1y OR 1uz9 OR 2l1z OR 7nhu OR 3w80 OR 4aiy OR 3utq OR 3ilg OR 5cjo OR 4ak0 OR 6b3q OR 4f1g OR 4wdi OR 1jco OR 1vkt OR 6tyh OR 4iyd OR 5ena OR 4f1b OR 4f1a OR 4iyf OR 4f1d OR 4f1c OR 4f1f OR 4ajx OR 4ajz OR 1ben OR 1tyl OR 1tym OR 2vk0 OR 6bfc OR 2om0 OR 2om1 OR 3uts OR 3utt OR 3tt8 OR 2omh OR 2omi OR 3u4n OR 6o17 OR 4fg3 OR 2vjz OR 4oga OR 2lgb OR 6ck2 OR 2omg OR 5uoz OR 2oly OR 1zeg OR 2olz OR 3inc OR 1zeh OR 4akj OR 4f51 OR 3w7y OR 3rov OR 3w7z OR 6b70 OR 5co9 OR 1j73 OR 5aiy OR 5co2 OR 1os4 OR 5uqa OR 1os3 OR 4f4t OR 2jv1 OR 5co6 OR 4f4v OR 7bw7 OR 5wdm OR 7bw8 OR 1rwe OR 2ceu OR 2omq OR 2r34 OR 2r35 OR 7s4y OR 2r36 OR 5cny OR 2juu OR 2juv OR 5mt9 OR 2jum OR 3exx OR 3ir0 OR 1htv OR 5mt3 OR 7bwa OR 3zqr OR 6h3m OR 1lkq OR 5mam OR 3zs2 OR 2mli OR 1ai0 OR 5usp OR 5uu2 OR 5uu4 OR 5uu3 OR 3e7y OR 3e7z OR 4ex0 OR 3jsd OR 6gv0 OR 4ex1 OR 2kxk OR 1sjt OR 1q4v OR 1sju OR 5uru OR 5urt OR 6jk8 OR 1xda OR 6z7y OR 1hui OR 5hyj OR 6z7w OR 4ey9 OR 4eww OR 1a7f OR 2k91 OR 4nib OR 1b9e OR 4ewx OR 4ewz OR 4ey1 OR 1jk8 OR 5uss OR 5usv OR 3zu1 OR 6p4z OR 4efx OR 6x4x OR 1xw7 OR 2kjj OR 1kmf OR 4eyd OR 1fu2 OR 4exx OR 2wc0 OR 2ws6 OR 1qj0 OR 2ws7 OR 2c8q OR 2c8r OR 5udp OR 5boq OR 4f8f OR 2ws0 OR 2ws1 OR 1guj OR 2ws4 OR 1lph OR 2wby OR 1qiz OR 1qiy OR 3i40 OR 2k9r OR 6sof OR 2wru OR 4fka OR 4eyp OR 2wrv OR 2wrw OR 2wrx OR 1xgl OR 5bpo OR 1aiy OR 5c0d OR 2kju OR 4eyn OR 3fq9 OR 3i3z OR 3p33 OR 1hiq OR 2mpg OR 5mwq OR 2mpi OR 1mso OR 2h67 OR 6vep OR 5bqq OR 6ves OR 4y19 OR 6vet OR 1fub OR 6ver OR 6tc2 OR 1t0c OR 1ev6 OR 1ev3 OR 2aiy OR 3zi3 OR 5viz OR 2g54 OR 4y1a OR 6nwv OR 5mhd OR 2g56 OR 3bxq OR 4cy7 OR 1hit OR 1his OR 2hh4 OR 6u46 OR 3w11 OR 2w44 OR 3w12 OR 3w13 OR 6hn5 OR 2hho OR 5e7w OR 1t1k OR 4xc4 OR 6jr3 OR 1trz OR 2qiu OR 1g7b OR 1g7a OR 4cxl OR 3p2x OR 4cxn OR 1znj) AND molecule_sequence:['' TO *] AND status:REL",
"fl":"pdb_id,title,experimental_method,resolution",
"start":"0",
"sort":"",
"rows":"500",
"wt":"json"}},
- "response":{"numFound":638,"start":0,"docs":[
+ "response":{"numFound":641,"start":0,"docs":[
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2ws6",
- "resolution":1.5,
- "title":"Semi-synthetic analogue of human insulin NMeTyrB26-insulin in hexamer form"},
+ "pdb_id":"3hyd",
+ "resolution":1.0,
+ "title":"LVEALYL peptide derived from human insulin chain B, residues 11-17"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"2ws6",
- "resolution":1.5,
- "title":"Semi-synthetic analogue of human insulin NMeTyrB26-insulin in hexamer form"},
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1t0c",
+ "title":"Solution Structure of Human Proinsulin C-Peptide"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"6u46",
+ "title":"Solution Structure of a Heat-Resistant Long-Acting Insulin Analog"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2ws6",
- "resolution":1.5,
- "title":"Semi-synthetic analogue of human insulin NMeTyrB26-insulin in hexamer form"},
+ "pdb_id":"2omq",
+ "resolution":2.0,
+ "title":"VEALYL peptide derived from human insulin chain B, residues 12-17"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"1hit",
- "title":"Receptor binding redefined by a structural switch in a mutant Human Insulin"},
+ "pdb_id":"1sju",
+ "title":"MINI-PROINSULIN, SINGLE CHAIN INSULIN ANALOG MUTANT: DES B30, HIS(B 10)ASP, PRO(B 28)ASP AND PEPTIDE BOND BETWEEN LYS B 29 AND GLY A 1, NMR, 20 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1efe",
+ "title":"AN ACTIVE MINI-PROINSULIN, M2PI"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5wdm",
+ "resolution":2.803,
+ "title":"An ultra-stable single-chain insulin analog resists thermal inactivation and exhibits biological signaling duration equivalent to the native protein"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"1his",
"title":"Receptor binding redefined by a structural switch in a mutant Human Insulin"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2m2o",
- "title":"Structure of [D-HisB24] insulin analogue at pH 1.9"},
+ "pdb_id":"1hit",
+ "title":"Receptor binding redefined by a structural switch in a mutant Human Insulin"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2m1d",
- "title":"Biosynthetic engineered B28K-B29P human insulin monomer structure in in water/acetonitrile solutions."},
+ "pdb_id":"1vkt",
+ "title":"HUMAN INSULIN TWO DISULFIDE MODEL, NMR, 10 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2m2n",
- "title":"Structure of [L-HisB24] insulin analogue at pH 8.0"},
+ "pdb_id":"2m1e",
+ "title":"Biosynthetic engineered B28K-B29P human insulin monomer structure in in water solutions."},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2m2n",
- "title":"Structure of [L-HisB24] insulin analogue at pH 8.0"},
+ "pdb_id":"2m2o",
+ "title":"Structure of [D-HisB24] insulin analogue at pH 1.9"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"1sjt",
- "title":"MINI-PROINSULIN, TWO CHAIN INSULIN ANALOG MUTANT: DES B30, HIS(B 10)ASP, PRO(B 28)ASP, NMR, 20 STRUCTURES"},
+ "pdb_id":"2m2p",
+ "title":"Structure of [D-HisB24] insulin analogue at pH 8.0"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"1vkt",
- "title":"HUMAN INSULIN TWO DISULFIDE MODEL, NMR, 10 STRUCTURES"},
+ "pdb_id":"2m1d",
+ "title":"Biosynthetic engineered B28K-B29P human insulin monomer structure in in water/acetonitrile solutions."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2c8q",
+ "resolution":1.95,
+ "title":"insuline(1sec) and UV laser excited fluorescence"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2c8q",
+ "resolution":1.95,
+ "title":"insuline(1sec) and UV laser excited fluorescence"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"2c8r",
"title":"PARADOXICAL STRUCTURE AND FUNCTION IN A MUTANT HUMAN INSULIN ASSOCIATED WITH DIABETES MELLITUS"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2c8q",
- "resolution":1.95,
- "title":"insuline(1sec) and UV laser excited fluorescence"},
+ "pdb_id":"7nhu",
+ "resolution":1.4,
+ "title":"Crystal structure of desB30 insulin produced by cell free protein synthesis"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2c8q",
- "resolution":1.95,
- "title":"insuline(1sec) and UV laser excited fluorescence"},
+ "pdb_id":"7nhu",
+ "resolution":1.4,
+ "title":"Crystal structure of desB30 insulin produced by cell free protein synthesis"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"6o17",
"resolution":1.58,
"title":"Recombinant Human Insulin"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"7nhu",
- "resolution":1.4,
- "title":"Crystal structure of desB30 insulin produced by cell free protein synthesis"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"7nhu",
- "resolution":1.4,
- "title":"Crystal structure of desB30 insulin produced by cell free protein synthesis"},
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mvc",
+ "title":"Solution structure of human insulin at pH 1.9"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"2mvd",
"title":"Solution structure of [GlnB22]-insulin mutant at pH 1.9"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2mvc",
- "title":"Solution structure of human insulin at pH 1.9"},
+ "pdb_id":"2m2n",
+ "title":"Structure of [L-HisB24] insulin analogue at pH 8.0"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2m1e",
- "title":"Biosynthetic engineered B28K-B29P human insulin monomer structure in in water solutions."},
+ "pdb_id":"2m2n",
+ "title":"Structure of [L-HisB24] insulin analogue at pH 8.0"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2m2p",
- "title":"Structure of [D-HisB24] insulin analogue at pH 8.0"},
+ "pdb_id":"1vkt",
+ "title":"HUMAN INSULIN TWO DISULFIDE MODEL, NMR, 10 STRUCTURES"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"2ws4",
"title":"Semi-synthetic analogue of human insulin ProB26-DTI in monomer form"},
{
"experimental_method":["Solution NMR"],
+ "pdb_id":"2m1e",
+ "title":"Biosynthetic engineered B28K-B29P human insulin monomer structure in in water solutions."},
+ {
+ "experimental_method":["Solution NMR"],
"pdb_id":"2m2o",
"title":"Structure of [D-HisB24] insulin analogue at pH 1.9"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2m1d",
- "title":"Biosynthetic engineered B28K-B29P human insulin monomer structure in in water/acetonitrile solutions."},
+ "pdb_id":"2m2p",
+ "title":"Structure of [D-HisB24] insulin analogue at pH 8.0"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2m1e",
- "title":"Biosynthetic engineered B28K-B29P human insulin monomer structure in in water solutions."},
+ "pdb_id":"2m1d",
+ "title":"Biosynthetic engineered B28K-B29P human insulin monomer structure in in water/acetonitrile solutions."},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"1sjt",
- "title":"MINI-PROINSULIN, TWO CHAIN INSULIN ANALOG MUTANT: DES B30, HIS(B 10)ASP, PRO(B 28)ASP, NMR, 20 STRUCTURES"},
+ "pdb_id":"1k3m",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-ALA, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"1vkt",
- "title":"HUMAN INSULIN TWO DISULFIDE MODEL, NMR, 10 STRUCTURES"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3ilg",
- "resolution":1.9,
- "title":"Crystal structure of humnan insulin Sr+2 complex"},
+ "pdb_id":"1k3m",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-ALA, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"1lkq",
"title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-GLY, VAL-A3-GLY, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 20 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"1k3m",
- "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-ALA, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ "pdb_id":"1sjt",
+ "title":"MINI-PROINSULIN, TWO CHAIN INSULIN ANALOG MUTANT: DES B30, HIS(B 10)ASP, PRO(B 28)ASP, NMR, 20 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"1k3m",
- "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-ALA, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ "pdb_id":"1sjt",
+ "title":"MINI-PROINSULIN, TWO CHAIN INSULIN ANALOG MUTANT: DES B30, HIS(B 10)ASP, PRO(B 28)ASP, NMR, 20 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"1lkq",
"title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-GLY, VAL-A3-GLY, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 20 STRUCTURES"},
{
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3ilg",
+ "resolution":1.9,
+ "title":"Crystal structure of humnan insulin Sr+2 complex"},
+ {
"experimental_method":["Solution NMR"],
"pdb_id":"5mwq",
"title":"Biosynthetic engineered A21K-B31K-B32R human insulin monomer structure in water/acetonitrile solution"},
{
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mvc",
+ "title":"Solution structure of human insulin at pH 1.9"},
+ {
"experimental_method":["X-ray diffraction"],
"pdb_id":"5ena",
"resolution":1.35,
"resolution":1.7,
"title":"X-Ray structure of Insulin Glargine"},
{
- "experimental_method":["Solution NMR"],
- "pdb_id":"2mvc",
- "title":"Solution structure of human insulin at pH 1.9"},
- {
"experimental_method":["X-ray diffraction"],
"pdb_id":"5en9",
"resolution":1.5,
"title":"High resolution x-ray crystal structure of isotope-labeled ester-insulin"},
{
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3i40",
+ "resolution":1.85,
+ "title":"Human insulin"},
+ {
"experimental_method":["Solution NMR"],
- "pdb_id":"2m2p",
- "title":"Structure of [D-HisB24] insulin analogue at pH 8.0"},
+ "pdb_id":"2kjj",
+ "title":"Dynamics of insulin probed by 1H-NMR amide proton exchange anomalous flexibility of the receptor-binding surface"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2kjj",
+ "title":"Dynamics of insulin probed by 1H-NMR amide proton exchange anomalous flexibility of the receptor-binding surface"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2juu",
+ "title":"allo-ThrA3 DKP-insulin"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"2jum",
"title":"ThrA3-DKP-insulin"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2kjj",
- "title":"Dynamics of insulin probed by 1H-NMR amide proton exchange anomalous flexibility of the receptor-binding surface"},
+ "pdb_id":"2jv1",
+ "title":"NMR structure of human insulin monomer in 35% CD3CN zinc free, 50 structures"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2kjj",
- "title":"Dynamics of insulin probed by 1H-NMR amide proton exchange anomalous flexibility of the receptor-binding surface"},
+ "pdb_id":"1iog",
+ "title":"INSULIN MUTANT A3 GLY,(B1, B10, B16, B27)GLU, DES-B30, NMR, 19 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2jv1",
- "title":"NMR structure of human insulin monomer in 35% CD3CN zinc free, 50 structures"},
+ "pdb_id":"1jco",
+ "title":"Solution structure of the monomeric [Thr(B27)->Pro,Pro(B28)->Thr] insulin mutant (PT insulin)"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2kju",
- "title":"NMR structure of human insulin mutant glu-b21-d-glu, his-b10 asp pro-b28-lys, lys-b29-pro, 20 structures"},
+ "pdb_id":"1xgl",
+ "title":"HUMAN INSULIN DISULFIDE ISOMER, NMR, 10 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2juu",
- "title":"allo-ThrA3 DKP-insulin"},
+ "pdb_id":"1xgl",
+ "title":"HUMAN INSULIN DISULFIDE ISOMER, NMR, 10 STRUCTURES"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2wrw",
- "resolution":2.41,
- "title":"Semi-synthetic highly active analogue of human insulin D-ProB26-DTI- NH2"},
+ "pdb_id":"2r35",
+ "resolution":2.08,
+ "title":"Crystal structure of RB human arg-insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2wrw",
- "resolution":2.41,
- "title":"Semi-synthetic highly active analogue of human insulin D-ProB26-DTI- NH2"},
+ "pdb_id":"2qiu",
+ "resolution":2.0,
+ "title":"Structure of Human Arg-Insulin"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"2ws4",
"title":"Semi-synthetic analogue of human insulin ProB26-DTI in monomer form"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2r34",
- "resolution":2.25,
- "title":"Crystal structure of MN human arg-insulin"},
+ "pdb_id":"2wrw",
+ "resolution":2.41,
+ "title":"Semi-synthetic highly active analogue of human insulin D-ProB26-DTI- NH2"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wrw",
+ "resolution":2.41,
+ "title":"Semi-synthetic highly active analogue of human insulin D-ProB26-DTI- NH2"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"2l1z",
"title":"NMR Structure of human insulin mutant GLY-B20-D-ALA, GLY-B23-D-ALA PRO-B28-LYS, LYS-B29-PRO, 20 Structures"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2qiu",
- "resolution":2.0,
- "title":"Structure of Human Arg-Insulin"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"1os4",
+ "pdb_id":"2r34",
"resolution":2.25,
- "title":"Dehydrated T6 human insulin at 295 K"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"1t1k",
- "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ALA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"1t1k",
- "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ALA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3ilg",
- "resolution":1.9,
- "title":"Crystal structure of humnan insulin Sr+2 complex"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3i40",
- "resolution":1.85,
- "title":"Human insulin"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"1xgl",
- "title":"HUMAN INSULIN DISULFIDE ISOMER, NMR, 10 STRUCTURES"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"1xgl",
- "title":"HUMAN INSULIN DISULFIDE ISOMER, NMR, 10 STRUCTURES"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"1iog",
- "title":"INSULIN MUTANT A3 GLY,(B1, B10, B16, B27)GLU, DES-B30, NMR, 19 STRUCTURES"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"1jco",
- "title":"Solution structure of the monomeric [Thr(B27)->Pro,Pro(B28)->Thr] insulin mutant (PT insulin)"},
+ "title":"Crystal structure of MN human arg-insulin"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"1kmf",
"title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT ILE-A2-ALLO-ILE, HIS-B10-ASP, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
+ "pdb_id":"1ioh",
+ "title":"INSULIN MUTANT A8 HIS,(B1, B10, B16, B27)GLU, DES-B30, NMR, 26 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
"pdb_id":"1hui",
"title":"INSULIN MUTANT (B1, B10, B16, B27)GLU, DES-B30, NMR, 25 STRUCTURES"},
{
"pdb_id":"1hui",
"title":"INSULIN MUTANT (B1, B10, B16, B27)GLU, DES-B30, NMR, 25 STRUCTURES"},
{
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1os4",
+ "resolution":2.25,
+ "title":"Dehydrated T6 human insulin at 295 K"},
+ {
"experimental_method":["Solution NMR"],
"pdb_id":"1a7f",
"title":"INSULIN MUTANT B16 GLU, B24 GLY, DES-B30, NMR, 20 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"1ioh",
- "title":"INSULIN MUTANT A8 HIS,(B1, B10, B16, B27)GLU, DES-B30, NMR, 26 STRUCTURES"},
+ "pdb_id":"2kju",
+ "title":"NMR structure of human insulin mutant glu-b21-d-glu, his-b10 asp pro-b28-lys, lys-b29-pro, 20 structures"},
{
- "experimental_method":["Electron Microscopy"],
- "pdb_id":"6jr3",
- "resolution":14.5,
- "title":"Crystal structure of insulin hexamer fitted into cryo EM density map where each dimer was kept as rigid body"},
- {
- "experimental_method":["Electron Microscopy"],
- "pdb_id":"6jr3",
- "resolution":14.5,
- "title":"Crystal structure of insulin hexamer fitted into cryo EM density map where each dimer was kept as rigid body"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"5mwq",
- "title":"Biosynthetic engineered A21K-B31K-B32R human insulin monomer structure in water/acetonitrile solution"},
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3ilg",
+ "resolution":1.9,
+ "title":"Crystal structure of humnan insulin Sr+2 complex"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"6x4x",
- "title":"B24Y DKP insulin"},
+ "pdb_id":"1t1k",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ALA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"6x4x",
- "title":"B24Y DKP insulin"},
+ "pdb_id":"1t1k",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ALA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"5t7r",
"resolution":1.55,
"title":"A6-A11 trans-dicarba human insulin"},
{
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"5mwq",
+ "title":"Biosynthetic engineered A21K-B31K-B32R human insulin monomer structure in water/acetonitrile solution"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6jr3",
+ "resolution":14.5,
+ "title":"Crystal structure of insulin hexamer fitted into cryo EM density map where each dimer was kept as rigid body"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6jr3",
+ "resolution":14.5,
+ "title":"Crystal structure of insulin hexamer fitted into cryo EM density map where each dimer was kept as rigid body"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"6x4x",
+ "title":"B24Y DKP insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"6x4x",
+ "title":"B24Y DKP insulin"},
+ {
"experimental_method":["X-ray diffraction"],
"pdb_id":"5ena",
"resolution":1.35,
"title":"Xray crystal structure of isotope-labeled human insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3zi3",
- "resolution":1.7,
- "title":"Crystal structure of the B24His-insulin - human analogue"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3zi3",
- "resolution":1.7,
- "title":"Crystal structure of the B24His-insulin - human analogue"},
- {
- "experimental_method":["X-ray diffraction"],
"pdb_id":"3u4n",
"resolution":1.98,
"title":"A novel covalently linked insulin dimer"},
"title":"A novel covalently linked insulin dimer"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2r35",
- "resolution":2.08,
- "title":"Crystal structure of RB human arg-insulin"},
+ "pdb_id":"3zi3",
+ "resolution":1.7,
+ "title":"Crystal structure of the B24His-insulin - human analogue"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3zi3",
+ "resolution":1.7,
+ "title":"Crystal structure of the B24His-insulin - human analogue"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"5en9",
"resolution":1.5,
"title":"High resolution x-ray crystal structure of isotope-labeled ester-insulin"},
{
- "experimental_method":["Solution NMR"],
- "pdb_id":"2h67",
- "title":"NMR structure of human insulin mutant HIS-B5-ALA, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7jp3",
+ "resolution":1.95,
+ "title":"Des-B29,B30-insulin"},
{
- "experimental_method":["Solution NMR"],
- "pdb_id":"2kju",
- "title":"NMR structure of human insulin mutant glu-b21-d-glu, his-b10 asp pro-b28-lys, lys-b29-pro, 20 structures"},
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3i40",
+ "resolution":1.85,
+ "title":"Human insulin"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"2hho",
"title":"NMR structure of human insulin mutant GLY-B8-SER, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2juv",
- "title":"AbaA3-DKP-insulin"},
+ "pdb_id":"2juu",
+ "title":"allo-ThrA3 DKP-insulin"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2juv",
- "title":"AbaA3-DKP-insulin"},
+ "pdb_id":"2h67",
+ "title":"NMR structure of human insulin mutant HIS-B5-ALA, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2h67",
+ "title":"NMR structure of human insulin mutant HIS-B5-ALA, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"2jv1",
"title":"NMR structure of human insulin monomer in 35% CD3CN zinc free, 50 structures"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2juu",
- "title":"allo-ThrA3 DKP-insulin"},
+ "pdb_id":"2juv",
+ "title":"AbaA3-DKP-insulin"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2h67",
- "title":"NMR structure of human insulin mutant HIS-B5-ALA, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
+ "pdb_id":"2juv",
+ "title":"AbaA3-DKP-insulin"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"2ws0",
"title":"Semi-synthetic analogue of human insulin NMeAlaB26-insulin at pH 7.5"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2rn5",
- "title":"Humal Insulin Mutant B31Lys-B32Arg"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"2rn5",
- "title":"Humal Insulin Mutant B31Lys-B32Arg"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"2qiu",
- "resolution":2.0,
- "title":"Structure of Human Arg-Insulin"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"2lgb",
- "title":"Modified A22Gly-B31Arg Human Insulin"},
+ "pdb_id":"1iog",
+ "title":"INSULIN MUTANT A3 GLY,(B1, B10, B16, B27)GLU, DES-B30, NMR, 19 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2lgb",
- "title":"Modified A22Gly-B31Arg Human Insulin"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"1os4",
- "resolution":2.25,
- "title":"Dehydrated T6 human insulin at 295 K"},
+ "pdb_id":"1jco",
+ "title":"Solution structure of the monomeric [Thr(B27)->Pro,Pro(B28)->Thr] insulin mutant (PT insulin)"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"1t1p",
"title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-THR, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2aiy",
- "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 20 STRUCTURES"},
+ "pdb_id":"1t1q",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ABA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1t1q",
+ "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ABA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"1sf1",
"pdb_id":"1sf1",
"title":"NMR STRUCTURE OF HUMAN INSULIN under Amyloidogenic Condition, 15 STRUCTURES"},
{
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2r35",
+ "resolution":2.08,
+ "title":"Crystal structure of RB human arg-insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2qiu",
+ "resolution":2.0,
+ "title":"Structure of Human Arg-Insulin"},
+ {
"experimental_method":["Solution NMR"],
- "pdb_id":"1t1q",
- "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ABA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ "pdb_id":"2rn5",
+ "title":"Humal Insulin Mutant B31Lys-B32Arg"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"1t1q",
- "title":"NMR STRUCTURE OF HUMAN INSULIN MUTANT HIS-B10-ASP, VAL-B12-ABA, PRO-B28-LYS, LYS-B29-PRO, 15 STRUCTURES"},
+ "pdb_id":"2rn5",
+ "title":"Humal Insulin Mutant B31Lys-B32Arg"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3i3z",
- "resolution":1.6,
- "title":"Human insulin"},
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2lgb",
+ "title":"Modified A22Gly-B31Arg Human Insulin"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3i3z",
- "resolution":1.6,
- "title":"Human insulin"},
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2lgb",
+ "title":"Modified A22Gly-B31Arg Human Insulin"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3i40",
- "resolution":1.85,
- "title":"Human insulin"},
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1ioh",
+ "title":"INSULIN MUTANT A8 HIS,(B1, B10, B16, B27)GLU, DES-B30, NMR, 26 STRUCTURES"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"1iog",
- "title":"INSULIN MUTANT A3 GLY,(B1, B10, B16, B27)GLU, DES-B30, NMR, 19 STRUCTURES"},
+ "pdb_id":"1a7f",
+ "title":"INSULIN MUTANT B16 GLU, B24 GLY, DES-B30, NMR, 20 STRUCTURES"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"1mso",
"resolution":1.0,
"title":"T6 Human Insulin at 1.0 A Resolution"},
{
- "experimental_method":["Solution NMR"],
- "pdb_id":"1jco",
- "title":"Solution structure of the monomeric [Thr(B27)->Pro,Pro(B28)->Thr] insulin mutant (PT insulin)"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"1a7f",
- "title":"INSULIN MUTANT B16 GLU, B24 GLY, DES-B30, NMR, 20 STRUCTURES"},
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1os4",
+ "resolution":2.25,
+ "title":"Dehydrated T6 human insulin at 295 K"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"1hls",
"pdb_id":"1hls",
"title":"NMR STRUCTURE OF THE HUMAN INSULIN-HIS(B16)"},
{
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3i3z",
+ "resolution":1.6,
+ "title":"Human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3i3z",
+ "resolution":1.6,
+ "title":"Human insulin"},
+ {
"experimental_method":["Solution NMR"],
- "pdb_id":"1ioh",
- "title":"INSULIN MUTANT A8 HIS,(B1, B10, B16, B27)GLU, DES-B30, NMR, 26 STRUCTURES"},
+ "pdb_id":"2kju",
+ "title":"NMR structure of human insulin mutant glu-b21-d-glu, his-b10 asp pro-b28-lys, lys-b29-pro, 20 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 20 STRUCTURES"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4iyd",
- "resolution":1.66,
- "title":"Insulin glargine crystal structure 1"},
+ "pdb_id":"6ves",
+ "resolution":1.85,
+ "title":"Human insulin analog: [GluB10,HisA8,ArgA9]-DOI"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4iyd",
- "resolution":1.66,
- "title":"Insulin glargine crystal structure 1"},
+ "pdb_id":"6ves",
+ "resolution":1.85,
+ "title":"Human insulin analog: [GluB10,HisA8,ArgA9]-DOI"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"6s34",
"title":"Zinc free, dimeric human insulin determined to 1.35 Angstrom resolution"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"6ves",
- "resolution":1.85,
- "title":"Human insulin analog: [GluB10,HisA8,ArgA9]-DOI"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"6ves",
- "resolution":1.85,
- "title":"Human insulin analog: [GluB10,HisA8,ArgA9]-DOI"},
+ "pdb_id":"4ung",
+ "resolution":1.81,
+ "title":"Human insulin B26Asn mutant crystal structure"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"4unh",
"title":"Solution structure of the [AibB8,LysB28,ProB29]-insulin analogue"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3w7y",
- "resolution":0.92,
- "title":"0.92A structure of 2Zn human insulin at 100K"},
+ "pdb_id":"4iyd",
+ "resolution":1.66,
+ "title":"Insulin glargine crystal structure 1"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3w7y",
- "resolution":0.92,
- "title":"0.92A structure of 2Zn human insulin at 100K"},
+ "pdb_id":"4iyd",
+ "resolution":1.66,
+ "title":"Insulin glargine crystal structure 1"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"3w7z",
"title":"1.15A structure of human 2Zn insulin at 293K"},
{
"experimental_method":["X-ray diffraction"],
+ "pdb_id":"3w7y",
+ "resolution":0.92,
+ "title":"0.92A structure of 2Zn human insulin at 100K"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3w7y",
+ "resolution":0.92,
+ "title":"0.92A structure of 2Zn human insulin at 100K"},
+ {
+ "experimental_method":["X-ray diffraction"],
"pdb_id":"4ak0",
"resolution":2.28,
"title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
"resolution":1.1746387,
"title":"Insulin with proline analog FyP at position B28 in the T2 state"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"4ung",
- "resolution":1.81,
- "title":"Human insulin B26Asn mutant crystal structure"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"2r35",
- "resolution":2.08,
- "title":"Crystal structure of RB human arg-insulin"},
- {
"experimental_method":["Solution NMR"],
"pdb_id":"2hiu",
"title":"NMR STRUCTURE OF HUMAN INSULIN IN 20% ACETIC ACID, ZINC-FREE, 10 STRUCTURES"},
"pdb_id":"2m2m",
"title":"Structure of [L-HisB24] insulin analogue at pH 1.9"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"2wrx",
- "resolution":1.5,
- "title":"Semi-synthetic analogue of human insulin NMeAlaB26-insulin at pH 3.0"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"2wrx",
- "resolution":1.5,
- "title":"Semi-synthetic analogue of human insulin NMeAlaB26-insulin at pH 3.0"},
- {
"experimental_method":["Solution NMR"],
"pdb_id":"2hho",
"title":"NMR structure of human insulin mutant GLY-B8-SER, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2hh4",
- "title":"NMR structure of human insulin mutant GLY-B8-D-SER, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
+ "pdb_id":"2k91",
+ "title":"Enhancing the activity of insulin by stereospecific unfolding"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2hh4",
- "title":"NMR structure of human insulin mutant GLY-B8-D-SER, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
+ "pdb_id":"2k91",
+ "title":"Enhancing the activity of insulin by stereospecific unfolding"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2kxk",
- "title":"Human Insulin Mutant A22Gly-B31Lys-B32Arg"},
+ "pdb_id":"2hh4",
+ "title":"NMR structure of human insulin mutant GLY-B8-D-SER, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2kxk",
- "title":"Human Insulin Mutant A22Gly-B31Lys-B32Arg"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"4cxn",
- "resolution":1.7,
- "title":"Crystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form I"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"4cxn",
- "resolution":1.7,
- "title":"Crystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form I"},
+ "pdb_id":"2hh4",
+ "title":"NMR structure of human insulin mutant GLY-B8-D-SER, HIS-B10-ASP PRO-B28-LYS, LYS-B29-PRO, 20 structures"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"2ws0",
"resolution":2.1,
"title":"Semi-synthetic analogue of human insulin NMeAlaB26-insulin at pH 7.5"},
{
- "experimental_method":["Solution NMR"],
- "pdb_id":"2kqq",
- "title":"NMR structure of human insulin mutant gly-b8-d-ala, his-b10-asp, pro-b28-lys, lys-b29-pro, 20 structures"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"2l1y",
- "title":"NMR Structure of human insulin mutant GLY-B20-D-ALA, GLY-B23-D-ALA PRO-B28-LYS, LYS-B29-PRO, 20 Structures"},
- {
"experimental_method":["X-ray diffraction"],
"pdb_id":"1os3",
"resolution":1.95,
"pdb_id":"3aiy",
"title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, REFINED AVERAGE STRUCTURE"},
{
- "experimental_method":["Solution NMR"],
- "pdb_id":"2aiy",
- "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 20 STRUCTURES"},
- {
"experimental_method":["X-ray diffraction"],
"pdb_id":"3inc",
"resolution":1.85,
"resolution":1.85,
"title":"Crystal structure of human insulin with Ni+2 complex"},
{
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2kxk",
+ "title":"Human Insulin Mutant A22Gly-B31Lys-B32Arg"},
+ {
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1mso",
- "resolution":1.0,
- "title":"T6 Human Insulin at 1.0 A Resolution"},
+ "pdb_id":"4cxn",
+ "resolution":1.7,
+ "title":"Crystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form I"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4cxn",
+ "resolution":1.7,
+ "title":"Crystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form I"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2r34",
+ "resolution":2.25,
+ "title":"Crystal structure of MN human arg-insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2kxk",
+ "title":"Human Insulin Mutant A22Gly-B31Lys-B32Arg"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wrx",
+ "resolution":1.5,
+ "title":"Semi-synthetic analogue of human insulin NMeAlaB26-insulin at pH 3.0"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2wrx",
+ "resolution":1.5,
+ "title":"Semi-synthetic analogue of human insulin NMeAlaB26-insulin at pH 3.0"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"1mhi",
"pdb_id":"1aiy",
"title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 10 STRUCTURES"},
{
- "experimental_method":["Solution NMR"],
- "pdb_id":"2k91",
- "title":"Enhancing the activity of insulin by stereospecific unfolding"},
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1mso",
+ "resolution":1.0,
+ "title":"T6 Human Insulin at 1.0 A Resolution"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2g56",
+ "resolution":2.2,
+ "title":"crystal structure of human insulin-degrading enzyme in complex with insulin B chain"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2k91",
- "title":"Enhancing the activity of insulin by stereospecific unfolding"},
+ "pdb_id":"2aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 20 STRUCTURES"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"4iyf",
- "resolution":1.8,
- "title":"Insulin glargine crystal structure 2"},
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2kqq",
+ "title":"NMR structure of human insulin mutant gly-b8-d-ala, his-b10-asp, pro-b28-lys, lys-b29-pro, 20 structures"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"4iyf",
- "resolution":1.8,
- "title":"Insulin glargine crystal structure 2"},
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2l1y",
+ "title":"NMR Structure of human insulin mutant GLY-B20-D-ALA, GLY-B23-D-ALA PRO-B28-LYS, LYS-B29-PRO, 20 Structures"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"5aiy",
- "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 'RED' SUBSTATE, AVERAGE STRUCTURE"},
+ "pdb_id":"2n2v",
+ "title":"Solution structure of [B26-B29 triazole cross-linked]-insulin analogue at pH 1.9"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"5aiy",
- "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 'RED' SUBSTATE, AVERAGE STRUCTURE"},
+ "pdb_id":"2n2w",
+ "title":"Solution structure of [B26-B29 triazole cross-linked]-insulin analogue at pH 8.0"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"4une",
"title":"Human insulin B26Phe mutant crystal structure"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5hqi",
- "resolution":0.97,
- "title":"Insulin with proline analog HzP at position B28 in the T2 state"},
+ "pdb_id":"4ung",
+ "resolution":1.81,
+ "title":"Human insulin B26Asn mutant crystal structure"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"5hqi",
- "resolution":0.97,
- "title":"Insulin with proline analog HzP at position B28 in the T2 state"},
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2mpi",
+ "title":"Solution structure of B24G insulin"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2mli",
- "title":"NMR structure of B25-(alpha, beta)-dehydro-phenylalanine insulin"},
+ "pdb_id":"2mpi",
+ "title":"Solution structure of B24G insulin"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"2mpg",
"title":"Solution structure of the [AibB8,LysB28,ProB29]-insulin analogue"},
{
"experimental_method":["Solution NMR"],
+ "pdb_id":"2mli",
+ "title":"NMR structure of B25-(alpha, beta)-dehydro-phenylalanine insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3w80",
+ "resolution":1.4,
+ "title":"Crystal structure of dodecamer human insulin with double C-axis length of the hexamer 2 Zn insulin cell"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3w80",
+ "resolution":1.4,
+ "title":"Crystal structure of dodecamer human insulin with double C-axis length of the hexamer 2 Zn insulin cell"},
+ {
+ "experimental_method":["Solution NMR"],
"pdb_id":"4aiy",
"title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 'GREEN' SUBSTATE, AVERAGE STRUCTURE"},
{
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4eww",
- "resolution":2.3,
- "title":"Human Insulin"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3w80",
- "resolution":1.4,
- "title":"Crystal structure of dodecamer human insulin with double C-axis length of the hexamer 2 Zn insulin cell"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3w80",
- "resolution":1.4,
- "title":"Crystal structure of dodecamer human insulin with double C-axis length of the hexamer 2 Zn insulin cell"},
- {
- "experimental_method":["X-ray diffraction"],
"pdb_id":"3tt8",
"resolution":1.12,
"title":"Crystal Structure Analysis of Cu Human Insulin Derivative"},
"resolution":1.12,
"title":"Crystal Structure Analysis of Cu Human Insulin Derivative"},
{
- "experimental_method":["Solution NMR"],
- "pdb_id":"2n2v",
- "title":"Solution structure of [B26-B29 triazole cross-linked]-insulin analogue at pH 1.9"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"2n2w",
- "title":"Solution structure of [B26-B29 triazole cross-linked]-insulin analogue at pH 8.0"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"2n2x",
- "title":"Solution structure of [GlyB24,B27-B29 triazole cross-linked]-insulin analogue at pH 1.9"},
- {
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4ung",
- "resolution":1.81,
- "title":"Human insulin B26Asn mutant crystal structure"},
+ "pdb_id":"4iyf",
+ "resolution":1.8,
+ "title":"Insulin glargine crystal structure 2"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2r34",
- "resolution":2.25,
- "title":"Crystal structure of MN human arg-insulin"},
+ "pdb_id":"4iyf",
+ "resolution":1.8,
+ "title":"Insulin glargine crystal structure 2"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2mpi",
- "title":"Solution structure of B24G insulin"},
+ "pdb_id":"5aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 'RED' SUBSTATE, AVERAGE STRUCTURE"},
{
"experimental_method":["Solution NMR"],
- "pdb_id":"2mpi",
- "title":"Solution structure of B24G insulin"},
+ "pdb_id":"5aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 'RED' SUBSTATE, AVERAGE STRUCTURE"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"5mhd",
"pdb_id":"5mhd",
"title":"Biosynthetic engineered A22S-B3K-B31R human insulin monomer structure in water/acetonitrile solutions."},
{
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2n2x",
+ "title":"Solution structure of [GlyB24,B27-B29 triazole cross-linked]-insulin analogue at pH 1.9"},
+ {
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2ws1",
- "resolution":1.6,
- "title":"Semi-synthetic analogue of human insulin NMeTyrB26-insulin in monomer form"},
+ "pdb_id":"5hqi",
+ "resolution":0.97,
+ "title":"Insulin with proline analog HzP at position B28 in the T2 state"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2ws1",
- "resolution":1.6,
- "title":"Semi-synthetic analogue of human insulin NMeTyrB26-insulin in monomer form"},
+ "pdb_id":"5hqi",
+ "resolution":0.97,
+ "title":"Insulin with proline analog HzP at position B28 in the T2 state"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f1c",
- "resolution":1.7,
+ "pdb_id":"4eww",
+ "resolution":2.3,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f1d",
- "resolution":1.637,
- "title":"Human Insulin"},
+ "pdb_id":"2wru",
+ "resolution":1.57,
+ "title":"Semi-synthetic highly active analogue of human insulin NMeAlaB26-DTI- NH2"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f0o",
- "resolution":1.672,
- "title":"Human Insulin"},
+ "pdb_id":"2wru",
+ "resolution":1.57,
+ "title":"Semi-synthetic highly active analogue of human insulin NMeAlaB26-DTI- NH2"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f1g",
- "resolution":1.637,
- "title":"Human insulin"},
+ "pdb_id":"4f1a",
+ "resolution":1.8,
+ "title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f4v",
- "resolution":1.637,
+ "pdb_id":"4f1a",
+ "resolution":1.8,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f8f",
- "resolution":1.676,
+ "pdb_id":"4f4t",
+ "resolution":1.637,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f1f",
- "resolution":1.684,
+ "pdb_id":"4f0o",
+ "resolution":1.672,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2wru",
- "resolution":1.57,
- "title":"Semi-synthetic highly active analogue of human insulin NMeAlaB26-DTI- NH2"},
+ "pdb_id":"2ws1",
+ "resolution":1.6,
+ "title":"Semi-synthetic analogue of human insulin NMeTyrB26-insulin in monomer form"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2wru",
- "resolution":1.57,
- "title":"Semi-synthetic highly active analogue of human insulin NMeAlaB26-DTI- NH2"},
+ "pdb_id":"2ws1",
+ "resolution":1.6,
+ "title":"Semi-synthetic analogue of human insulin NMeTyrB26-insulin in monomer form"},
{
- "experimental_method":["Solution NMR"],
- "pdb_id":"2kqq",
- "title":"NMR structure of human insulin mutant gly-b8-d-ala, his-b10-asp, pro-b28-lys, lys-b29-pro, 20 structures"},
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4fka",
+ "resolution":1.08,
+ "title":"High resolution structure of the manganese derivative of insulin"},
{
- "experimental_method":["Solution NMR"],
- "pdb_id":"2l1y",
- "title":"NMR Structure of human insulin mutant GLY-B20-D-ALA, GLY-B23-D-ALA PRO-B28-LYS, LYS-B29-PRO, 20 Structures"},
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4f1g",
+ "resolution":1.637,
+ "title":"Human insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f1a",
- "resolution":1.8,
+ "pdb_id":"4f8f",
+ "resolution":1.676,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f1a",
- "resolution":1.8,
+ "pdb_id":"4f1d",
+ "resolution":1.637,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f4t",
- "resolution":1.637,
+ "pdb_id":"4f1b",
+ "resolution":1.591,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f1b",
- "resolution":1.591,
+ "pdb_id":"4f1c",
+ "resolution":1.7,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1jca",
- "resolution":2.5,
- "title":"Non-standard Design of Unstable Insulin Analogues with Enhanced Activity"},
+ "pdb_id":"4f1f",
+ "resolution":1.684,
+ "title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3bxq",
- "resolution":1.3,
- "title":"The structure of a mutant insulin uncouples receptor binding from protein allostery. An electrostatic block to the TR transition"},
+ "pdb_id":"4f4v",
+ "resolution":1.637,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"1aiy",
+ "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 10 STRUCTURES"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"1htv",
"pdb_id":"1ai0",
"title":"R6 HUMAN INSULIN HEXAMER (NON-SYMMETRIC), NMR, 10 STRUCTURES"},
{
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3bxq",
+ "resolution":1.3,
+ "title":"The structure of a mutant insulin uncouples receptor binding from protein allostery. An electrostatic block to the TR transition"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1jca",
+ "resolution":2.5,
+ "title":"Non-standard Design of Unstable Insulin Analogues with Enhanced Activity"},
+ {
"experimental_method":["Solution NMR"],
- "pdb_id":"1aiy",
- "title":"R6 HUMAN INSULIN HEXAMER (SYMMETRIC), NMR, 10 STRUCTURES"},
+ "pdb_id":"2kqq",
+ "title":"NMR structure of human insulin mutant gly-b8-d-ala, his-b10-asp, pro-b28-lys, lys-b29-pro, 20 structures"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2l1y",
+ "title":"NMR Structure of human insulin mutant GLY-B20-D-ALA, GLY-B23-D-ALA PRO-B28-LYS, LYS-B29-PRO, 20 Structures"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6ver",
+ "resolution":1.047,
+ "title":"Human insulin analog: [GluB10,TyrB20]-DOI"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6ver",
+ "resolution":1.047,
+ "title":"Human insulin analog: [GluB10,TyrB20]-DOI"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"5bts",
"title":"Structural and biophysical characterization of a covalent insulin dimer formed during storage of neutral formulation of human insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5usp",
- "resolution":1.174,
- "title":"Insulin with proline analog Pip at position B28 in the T2 state"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"5usp",
- "resolution":1.174,
- "title":"Insulin with proline analog Pip at position B28 in the T2 state"},
- {
- "experimental_method":["X-ray diffraction"],
"pdb_id":"5bpo",
"resolution":1.9,
"title":"Human insulin with intra-chain chemical crosslink between modified B27 and B29"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5uu2",
- "resolution":1.223,
- "title":"Insulin with proline analog ThioP at position B28 in the T2 state"},
- {
- "experimental_method":["X-ray diffraction"],
"pdb_id":"5urt",
"resolution":1.18,
"title":"Insulin with proline analog DhP at position B28 in the T2 state"},
{
"experimental_method":["X-ray diffraction"],
+ "pdb_id":"5usp",
+ "resolution":1.174,
+ "title":"Insulin with proline analog Pip at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5usp",
+ "resolution":1.174,
+ "title":"Insulin with proline analog Pip at position B28 in the T2 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
"pdb_id":"6h3m",
"resolution":1.821,
"title":"The crystal structure of a human seleno-insulin analog"},
"title":"The crystal structure of a human seleno-insulin analog"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"6ver",
- "resolution":1.047,
- "title":"Human insulin analog: [GluB10,TyrB20]-DOI"},
+ "pdb_id":"4rxw",
+ "resolution":1.73,
+ "title":"Crystal Structure of the cobalt human insulin derivative"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"6ver",
- "resolution":1.047,
- "title":"Human insulin analog: [GluB10,TyrB20]-DOI"},
+ "pdb_id":"4rxw",
+ "resolution":1.73,
+ "title":"Crystal Structure of the cobalt human insulin derivative"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2n2v",
+ "title":"Solution structure of [B26-B29 triazole cross-linked]-insulin analogue at pH 1.9"},
+ {
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2n2w",
+ "title":"Solution structure of [B26-B29 triazole cross-linked]-insulin analogue at pH 8.0"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4ewx",
- "resolution":2.201,
+ "pdb_id":"4eyd",
+ "resolution":1.471,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4eyd",
+ "resolution":1.471,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4eyn",
+ "resolution":1.532,
+ "title":"Human Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4eyn",
+ "resolution":1.532,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4eww",
- "resolution":2.3,
+ "pdb_id":"4ewx",
+ "resolution":2.201,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4exx",
- "resolution":1.55,
+ "pdb_id":"4eyp",
+ "resolution":1.591,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4eyp",
- "resolution":1.591,
+ "pdb_id":"4exx",
+ "resolution":1.55,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4ewz",
- "resolution":1.791,
- "title":"Human Insulin"},
+ "pdb_id":"5usv",
+ "resolution":1.3,
+ "title":"Insulin with proline analog AzeP at position B28 in the T2 state"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4ewz",
- "resolution":1.791,
- "title":"Human Insulin"},
+ "pdb_id":"5usv",
+ "resolution":1.3,
+ "title":"Insulin with proline analog AzeP at position B28 in the T2 state"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4ex0",
- "resolution":1.86,
- "title":"Human Insulin"},
+ "pdb_id":"5uu2",
+ "resolution":1.223,
+ "title":"Insulin with proline analog ThioP at position B28 in the T2 state"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4ex0",
- "resolution":1.86,
+ "pdb_id":"4ex1",
+ "resolution":1.657,
"title":"Human Insulin"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"4eyd",
- "resolution":1.471,
- "title":"Human Insulin"},
+ "experimental_method":["Solution NMR"],
+ "pdb_id":"2n2x",
+ "title":"Solution structure of [GlyB24,B27-B29 triazole cross-linked]-insulin analogue at pH 1.9"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4eyd",
+ "pdb_id":"4ey9",
"resolution":1.471,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4ex1",
- "resolution":1.657,
+ "pdb_id":"4ey9",
+ "resolution":1.471,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
"resolution":2.05,
"title":"Human insulin in complex with cucurbit[7]uril"},
{
- "experimental_method":["Solution NMR"],
- "pdb_id":"2n2v",
- "title":"Solution structure of [B26-B29 triazole cross-linked]-insulin analogue at pH 1.9"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"2n2w",
- "title":"Solution structure of [B26-B29 triazole cross-linked]-insulin analogue at pH 8.0"},
- {
- "experimental_method":["Solution NMR"],
- "pdb_id":"2n2x",
- "title":"Solution structure of [GlyB24,B27-B29 triazole cross-linked]-insulin analogue at pH 1.9"},
- {
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4ey9",
- "resolution":1.471,
+ "pdb_id":"4ex0",
+ "resolution":1.86,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4ey9",
- "resolution":1.471,
+ "pdb_id":"4ex0",
+ "resolution":1.86,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4fka",
- "resolution":1.08,
- "title":"High resolution structure of the manganese derivative of insulin"},
+ "pdb_id":"4eww",
+ "resolution":2.3,
+ "title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4eyn",
- "resolution":1.532,
+ "pdb_id":"4ewz",
+ "resolution":1.791,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4eyn",
- "resolution":1.532,
+ "pdb_id":"4ewz",
+ "resolution":1.791,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4rxw",
- "resolution":1.73,
- "title":"Crystal Structure of the cobalt human insulin derivative"},
+ "pdb_id":"5c0d",
+ "resolution":1.68,
+ "title":"HLA-A02 carrying AQWGPDPAAA"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4rxw",
- "resolution":1.73,
- "title":"Crystal Structure of the cobalt human insulin derivative"},
+ "pdb_id":"3ir0",
+ "resolution":2.2,
+ "title":"Crystal Structure of Human Insulin complexed with Cu+2 metal ion"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5usv",
- "resolution":1.3,
- "title":"Insulin with proline analog AzeP at position B28 in the T2 state"},
+ "pdb_id":"3ir0",
+ "resolution":2.2,
+ "title":"Crystal Structure of Human Insulin complexed with Cu+2 metal ion"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5usv",
- "resolution":1.3,
- "title":"Insulin with proline analog AzeP at position B28 in the T2 state"},
+ "pdb_id":"3exx",
+ "resolution":1.35,
+ "title":"Structure of the T6 human insulin derivative with nickel at 1.35 A resolution"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3exx",
+ "resolution":1.35,
+ "title":"Structure of the T6 human insulin derivative with nickel at 1.35 A resolution"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"2wrv",
"title":"Crystal structure form ultalente insulin microcrystals"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3exx",
- "resolution":1.35,
- "title":"Structure of the T6 human insulin derivative with nickel at 1.35 A resolution"},
+ "pdb_id":"1b9e",
+ "resolution":2.5,
+ "title":"HUMAN INSULIN MUTANT SERB9GLU"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3exx",
- "resolution":1.35,
- "title":"Structure of the T6 human insulin derivative with nickel at 1.35 A resolution"},
+ "pdb_id":"1b9e",
+ "resolution":2.5,
+ "title":"HUMAN INSULIN MUTANT SERB9GLU"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"2vjz",
- "resolution":1.8,
- "title":"Crystal structure form ultalente insulin microcrystals"},
+ "experimental_method":["X-ray powder diffraction"],
+ "pdb_id":"1fub",
+ "title":"FIRST PROTEIN STRUCTURE DETERMINED FROM X-RAY POWDER DIFFRACTION DATA"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f1c",
- "resolution":1.7,
+ "pdb_id":"4f51",
+ "resolution":1.637,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f1d",
+ "pdb_id":"4f4t",
"resolution":1.637,
"title":"Human Insulin"},
{
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4gbc",
- "resolution":1.778,
- "title":"Crystal structure of aspart insulin at pH 6.5"},
+ "pdb_id":"2vjz",
+ "resolution":1.8,
+ "title":"Crystal structure form ultalente insulin microcrystals"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4gbn",
- "resolution":1.872,
- "title":"Crystal structure of aspart insulin at pH 6.5"},
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+ "resolution":1.08,
+ "title":"High resolution structure of the manganese derivative of insulin"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"4f1g",
"title":"Human insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f4v",
- "resolution":1.637,
- "title":"Human Insulin"},
+ "pdb_id":"2r36",
+ "resolution":2.0,
+ "title":"Crystal structure of ni human ARG-insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f51",
- "resolution":1.637,
- "title":"Human Insulin"},
+ "pdb_id":"4gbi",
+ "resolution":2.502,
+ "title":"Crystal structure of aspart insulin at pH 6.5"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f1f",
- "resolution":1.684,
+ "pdb_id":"4f8f",
+ "resolution":1.676,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f8f",
- "resolution":1.676,
+ "pdb_id":"4f1d",
+ "resolution":1.637,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4gbi",
- "resolution":2.502,
+ "pdb_id":"4gbc",
+ "resolution":1.778,
+ "title":"Crystal structure of aspart insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbn",
+ "resolution":1.872,
"title":"Crystal structure of aspart insulin at pH 6.5"},
{
"experimental_method":["X-ray diffraction"],
"title":"Human insulin analogue (D-ProB8)-insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2r36",
- "resolution":2.0,
- "title":"Crystal structure of ni human ARG-insulin"},
+ "pdb_id":"4f1b",
+ "resolution":1.591,
+ "title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f4t",
- "resolution":1.637,
+ "pdb_id":"4f1c",
+ "resolution":1.7,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4f1b",
- "resolution":1.591,
+ "pdb_id":"4f1f",
+ "resolution":1.684,
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3ir0",
- "resolution":2.2,
- "title":"Crystal Structure of Human Insulin complexed with Cu+2 metal ion"},
+ "pdb_id":"4f4v",
+ "resolution":1.637,
+ "title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3ir0",
- "resolution":2.2,
- "title":"Crystal Structure of Human Insulin complexed with Cu+2 metal ion"},
+ "pdb_id":"2ceu",
+ "resolution":1.8,
+ "title":"Despentapeptide insulin in acetic acid (pH 2)"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1jca",
- "resolution":2.5,
- "title":"Non-standard Design of Unstable Insulin Analogues with Enhanced Activity"},
+ "pdb_id":"2ceu",
+ "resolution":1.8,
+ "title":"Despentapeptide insulin in acetic acid (pH 2)"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"3bxq",
"title":"The structure of a mutant insulin uncouples receptor binding from protein allostery. An electrostatic block to the TR transition"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1b9e",
- "resolution":2.5,
- "title":"HUMAN INSULIN MUTANT SERB9GLU"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"1b9e",
+ "pdb_id":"1jca",
"resolution":2.5,
- "title":"HUMAN INSULIN MUTANT SERB9GLU"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"2ceu",
- "resolution":1.8,
- "title":"Despentapeptide insulin in acetic acid (pH 2)"},
+ "title":"Non-standard Design of Unstable Insulin Analogues with Enhanced Activity"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2ceu",
- "resolution":1.8,
- "title":"Despentapeptide insulin in acetic acid (pH 2)"},
- {
- "experimental_method":["X-ray powder diffraction"],
- "pdb_id":"1fub",
- "title":"FIRST PROTEIN STRUCTURE DETERMINED FROM X-RAY POWDER DIFFRACTION DATA"},
+ "pdb_id":"5cny",
+ "resolution":1.7,
+ "title":"Crystal Structure of human zinc insulin at pH 5.5"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"5bpo",
"title":"Human insulin with intra-chain chemical crosslink between modified B27 and B29"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5uu2",
- "resolution":1.223,
- "title":"Insulin with proline analog ThioP at position B28 in the T2 state"},
+ "pdb_id":"5urt",
+ "resolution":1.18,
+ "title":"Insulin with proline analog DhP at position B28 in the T2 state"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"2mli",
"title":"NMR structure of B25-(alpha, beta)-dehydro-phenylalanine insulin"},
{
"experimental_method":["X-ray diffraction"],
+ "pdb_id":"4iuz",
+ "resolution":1.6,
+ "title":"High resolution crystal structure of racemic ester insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
"pdb_id":"4ey1",
"resolution":1.471,
"title":"Human Insulin"},
"title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
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- "resolution":1.657,
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- "experimental_method":["X-ray diffraction"],
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- "resolution":1.6,
- "title":"High resolution crystal structure of racemic ester insulin"},
- {
- "experimental_method":["X-ray diffraction"],
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- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"4fka",
- "resolution":1.08,
- "title":"High resolution structure of the manganese derivative of insulin"},
+ "pdb_id":"5uu2",
+ "resolution":1.223,
+ "title":"Insulin with proline analog ThioP at position B28 in the T2 state"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5cny",
- "resolution":1.7,
- "title":"Crystal Structure of human zinc insulin at pH 5.5"},
+ "pdb_id":"4ex1",
+ "resolution":1.657,
+ "title":"Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2vk0",
- "resolution":2.2,
- "title":"Crystal structure form ultalente insulin microcrystals"},
+ "pdb_id":"2omi",
+ "resolution":2.24,
+ "title":"Structure of human insulin cocrystallized with protamine"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"2k9r",
"title":"Enhancing the activity of insulin by stereospecific unfolding"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2omi",
- "resolution":2.24,
- "title":"Structure of human insulin cocrystallized with protamine"},
+ "pdb_id":"2g54",
+ "resolution":2.25,
+ "title":"Crystal structure of Zn-bound human insulin-degrading enzyme in complex with insulin B chain"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2vk0",
+ "resolution":2.2,
+ "title":"Crystal structure form ultalente insulin microcrystals"},
+ {
+ "experimental_method":["X-ray powder diffraction"],
+ "pdb_id":"1fub",
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{
"experimental_method":["X-ray diffraction"],
"pdb_id":"2vjz",
"title":"Crystal structure form ultalente insulin microcrystals"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4gbn",
- "resolution":1.872,
- "title":"Crystal structure of aspart insulin at pH 6.5"},
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+ "resolution":2.0,
+ "title":"Crystal structure of ni human ARG-insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4gbl",
- "resolution":2.5,
+ "pdb_id":"4gbk",
+ "resolution":2.4,
"title":"Crystal structure of aspart insulin at pH 8.5"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4gbl",
- "resolution":2.5,
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+ "resolution":2.4,
"title":"Crystal structure of aspart insulin at pH 8.5"},
{
"experimental_method":["X-ray diffraction"],
"title":"Crystal structure of aspart insulin at pH 6.5"},
{
"experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbc",
+ "resolution":1.778,
+ "title":"Crystal structure of aspart insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
"pdb_id":"4cy7",
"resolution":1.4,
"title":"Crystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form II"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2r36",
- "resolution":2.0,
- "title":"Crystal structure of ni human ARG-insulin"},
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+ "resolution":1.872,
+ "title":"Crystal structure of aspart insulin at pH 6.5"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4gbc",
- "resolution":1.778,
- "title":"Crystal structure of aspart insulin at pH 6.5"},
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+ "resolution":2.5,
+ "title":"Crystal structure of aspart insulin at pH 8.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gbl",
+ "resolution":2.5,
+ "title":"Crystal structure of aspart insulin at pH 8.5"},
{
"experimental_method":["X-ray powder diffraction"],
"pdb_id":"1fu2",
"resolution":2.0,
"title":"Crystal structure of an unstable insulin analog with native activity."},
{
- "experimental_method":["X-ray powder diffraction"],
- "pdb_id":"1fub",
- "title":"FIRST PROTEIN STRUCTURE DETERMINED FROM X-RAY POWDER DIFFRACTION DATA"},
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6s4i",
+ "resolution":1.511,
+ "title":"Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB30 human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6s4i",
+ "resolution":1.511,
+ "title":"Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB30 human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6p4z",
+ "resolution":1.8,
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+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5co9",
+ "resolution":1.92,
+ "title":"Crystal structure of human zinc insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5cny",
+ "resolution":1.7,
+ "title":"Crystal Structure of human zinc insulin at pH 5.5"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"5co2",
"title":"Human insulin with intra-chain chemical crosslink between modified B24 and B29"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"6s4i",
- "resolution":1.511,
- "title":"Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB30 human insulin"},
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- "experimental_method":["X-ray diffraction"],
- "pdb_id":"6s4i",
- "resolution":1.511,
- "title":"Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB30 human insulin"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"6p4z",
- "resolution":1.8,
- "title":"Structure of gadolinium-caged cobalt (III) insulin hexamer"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"6gv0",
- "resolution":1.26,
- "title":"Insulin glulisine"},
- {
- "experimental_method":["X-ray diffraction"],
"pdb_id":"6vet",
"resolution":1.46,
"title":"Human insulin analog: [GluB10,HisA8,ArgA9,TyrB20]-DOI"},
"title":"Human insulin analog: [GluB10,HisA8,ArgA9,TyrB20]-DOI"},
{
"experimental_method":["X-ray diffraction"],
+ "pdb_id":"6gv0",
+ "resolution":1.26,
+ "title":"Insulin glulisine"},
+ {
+ "experimental_method":["X-ray diffraction"],
"pdb_id":"4iuz",
"resolution":1.6,
"title":"High resolution crystal structure of racemic ester insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4gbk",
- "resolution":2.4,
- "title":"Crystal structure of aspart insulin at pH 8.5"},
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- "experimental_method":["X-ray diffraction"],
- "pdb_id":"4gbk",
- "resolution":2.4,
- "title":"Crystal structure of aspart insulin at pH 8.5"},
- {
- "experimental_method":["X-ray diffraction"],
"pdb_id":"4efx",
"resolution":1.98,
"title":"Highly biologically active insulin with additional disulfide bond"},
"resolution":1.98,
"title":"Highly biologically active insulin with additional disulfide bond"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"5co9",
- "resolution":1.92,
- "title":"Crystal structure of human zinc insulin at pH 6.5"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"5cny",
- "resolution":1.7,
- "title":"Crystal Structure of human zinc insulin at pH 5.5"},
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6ce7",
+ "resolution":7.4,
+ "title":"Insulin Receptor ectodomain in complex with one insulin molecule"},
{
"experimental_method":["Solution NMR"],
"pdb_id":"2jmn",
"title":"NMR structure of human insulin mutant His-B10-Asp, Pro-B28-Lys, Lys-B29-Pro, 20 structures"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3e7z",
- "resolution":1.7,
- "title":"Structure of human insulin"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3e7z",
- "resolution":1.7,
- "title":"Structure of human insulin"},
+ "pdb_id":"3utq",
+ "resolution":1.67,
+ "title":"Human HLA-A*0201-ALWGPDPAAA"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2w44",
- "resolution":2.0,
- "title":"Structure DeltaA1-A4 insulin"},
+ "pdb_id":"2omi",
+ "resolution":2.24,
+ "title":"Structure of human insulin cocrystallized with protamine"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"3e7y",
"title":"Structure of human insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2omi",
- "resolution":2.24,
- "title":"Structure of human insulin cocrystallized with protamine"},
+ "pdb_id":"1ev6",
+ "resolution":1.9,
+ "title":"Structure of the monoclinic form of the M-cresol/insulin R6 hexamer"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1trz",
+ "resolution":1.6,
+ "title":"CRYSTALLOGRAPHIC EVIDENCE FOR DUAL COORDINATION AROUND ZINC IN THE T3R3 HUMAN INSULIN HEXAMER"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1trz",
+ "resolution":1.6,
+ "title":"CRYSTALLOGRAPHIC EVIDENCE FOR DUAL COORDINATION AROUND ZINC IN THE T3R3 HUMAN INSULIN HEXAMER"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"2ws7",
"title":"Semi-synthetic analogue of human insulin ProB26-DTI"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4cy7",
+ "pdb_id":"4nib",
"resolution":1.4,
- "title":"Crystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form II"},
+ "title":"Crystal structure of human insulin mutant B20 D-ala, B23 D-ala"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"4nib",
"title":"Crystal structure of human insulin mutant B20 D-ala, B23 D-ala"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4nib",
+ "pdb_id":"4cy7",
"resolution":1.4,
- "title":"Crystal structure of human insulin mutant B20 D-ala, B23 D-ala"},
+ "title":"Crystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form II"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"1qj0",
"resolution":2.4,
"title":"HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"1uz9",
- "resolution":1.6,
- "title":"Crystallographic and solution studies of N-lithocholyl insulin: a new generation of prolonged-acting insulins."},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"1uz9",
- "resolution":1.6,
- "title":"Crystallographic and solution studies of N-lithocholyl insulin: a new generation of prolonged-acting insulins."},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"1trz",
- "resolution":1.6,
- "title":"CRYSTALLOGRAPHIC EVIDENCE FOR DUAL COORDINATION AROUND ZINC IN THE T3R3 HUMAN INSULIN HEXAMER"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"1trz",
- "resolution":1.6,
- "title":"CRYSTALLOGRAPHIC EVIDENCE FOR DUAL COORDINATION AROUND ZINC IN THE T3R3 HUMAN INSULIN HEXAMER"},
- {
"experimental_method":["X-ray powder diffraction"],
"pdb_id":"1fu2",
"title":"FIRST PROTEIN STRUCTURE DETERMINED FROM X-RAY POWDER DIFFRACTION DATA"},
"title":"The structure of the resorcinol/insulin R6 hexamer"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1ev3",
- "resolution":1.78,
- "title":"Structure of the rhombohedral form of the M-cresol/insulin R6 hexamer"},
+ "pdb_id":"1ev6",
+ "resolution":1.9,
+ "title":"Structure of the monoclinic form of the M-cresol/insulin R6 hexamer"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"1guj",
"title":"Insulin at pH 2: structural analysis of the conditions promoting insulin fibre formation."},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1ev6",
- "resolution":1.9,
- "title":"Structure of the monoclinic form of the M-cresol/insulin R6 hexamer"},
+ "pdb_id":"1ev3",
+ "resolution":1.78,
+ "title":"Structure of the rhombohedral form of the M-cresol/insulin R6 hexamer"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1ev6",
- "resolution":1.9,
- "title":"Structure of the monoclinic form of the M-cresol/insulin R6 hexamer"},
+ "pdb_id":"2w44",
+ "resolution":2.0,
+ "title":"Structure DeltaA1-A4 insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"6s4j",
- "resolution":1.5,
- "title":"Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB27, desB30 human insulin"},
+ "pdb_id":"1uz9",
+ "resolution":1.6,
+ "title":"Crystallographic and solution studies of N-lithocholyl insulin: a new generation of prolonged-acting insulins."},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"6s4j",
- "resolution":1.5,
- "title":"Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB27, desB30 human insulin"},
+ "pdb_id":"1uz9",
+ "resolution":1.6,
+ "title":"Crystallographic and solution studies of N-lithocholyl insulin: a new generation of prolonged-acting insulins."},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3e7z",
+ "resolution":1.7,
+ "title":"Structure of human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3e7z",
+ "resolution":1.7,
+ "title":"Structure of human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6gnq",
+ "resolution":2.2,
+ "title":"Monoclinic crystalline form of human insulin, complexed with meta-cresol"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7s4y",
+ "resolution":1.71,
+ "title":"Serial Macromolecular Crystallography at ALBA Synchrotron Light Source - Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7s4y",
+ "resolution":1.71,
+ "title":"Serial Macromolecular Crystallography at ALBA Synchrotron Light Source - Insulin"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"5co6",
"title":"Structure of gadolinium-caged cobalt (III) insulin hexamer"},
{
"experimental_method":["X-ray diffraction"],
+ "pdb_id":"5co9",
+ "resolution":1.92,
+ "title":"Crystal structure of human zinc insulin at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6s4j",
+ "resolution":1.5,
+ "title":"Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB27, desB30 human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6s4j",
+ "resolution":1.5,
+ "title":"Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB27, desB30 human insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
"pdb_id":"6gv0",
"resolution":1.26,
"title":"Insulin glulisine"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"6gnq",
- "resolution":2.2,
- "title":"Monoclinic crystalline form of human insulin, complexed with meta-cresol"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"5ems",
- "resolution":2.3,
- "title":"Crystal Structure of an iodinated insulin analog"},
- {
- "experimental_method":["X-ray diffraction"],
"pdb_id":"3zu1",
"resolution":1.6,
"title":"Structure of LysB29(Nepsilon omega-carboxyheptadecanoyl) des(B30) Human Insulin"},
"title":"Structure of LysB29(Nepsilon omega-carboxyheptadecanoyl) des(B30) Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5co9",
- "resolution":1.92,
- "title":"Crystal structure of human zinc insulin at pH 6.5"},
+ "pdb_id":"5ems",
+ "resolution":2.3,
+ "title":"Crystal Structure of an iodinated insulin analog"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6ce7",
+ "resolution":7.4,
+ "title":"Insulin Receptor ectodomain in complex with one insulin molecule"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1jk8",
+ "resolution":2.4,
+ "title":"Crystal structure of a human insulin peptide-HLA-DQ8 complex"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"2wby",
"title":"Leucine-zippered human insulin receptor ectodomain with single bound insulin - \"upper\" membrane-distal part"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2olz",
- "resolution":1.7,
- "title":"Structure of human insulin in presence of thiocyanate at pH 7.0"},
+ "pdb_id":"2om1",
+ "resolution":1.97,
+ "title":"Structure of human insulin in presence of thiocyanate at pH 6.5"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2olz",
- "resolution":1.7,
- "title":"Structure of human insulin in presence of thiocyanate at pH 7.0"},
+ "pdb_id":"2om0",
+ "resolution":2.05,
+ "title":"Structure of human insulin in presence of urea at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2om0",
+ "resolution":2.05,
+ "title":"Structure of human insulin in presence of urea at pH 6.5"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3p33",
+ "resolution":2.3,
+ "title":"Insulin fibrillation is the Janus face of induced fit. A chiral clamp stabilizes the native state at the expense of activity"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"2omg",
"title":"Structure of human insulin cocrystallized with protamine and urea"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2w44",
- "resolution":2.0,
- "title":"Structure DeltaA1-A4 insulin"},
+ "pdb_id":"2olz",
+ "resolution":1.7,
+ "title":"Structure of human insulin in presence of thiocyanate at pH 7.0"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2ws7",
- "resolution":2.59,
- "title":"Semi-synthetic analogue of human insulin ProB26-DTI"},
+ "pdb_id":"2olz",
+ "resolution":1.7,
+ "title":"Structure of human insulin in presence of thiocyanate at pH 7.0"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4fg3",
- "resolution":2.001,
- "title":"Crystal Structure Analysis of the Human Insulin"},
+ "pdb_id":"1ben",
+ "resolution":1.4,
+ "title":"INSULIN COMPLEXED WITH 4-HYDROXYBENZAMIDE"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4fg3",
- "resolution":2.001,
- "title":"Crystal Structure Analysis of the Human Insulin"},
+ "pdb_id":"1g7a",
+ "resolution":1.2,
+ "title":"1.2 A structure of T3R3 human insulin at 100 K"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1g7a",
+ "resolution":1.2,
+ "title":"1.2 A structure of T3R3 human insulin at 100 K"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"1w8p",
"title":"Structural properties of the B25Tyr-NMe-B26Phe insulin mutant."},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3p33",
- "resolution":2.3,
- "title":"Insulin fibrillation is the Janus face of induced fit. A chiral clamp stabilizes the native state at the expense of activity"},
+ "pdb_id":"1rwe",
+ "resolution":1.8,
+ "title":"Enhancing the activity of insulin at receptor edge: crystal structure and photo-cross-linking of A8 analogues"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1rwe",
+ "resolution":1.8,
+ "title":"Enhancing the activity of insulin at receptor edge: crystal structure and photo-cross-linking of A8 analogues"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"1znj",
"title":"Diabetes-Associated Mutations in Human Insulin: Crystal Structure and Photo-Cross-Linking Studies of A-Chain Variant Insulin Wakayama"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1qj0",
- "resolution":2.4,
- "title":"HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR"},
+ "pdb_id":"4fg3",
+ "resolution":2.001,
+ "title":"Crystal Structure Analysis of the Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1rwe",
- "resolution":1.8,
- "title":"Enhancing the activity of insulin at receptor edge: crystal structure and photo-cross-linking of A8 analogues"},
+ "pdb_id":"4fg3",
+ "resolution":2.001,
+ "title":"Crystal Structure Analysis of the Human Insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1rwe",
- "resolution":1.8,
- "title":"Enhancing the activity of insulin at receptor edge: crystal structure and photo-cross-linking of A8 analogues"},
+ "pdb_id":"2ws7",
+ "resolution":2.59,
+ "title":"Semi-synthetic analogue of human insulin ProB26-DTI"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1evr",
- "resolution":1.9,
- "title":"The structure of the resorcinol/insulin R6 hexamer"},
+ "pdb_id":"1lph",
+ "resolution":2.3,
+ "title":"LYS(B28)PRO(B29)-HUMAN INSULIN"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"1qj0",
+ "resolution":2.4,
+ "title":"HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"1g7b",
"title":"1.3 A STRUCTURE OF T3R3 HUMAN INSULIN AT 100 K"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1ben",
- "resolution":1.4,
- "title":"INSULIN COMPLEXED WITH 4-HYDROXYBENZAMIDE"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"1lph",
- "resolution":2.3,
- "title":"LYS(B28)PRO(B29)-HUMAN INSULIN"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"1lph",
- "resolution":2.3,
- "title":"LYS(B28)PRO(B29)-HUMAN INSULIN"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"2om1",
- "resolution":1.97,
- "title":"Structure of human insulin in presence of thiocyanate at pH 6.5"},
+ "pdb_id":"1evr",
+ "resolution":1.9,
+ "title":"The structure of the resorcinol/insulin R6 hexamer"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2om0",
- "resolution":2.05,
- "title":"Structure of human insulin in presence of urea at pH 6.5"},
+ "pdb_id":"2w44",
+ "resolution":2.0,
+ "title":"Structure DeltaA1-A4 insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2om0",
- "resolution":2.05,
- "title":"Structure of human insulin in presence of urea at pH 6.5"},
+ "pdb_id":"6gnq",
+ "resolution":2.2,
+ "title":"Monoclinic crystalline form of human insulin, complexed with meta-cresol"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1g7a",
- "resolution":1.2,
- "title":"1.2 A structure of T3R3 human insulin at 100 K"},
+ "pdb_id":"5uru",
+ "resolution":2.41,
+ "title":"Insulin with proline analog DhP at position B28 in the R6 state"},
{
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"1g7a",
- "resolution":1.2,
- "title":"1.2 A structure of T3R3 human insulin at 100 K"},
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"7bw7",
+ "resolution":4.1,
+ "title":"Cryo-EM Structure for the Ectodomain of the Full-length Human Insulin Receptor in Complex with 1 Insulin."},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"6ck2",
"title":"Insulin analog containing a YB26W mutation"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5udp",
- "resolution":1.348,
- "title":"High resolution x-ray crystal structure of synthetic insulin lispro"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"5udp",
- "resolution":1.348,
- "title":"High resolution x-ray crystal structure of synthetic insulin lispro"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"5mt3",
- "resolution":2.02,
- "title":"Human insulin in complex with serotonin and arginine"},
- {
- "experimental_method":["X-ray diffraction"],
"pdb_id":"6nwv",
"resolution":1.601,
"title":"Insulin Lispro Analog"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"6gnq",
- "resolution":2.2,
- "title":"Monoclinic crystalline form of human insulin, complexed with meta-cresol"},
- {
- "experimental_method":["X-ray diffraction"],
"pdb_id":"5hrq",
"resolution":1.28,
"title":"Insulin with proline analog HzP at position B28 in the R6 state"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5hpr",
- "resolution":1.33,
- "title":"Insulin with proline analog HyP at position B28 in the T2 state"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"5hpr",
- "resolution":1.33,
- "title":"Insulin with proline analog HyP at position B28 in the T2 state"},
+ "pdb_id":"3zqr",
+ "resolution":1.9,
+ "title":"NMePheB25 insulin analogue crystal structure"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5ems",
- "resolution":2.3,
- "title":"Crystal Structure of an iodinated insulin analog"},
+ "pdb_id":"3zqr",
+ "resolution":1.9,
+ "title":"NMePheB25 insulin analogue crystal structure"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"4ajx",
"title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3v1g",
- "resolution":2.2,
- "title":"Forestalling insulin fibrillation by insertion of a chiral clamp mechanism-based application of protein engineering to global health"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3v1g",
- "resolution":2.2,
- "title":"Forestalling insulin fibrillation by insertion of a chiral clamp mechanism-based application of protein engineering to global health"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3zqr",
- "resolution":1.9,
- "title":"NMePheB25 insulin analogue crystal structure"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3zqr",
- "resolution":1.9,
- "title":"NMePheB25 insulin analogue crystal structure"},
+ "pdb_id":"4akj",
+ "resolution":2.01,
+ "title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"4ajz",
"title":"TyrB25,NMePheB26,LysB28,ProB29-insulin analogue crystal structure"},
{
"experimental_method":["X-ray diffraction"],
+ "pdb_id":"3v1g",
+ "resolution":2.2,
+ "title":"Forestalling insulin fibrillation by insertion of a chiral clamp mechanism-based application of protein engineering to global health"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3v1g",
+ "resolution":2.2,
+ "title":"Forestalling insulin fibrillation by insertion of a chiral clamp mechanism-based application of protein engineering to global health"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uu3",
+ "resolution":2.25,
+ "title":"Insulin with proline analog DfP at position B28 in the R6 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uss",
+ "resolution":2.061,
+ "title":"Insulin with proline analog PiP at position B28 in the R6 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5uss",
+ "resolution":2.061,
+ "title":"Insulin with proline analog PiP at position B28 in the R6 state"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5udp",
+ "resolution":1.348,
+ "title":"High resolution x-ray crystal structure of synthetic insulin lispro"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5udp",
+ "resolution":1.348,
+ "title":"High resolution x-ray crystal structure of synthetic insulin lispro"},
+ {
+ "experimental_method":["X-ray diffraction"],
"pdb_id":"5mt9",
"resolution":1.88,
"title":"Human insulin in complex with serotonin and arginine"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5uru",
- "resolution":2.41,
- "title":"Insulin with proline analog DhP at position B28 in the R6 state"},
+ "pdb_id":"5ems",
+ "resolution":2.3,
+ "title":"Crystal Structure of an iodinated insulin analog"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5hpr",
+ "resolution":1.33,
+ "title":"Insulin with proline analog HyP at position B28 in the T2 state"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5uu3",
- "resolution":2.25,
- "title":"Insulin with proline analog DfP at position B28 in the R6 state"},
+ "pdb_id":"5hpr",
+ "resolution":1.33,
+ "title":"Insulin with proline analog HyP at position B28 in the T2 state"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"3kq6",
"title":"Enhancing the Therapeutic Properties of a Protein by a Designed Zinc-Binding Site, Structural principles of a novel long-acting insulin analog"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4akj",
- "resolution":2.01,
- "title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"5uss",
- "resolution":2.061,
- "title":"Insulin with proline analog PiP at position B28 in the R6 state"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"5uss",
- "resolution":2.061,
- "title":"Insulin with proline analog PiP at position B28 in the R6 state"},
+ "pdb_id":"5mt3",
+ "resolution":2.02,
+ "title":"Human insulin in complex with serotonin and arginine"},
{
"experimental_method":["Electron Microscopy"],
"pdb_id":"6hn5",
"title":"Leucine-zippered human insulin receptor ectodomain with single bound insulin - \"upper\" membrane-distal part"},
{
"experimental_method":["X-ray diffraction"],
+ "pdb_id":"4wdi",
+ "resolution":2.313,
+ "title":"Weak TCR binding to an unstable insulin epitope drives type 1 diabetes"},
+ {
+ "experimental_method":["X-ray diffraction"],
"pdb_id":"2wc0",
"resolution":2.8,
"title":"crystal structure of human insulin degrading enzyme in complex with iodinated insulin"},
"resolution":2.8,
"title":"crystal structure of human insulin degrading enzyme in complex with iodinated insulin"},
{
- "experimental_method":["Electron Microscopy"],
- "pdb_id":"6sof",
- "resolution":4.3,
- "title":"human insulin receptor ectodomain bound by 4 insulin"},
- {
"experimental_method":["X-ray diffraction"],
"pdb_id":"6z7y",
"resolution":2.2,
"resolution":2.2,
"title":"Human insulin in complex with the analytical antibody OXI-005 Fab"},
{
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6sof",
+ "resolution":4.3,
+ "title":"human insulin receptor ectodomain bound by 4 insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3p2x",
+ "resolution":2.0,
+ "title":"Insulin fibrillation is the Janus face of induced fit. A chiaral clamp stabilizes the native state at the expense of activity"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3p2x",
+ "resolution":2.0,
+ "title":"Insulin fibrillation is the Janus face of induced fit. A chiaral clamp stabilizes the native state at the expense of activity"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3jsd",
+ "resolution":2.5,
+ "title":"Insulin's biosynthesis and activity have opposing structural requirements: a new factor in neonatal diabetes mellitus"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"3jsd",
+ "resolution":2.5,
+ "title":"Insulin's biosynthesis and activity have opposing structural requirements: a new factor in neonatal diabetes mellitus"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"2om1",
+ "resolution":1.97,
+ "title":"Structure of human insulin in presence of thiocyanate at pH 6.5"},
+ {
"experimental_method":["X-ray diffraction"],
"pdb_id":"2omh",
"resolution":1.36,
"title":"Structure of human insulin cocrystallized with ARG-12 peptide in presence of urea"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2omg",
- "resolution":1.52,
- "title":"Structure of human insulin cocrystallized with protamine and urea"},
- {
- "experimental_method":["X-ray diffraction"],
"pdb_id":"3fq9",
"resolution":1.35,
"title":"Design of an insulin analog with enhanced receptor-binding selectivity. Rationale, structure, and therapeutic implications"},
"title":"Design of an insulin analog with enhanced receptor-binding selectivity. Rationale, structure, and therapeutic implications"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3jsd",
- "resolution":2.5,
- "title":"Insulin's biosynthesis and activity have opposing structural requirements: a new factor in neonatal diabetes mellitus"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"3jsd",
- "resolution":2.5,
- "title":"Insulin's biosynthesis and activity have opposing structural requirements: a new factor in neonatal diabetes mellitus"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"4p65",
- "resolution":1.5,
- "title":"Crystal structure of an cyclohexylalanine substituted insulin analog."},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"4p65",
- "resolution":1.5,
- "title":"Crystal structure of an cyclohexylalanine substituted insulin analog."},
- {
- "experimental_method":["X-ray diffraction"],
"pdb_id":"3p33",
"resolution":2.3,
"title":"Insulin fibrillation is the Janus face of induced fit. A chiral clamp stabilizes the native state at the expense of activity"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3p2x",
- "resolution":2.0,
- "title":"Insulin fibrillation is the Janus face of induced fit. A chiaral clamp stabilizes the native state at the expense of activity"},
+ "pdb_id":"2omg",
+ "resolution":1.52,
+ "title":"Structure of human insulin cocrystallized with protamine and urea"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"3p2x",
- "resolution":2.0,
- "title":"Insulin fibrillation is the Janus face of induced fit. A chiaral clamp stabilizes the native state at the expense of activity"},
+ "pdb_id":"1ben",
+ "resolution":1.4,
+ "title":"INSULIN COMPLEXED WITH 4-HYDROXYBENZAMIDE"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"1qiz",
"title":"HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR COMPLEXED WITH RESORCINOL"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"1ben",
- "resolution":1.4,
- "title":"INSULIN COMPLEXED WITH 4-HYDROXYBENZAMIDE"},
+ "pdb_id":"4p65",
+ "resolution":1.5,
+ "title":"Crystal structure of an cyclohexylalanine substituted insulin analog."},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2oly",
- "resolution":1.7,
- "title":"Structure of human insulin in presence of urea at pH 7.0"},
+ "pdb_id":"4p65",
+ "resolution":1.5,
+ "title":"Crystal structure of an cyclohexylalanine substituted insulin analog."},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"2om1",
- "resolution":1.97,
- "title":"Structure of human insulin in presence of thiocyanate at pH 6.5"},
+ "pdb_id":"1lph",
+ "resolution":2.3,
+ "title":"LYS(B28)PRO(B29)-HUMAN INSULIN"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"6ck2",
- "resolution":2.25,
- "title":"Insulin analog containing a YB26W mutation"},
+ "pdb_id":"2oly",
+ "resolution":1.7,
+ "title":"Structure of human insulin in presence of urea at pH 7.0"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"6tyh",
"title":"Four-Disulfide Insulin Analog A22/B22"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5mt3",
- "resolution":2.02,
- "title":"Human insulin in complex with serotonin and arginine"},
+ "pdb_id":"5uru",
+ "resolution":2.41,
+ "title":"Insulin with proline analog DhP at position B28 in the R6 state"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"7bw8",
+ "resolution":3.8,
+ "title":"Cryo-EM Structure for the Insulin Binding Region in the Ectodomain of the Full-length Human Insulin Receptor in Complex with 1 Insulin"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6ck2",
+ "resolution":2.25,
+ "title":"Insulin analog containing a YB26W mutation"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6bfc",
+ "resolution":3.7,
+ "title":"Cryo-EM structure of human insulin degrading enzyme in complex with insulin"},
+ {
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"6b3q",
+ "resolution":3.7,
+ "title":"Cryo-EM structure of human insulin degrading enzyme in complex with insulin"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"6nwv",
"resolution":1.601,
"title":"Insulin Lispro Analog"},
{
+ "experimental_method":["Electron Microscopy"],
+ "pdb_id":"7bwa",
+ "resolution":4.9,
+ "title":"Cryo-EM Structure for the Ectodomain of the Full-length Human Insulin Receptor in Complex with 2 Insulin"},
+ {
"experimental_method":["X-ray diffraction"],
"pdb_id":"5hpu",
"resolution":2.2,
"title":"Insulin with proline analog HzP at position B28 in the R6 state"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"4ajz",
- "resolution":1.8,
+ "pdb_id":"4akj",
+ "resolution":2.01,
"title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5mt9",
- "resolution":1.88,
- "title":"Human insulin in complex with serotonin and arginine"},
- {
- "experimental_method":["X-ray diffraction"],
- "pdb_id":"5uru",
- "resolution":2.41,
- "title":"Insulin with proline analog DhP at position B28 in the R6 state"},
+ "pdb_id":"4ajz",
+ "resolution":1.8,
+ "title":"Ligand controlled assembly of hexamers, dihexamers, and linear multihexamer structures by an engineered acylated insulin"},
{
"experimental_method":["X-ray diffraction"],
"pdb_id":"5uu3",
"title":"Insulin with proline analog ThioP at position B28 in the R6 state"},
{
"experimental_method":["X-ray diffraction"],
- "pdb_id":"5bqq",
- "resolution":1.54,
- "title":"Human insulin with intra-chain chemical crosslink between modified B27 and B30"},
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\ No newline at end of file
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- Sequence seq,upSeq;
+ Sequence seq,upSeq,upSeq_nocanonical;
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
+ "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
+ "", 1,
1863);
- upSeq.createDatasetSequence();
upSeq.setDescription("Breast cancer type 1 susceptibility protein");
+ upSeq_nocanonical = new Sequence(upSeq);
+ upSeq.createDatasetSequence();
upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
+
+ upSeq_nocanonical.createDatasetSequence();
+ // not a canonical reference
+ upSeq_nocanonical.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,false));
+
}
@AfterMethod(alwaysRun = true)
{
seq = null;
upSeq=null;
+ upSeq_nocanonical=null;
}
@Test(groups = { "Functional" })
}
+ @Test(groups = { "Functional" })
+ public void displayTDBQueryTest() throws InterruptedException
+ {
+ TDBeaconsFTSRestClientTest.setMock();
+ PDBFTSRestClientTest.setMock();
+
+ SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
+ StructureChooser sc = new StructureChooser(selectedSeqs, upSeq_nocanonical, null);
+ // mock so should be quick. Exceptions from mocked PDBFTS are expected too
+ ThreadwaitFor(500, sc);
+
+ assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
+ }
+
@Test(groups = { "Network" })
public void fetchStructuresInfoTest()
{
cleanupTmpFiles(newFile, suffix, digits);
}
- private void cleanupTmpFiles(String file, String mysuffix, int mydigits)
+ protected static void cleanupTmpFiles(String file, String mysuffix,
+ int mydigits)
{
File newfile = new File(file);
if (newfile.exists())
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.StandardCopyOption;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.datamodel.AlignmentI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+
+/**
+ * WindowsFileSaveTest simply opens an alignment file and then tries to save it.
+ * This failed in Windows from 2.11.0 to 2.11.1.6 due to a combination of the
+ * opening file handle being left open ad infinitum, causing the BackupFiles
+ * operation of moving the saved (temp) file onto the original filename to fail,
+ * but only in Windows. See: https://issues.jalview.org/browse/JAL-3628
+ * https://issues.jalview.org/browse/JAL-3703
+ * https://issues.jalview.org/browse/JAL-3935 These issues are really all fixed
+ * by JAL-3703 This test is to ensure it doesn't start again, but note that this
+ * test will only fail in Windows.
+ */
+public class WindowsFileLoadAndSaveTest
+{
+
+ private final static String fileName = "examples" + File.separator
+ + "uniref50.fa";
+
+ private final static String testFileName = fileName + "-TEST";
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ /**
+ * Test saving and re-reading in a specified format
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void loadAndSaveAlignment() throws IOException
+ {
+ File file = new File(fileName);
+ File testFile = new File(testFileName);
+ Files.copy(file.toPath(), testFile.toPath(),
+ StandardCopyOption.REPLACE_EXISTING);
+ FormatAdapter fa = new FormatAdapter();
+ AlignmentI a = fa.readFile(testFile, DataSourceType.FILE,
+ FileFormat.Fasta);
+
+ AlignFrame af = new AlignFrame(a, 500, 500);
+ af.saveAlignment(testFileName, FileFormat.Fasta);
+
+ Assert.assertTrue(af.isSaveAlignmentSuccessful());
+ }
+
+ @AfterClass(alwaysRun = true)
+ private void cleanupTmpFiles()
+ {
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
+ BackupFilesTest.cleanupTmpFiles(testFileName, bfpe.suffix, bfpe.digits);
+ }
+
+}
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import javax.swing.JInternalFrame;
"Mismatch PDBEntry 'Type'");
Assert.assertNotNull(recov.getFile(),
"Recovered PDBEntry should have a non-null file entry");
+ Assert.assertEquals(recov.getFile().toLowerCase(Locale.ENGLISH).lastIndexOf("pdb"),recov.getFile().length()-3, "Recovered PDBEntry file should have PDB suffix");
}
}
{
Cache.initLogger();
}
-
+
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
assertArrayEquals(new int[] { 5, 6 }, merged.get(1));
assertArrayEquals(new int[] { 12, 8 }, merged.get(2));
assertArrayEquals(new int[] { 8, 7 }, merged.get(3));
-
+
// 'subsumed' ranges are preserved
ranges.clear();
ranges.add(new int[] { 10, 30 });
- ranges.add(new int[] { 15, 25 });
+ ranges.add(new int[] { 15, 25 });
+
merged = MapList.coalesceRanges(ranges);
assertEquals(2, merged.size());
assertArrayEquals(new int[] { 10, 30 }, merged.get(0));
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.commands.EditCommand;
protein.setCodonFrames(acfList);
/*
- * Select Seq1 and Seq3 in the protein (startRes=endRes=0)
+ * Select Seq1 and Seq3 in the protein
*/
SequenceGroup sg = new SequenceGroup();
sg.setColourText(true);
sg.setOutlineColour(Color.LIGHT_GRAY);
sg.addSequence(protein.getSequenceAt(0), false);
sg.addSequence(protein.getSequenceAt(2), false);
+ sg.setEndRes(protein.getWidth() - 1);
/*
* Verify the mapped sequence group in dna
assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(1));
assertEquals(0, mappedGroup.getStartRes());
- assertEquals(2, mappedGroup.getEndRes());
+ assertEquals(2, mappedGroup.getEndRes()); // 3 columns (1 codon)
/*
* Verify mapping sequence group from dna to protein
overlap = MappingUtils.findOverlap(ranges, 13, 15);
assertNull(overlap);
}
+
+ /**
+ * Test mapping a sequence group where sequences in and outside the group
+ * share a dataset sequence (e.g. alternative CDS for the same gene)
+ * <p>
+ * This scenario doesn't arise after JAL-3763 changes, but test left as still valid
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testMapSequenceGroup_sharedDataset() throws IOException
+ {
+ /*
+ * Set up dna and protein Seq1/2/3 with mappings (held on the protein
+ * viewport). CDS sequences share the same 'gene' dataset sequence.
+ */
+ SequenceI dna = new Sequence("dna", "aaatttgggcccaaatttgggccc");
+ SequenceI cds1 = new Sequence("cds1/1-6", "aaattt");
+ SequenceI cds2 = new Sequence("cds1/4-9", "tttggg");
+ SequenceI cds3 = new Sequence("cds1/19-24", "gggccc");
+
+ cds1.setDatasetSequence(dna);
+ cds2.setDatasetSequence(dna);
+ cds3.setDatasetSequence(dna);
+
+ SequenceI pep1 = new Sequence("pep1", "KF");
+ SequenceI pep2 = new Sequence("pep2", "FG");
+ SequenceI pep3 = new Sequence("pep3", "GP");
+ pep1.createDatasetSequence();
+ pep2.createDatasetSequence();
+ pep3.createDatasetSequence();
+
+ /*
+ * add mappings from coding positions of dna to respective peptides
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna, pep1,
+ new MapList(new int[]
+ { 1, 6 }, new int[] { 1, 2 }, 3, 1));
+ acf.addMap(dna, pep2,
+ new MapList(new int[]
+ { 4, 9 }, new int[] { 1, 2 }, 3, 1));
+ acf.addMap(dna, pep3,
+ new MapList(new int[]
+ { 19, 24 }, new int[] { 1, 2 }, 3, 1));
+
+ List<AlignedCodonFrame> acfList = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
+
+ AlignmentI cdna = new Alignment(new SequenceI[] { cds1, cds2, cds3 });
+ AlignmentI protein = new Alignment(
+ new SequenceI[]
+ { pep1, pep2, pep3 });
+ AlignViewportI cdnaView = new AlignViewport(cdna);
+ AlignViewportI peptideView = new AlignViewport(protein);
+ protein.setCodonFrames(acfList);
+
+ /*
+ * Select pep1 and pep3 in the protein alignment
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setColourText(true);
+ sg.setIdColour(Color.GREEN);
+ sg.setOutlineColour(Color.LIGHT_GRAY);
+ sg.addSequence(pep1, false);
+ sg.addSequence(pep3, false);
+ sg.setEndRes(protein.getWidth() - 1);
+
+ /*
+ * Verify the mapped sequence group in dna is cds1 and cds3
+ */
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
+ peptideView, cdnaView);
+ assertTrue(mappedGroup.getColourText());
+ assertSame(sg.getIdColour(), mappedGroup.getIdColour());
+ assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
+ assertEquals(2, mappedGroup.getSequences().size());
+ assertSame(cds1, mappedGroup.getSequences().get(0));
+ assertSame(cds3, mappedGroup.getSequences().get(1));
+ // columns 1-6 selected (0-5 base zero)
+ assertEquals(0, mappedGroup.getStartRes());
+ assertEquals(5, mappedGroup.getEndRes());
+
+ /*
+ * Select mapping sequence group from dna to protein
+ */
+ sg.clear();
+ sg.addSequence(cds2, false);
+ sg.addSequence(cds1, false);
+ sg.setStartRes(0);
+ sg.setEndRes(cdna.getWidth() - 1);
+ mappedGroup = MappingUtils.mapSequenceGroup(sg, cdnaView, peptideView);
+ assertTrue(mappedGroup.getColourText());
+ assertSame(sg.getIdColour(), mappedGroup.getIdColour());
+ assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
+ assertEquals(2, mappedGroup.getSequences().size());
+ assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(0));
+ assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(1));
+ assertEquals(0, mappedGroup.getStartRes());
+ assertEquals(1, mappedGroup.getEndRes()); // two columns
+ }
}
uod_banner.30=/images/UoD_banner-30.png
uod_banner.32=/images/UoD_banner-32.png
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+preferences.filename=.jalview_nonrelease_properties
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- width="210mm"
- height="297mm"
- viewBox="0 0 210 297"
+ width="132.29233mm"
+ height="132.29326mm"
+ viewBox="0 0 132.29233 132.29326"
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- inkscape:version="1.0.1 (0767f8302a, 2020-10-17)"
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+ inkscape:version="0.92.5 (2060ec1f9f, 2020-04-08)"
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### and
### ./tgz/jre-VERSION-OS-ARCH.tgz
### which is an archive of the _contents_ of ./jre-VERSION-OS-ARCH/jre/ and used by install4j for the installer
+### bs 2021-10-26
+### Edited to use adoptium domain to gain access to Java 17 (LTS) versions.
-BASE=https://api.adoptopenjdk.net/v3/binary/latest
+BASE=https://api.adoptium.net/v3/binary/latest
RELEASE_TYPE=ga
JVM_IMPL=hotspot
HEAP_SIZE=normal
-VENDOR=adoptopenjdk
+VENDOR=eclipse
IMAGE_TYPE=jdk
RM=/bin/rm
fi && rmdir "$temp"/* "$temp"
)
-for FEATURE_VERSION in 8 11 12 13; do
- for OS in mac; do
- #for OS in linux mac windows; do
- for ARCH in x64; do
- #for ARCH in aarch64 arm x32 x64; do
- NAME="${IMAGE_TYPE}-${FEATURE_VERSION}-${OS}-${ARCH}"
- TARFILE="${NAME}.tgz"
- echo "* Downloading ${TARFILE}"
- URL="${BASE}/${FEATURE_VERSION}/${RELEASE_TYPE}/${OS}/${ARCH}/${IMAGE_TYPE}/${JVM_IMPL}/${HEAP_SIZE}/${VENDOR}"
- wget -q -O "${TARFILE}" "${URL}"
- if [ "$?" != 0 ]; then
- echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}'"
- $RM -f "${TARFILE}"
- continue;
- fi
- echo "Unpacking ${TARFILE}"
- JREDIR="${NAME}/${IMAGE_TYPE}"
- [ x$NAME != x -a -e "${JREDIR}" ] && $RM -rf "${JREDIR}"
- mkdir -p "${JREDIR}"
- if [ x$OS = xwindows ]; then
- echo "using unzip"
- unzip-strip "${TARFILE}" "${JREDIR}"
- RET=$?
- else
- echo "using tar"
- tar --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
- RET=$?
- fi
- if [ "$RET" != 0 ]; then
- echo "Error unpacking ${TARFILE}"
- exit 1
- fi
- $RM "${TARFILE}"
- done
+for FEATURE_VERSION in 8 11 17; do
+ for OS_ARCH in mac:x64 mac:aarch64 windows:x64 linux:x64 linux:arm linux:aarch64; do
+ OS=${OS_ARCH%:*}
+ ARCH=${OS_ARCH#*:}
+ NAME="${IMAGE_TYPE}-${FEATURE_VERSION}-${OS}-${ARCH}"
+ TARFILE="${NAME}.tgz"
+ echo "* Downloading ${TARFILE}"
+ URL="${BASE}/${FEATURE_VERSION}/${RELEASE_TYPE}/${OS}/${ARCH}/${IMAGE_TYPE}/${JVM_IMPL}/${HEAP_SIZE}/${VENDOR}"
+ wget -q -O "${TARFILE}" "${URL}"
+ if [ "$?" != 0 ]; then
+ echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}'"
+ $RM -f "${TARFILE}"
+ continue;
+ fi
+ echo "Unpacking ${TARFILE}"
+ JREDIR="${NAME}/${IMAGE_TYPE}"
+ [ x$NAME != x -a -e "${JREDIR}" ] && $RM -rf "${JREDIR}"
+ mkdir -p "${JREDIR}"
+ if [ x$OS = xwindows ]; then
+ echo "using unzip"
+ unzip-strip "${TARFILE}" "${JREDIR}"
+ RET=$?
+ else
+ echo "using tar"
+ tar --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
+ RET=$?
+ fi
+ if [ "$RET" != 0 ]; then
+ echo "Error unpacking ${TARFILE}"
+ exit 1
+ fi
+ $RM "${TARFILE}"
done
done
### and
### ./tgz/jre-VERSION-OS-ARCH.tgz
### which is an archive of the _contents_ of ./jre-VERSION-OS-ARCH/jre/ and used by install4j for the installer
+### bs 2021-10-26
+### Edited to use adoptium domain to gain access to Java 17 (LTS) versions.
-BASE=https://api.adoptopenjdk.net/v3/binary/latest
+BASE=https://api.adoptium.net/v3/binary/latest
RELEASE_TYPE=ga
JVM_IMPL=hotspot
HEAP_SIZE=normal
-VENDOR=adoptopenjdk
+VENDOR=eclipse
IMAGE_TYPE=jre
TAR=tar
ZIP=zip
fi && rmdir "$temp"/* "$temp"
)
-for FEATURE_VERSION in 8 11; do
- for OS in linux mac windows; do
- for ARCH in x64 x32 arm; do
- #for ARCH in aarch64 arm x32 x64; do
- NAME="${IMAGE_TYPE}-${FEATURE_VERSION}-${OS}-${ARCH}"
- TARFILE="${NAME}.tgz"
- echo "* Downloading ${TARFILE}"
- URL="${BASE}/${FEATURE_VERSION}/${RELEASE_TYPE}/${OS}/${ARCH}/${IMAGE_TYPE}/${JVM_IMPL}/${HEAP_SIZE}/${VENDOR}"
- wget -q -O "${TARFILE}" "${URL}"
- if [ "$?" != 0 ]; then
- echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}'"
- $RM -f "${TARFILE}"
- continue;
- fi
- echo "Unpacking ${TARFILE}"
- JREDIR="${NAME}/${IMAGE_TYPE}"
- [ x$NAME != x -a -e "${JREDIR}" ] && $RM -rf "${JREDIR}"
- mkdir -p "${JREDIR}"
- if [ x$OS = xwindows ]; then
- echo "using unzip"
- unzip-strip "${TARFILE}" "${JREDIR}"
+for FEATURE_VERSION in 8 11 17; do
+ for OS_ARCH in mac:x64 mac:aarch64 windows:x64 linux:x64 linux:arm linux:aarch64; do
+ OS=${OS_ARCH%:*}
+ ARCH=${OS_ARCH#*:}
+ NAME="${IMAGE_TYPE}-${FEATURE_VERSION}-${OS}-${ARCH}"
+ TARFILE="${NAME}.tgz"
+ echo "* Downloading ${TARFILE}"
+ URL="${BASE}/${FEATURE_VERSION}/${RELEASE_TYPE}/${OS}/${ARCH}/${IMAGE_TYPE}/${JVM_IMPL}/${HEAP_SIZE}/${VENDOR}"
+ wget -q -O "${TARFILE}" "${URL}"
+ if [ "$?" != 0 ]; then
+ echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}'"
+ $RM -f "${TARFILE}"
+ continue;
+ fi
+ echo "Unpacking ${TARFILE}"
+ JREDIR="${NAME}/${IMAGE_TYPE}"
+ [ x$NAME != x -a -e "${JREDIR}" ] && $RM -rf "${JREDIR}"
+ mkdir -p "${JREDIR}"
+ if [ x$OS = xwindows ]; then
+ echo "using unzip"
+ unzip-strip "${TARFILE}" "${JREDIR}"
+ RET=$?
+ else
+ echo "using tar"
+ if [ x$OS = xmac -a x$STRIP_MAC_APP_BUNDLING = xtrue ]; then
+ $TAR --strip-components=3 -C "${JREDIR}" -zxf "${TARFILE}" "*/Contents/Home"
RET=$?
else
- echo "using tar"
- if [ x$OS = xmac -a x$STRIP_MAC_APP_BUNDLING = xtrue ]; then
- $TAR --strip-components=3 -C "${JREDIR}" -zxf "${TARFILE}" "*/Contents/Home"
- RET=$?
- else
- $TAR --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
- RET=$?
- fi
- fi
- if [ "$RET" != 0 ]; then
- echo "Error unpacking ${TARFILE}"
- exit 1
- fi
- $RM "${TARFILE}"
- if [ \! -z "$CREATE_ARCHIVES" ]; then
- for CREATEARCHIVE in ${CREATE_ARCHIVES}; do
- ARCHIVEDIR=$CREATEARCHIVE
- case $CREATEARCHIVE in
- zip)
- EXT=${CREATEARCHIVE}
- echo "Creating ${NAME}.${EXT} for getdown updates"
- [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
- ABSARCHIVEDIR="${PWD}/$ARCHIVEDIR"
- ZIPFILE="${ABSARCHIVEDIR}/${NAME}.${CREATEARCHIVE}"
- [ -e "${ZIPFILE}" ] && $RM "${ZIPFILE}"
- cd ${NAME}
- $ZIP -X -r "${ZIPFILE}" "${IMAGE_TYPE}"
- cd -
- ;;
- tgz)
- EXT=tar.gz
- echo "Creating ${NAME}.${EXT} for install4j bundling"
- [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
- $TAR -C "${JREDIR}" -zcf "${ARCHIVEDIR}/${NAME}.${EXT}" .
- ;;
- *)
- echo "Archiving as '${CREATEARCHIVE}' file not supported"
- ;;
- esac
- done
+ $TAR --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
+ RET=$?
fi
- done
+ fi
+ if [ "$RET" != 0 ]; then
+ echo "Error unpacking ${TARFILE}"
+ exit 1
+ fi
+ $RM "${TARFILE}"
+ if [ \! -z "$CREATE_ARCHIVES" ]; then
+ for CREATEARCHIVE in ${CREATE_ARCHIVES}; do
+ ARCHIVEDIR=$CREATEARCHIVE
+ case $CREATEARCHIVE in
+ zip)
+ EXT=${CREATEARCHIVE}
+ echo "Creating ${NAME}.${EXT} for getdown updates"
+ [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
+ ABSARCHIVEDIR="${PWD}/$ARCHIVEDIR"
+ ZIPFILE="${ABSARCHIVEDIR}/${NAME}.${CREATEARCHIVE}"
+ [ -e "${ZIPFILE}" ] && $RM "${ZIPFILE}"
+ cd ${NAME}
+ $ZIP -X -r "${ZIPFILE}" "${IMAGE_TYPE}"
+ cd -
+ ;;
+ tgz)
+ EXT=tar.gz
+ echo "Creating ${NAME}.${EXT} for install4j bundling"
+ [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
+ $TAR -C "${JREDIR}" -zcf "${ARCHIVEDIR}/${NAME}.${EXT}" .
+ # make symbolic link with _ instead of - for install4j9
+ NEWNAME=${NAME//-/_}
+ echo "Linking from ${NEWNAME}.${EXT} for install4j9"
+ ln -s "${NAME}.${EXT}" "${ARCHIVEDIR}/${NEWNAME}.${EXT}"
+ ;;
+ *)
+ echo "Archiving as '${CREATEARCHIVE}' file not supported"
+ ;;
+ esac
+ done
+ fi
done
done
<serializedBean>
<property name="description" type="string">Jalview File</property>
<property name="extension" type="string">jvp</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Jalview Launch File</property>
<property name="extension" type="string">jvl</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-Launch.icns</string>
<serializedBean>
<property name="description" type="string">CIF File</property>
<property name="extension" type="string">cif</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">mmCIF File</property>
<property name="extension" type="string">mcif,mmcif</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">PDB File</property>
<property name="extension" type="string">ent,pdb</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">AMSA File</property>
<property name="extension" type="string">amsa</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Jalview Annotations File</property>
<property name="extension" type="string">annotations,jvannotations</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">BioJSON File</property>
<property name="extension" type="string">biojson</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">BLC File</property>
<property name="extension" type="string">blc</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Clustal File</property>
<property name="extension" type="string">aln</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">ENA Flatfile File</property>
<property name="extension" type="string">txt</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Fasta File</property>
<property name="extension" type="string">fa,fasta</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Jalview Features File</property>
<property name="extension" type="string">features,jvfeatures</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">GenBank Flatfile File</property>
<property name="extension" type="string">gb,gbk</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Generic Features Format v2 File</property>
<property name="extension" type="string">gff2</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Generic Features Format v3 File</property>
<property name="extension" type="string">gff3</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">JnetFile File</property>
<property name="extension" type="string">concise,jnet</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">MSF File</property>
<property name="extension" type="string">msf</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">PFAM File</property>
<property name="extension" type="string">pfam</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">PHYLIP File</property>
<property name="extension" type="string">phy</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">PileUp File</property>
<property name="extension" type="string">pileup</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">PIR File</property>
<property name="extension" type="string">pir</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">RNAML File</property>
<property name="extension" type="string">rnaml</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Substitution Matrix File</property>
<property name="extension" type="string">mat</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Stockholm File</property>
<property name="extension" type="string">stk,sto</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">$$NAME$$ File</property>
<property name="extension" type="string">$$EXTENSION$$</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>$$ICONFILE$$.icns</string>
</components>
</files>
<launchers>
- <launcher name="Jalview Launcher" id="737" menuName="${compiler:JALVIEW_APPLICATION_NAME}" icnsFile="${compiler:JALVIEW_DIR}/${compiler:MAC_ICONS_FILE}" customMacBundleIdentifier="true" macBundleIdentifier="${compiler:BUNDLE_ID}" fileset="734" useCustomMacosExecutableName="true" customMacosExecutableName="${compiler:JALVIEW_APPLICATION_NAME}">
+ <launcher name="Jalview Launcher" id="737" customizedId="JALVIEW" menuName="${compiler:JALVIEW_APPLICATION_NAME}" icnsFile="${compiler:JALVIEW_DIR}/${compiler:MAC_ICONS_FILE}" customMacBundleIdentifier="true" macBundleIdentifier="${compiler:BUNDLE_ID}" fileset="734" useCustomMacosExecutableName="true" customMacosExecutableName="${compiler:JALVIEW_APPLICATION_NAME}">
<executable name="${compiler:EXECUTABLE_NAME}" iconSet="true" iconFile="${compiler:JALVIEW_DIR}/${compiler:WINDOWS_ICONS_FILE}" redirectStdout="true" executableMode="gui" changeWorkingDirectory="false" singleInstance="true" checkConsoleParameter="true">
<versionInfo include="true" fileDescription="${compiler:sys.fullName}" legalCopyright="${compiler:COPYRIGHT_MESSAGE}" internalName="${compiler:INTERNAL_ID}" productName="${compiler:sys.fullName}" />
</executable>
</group>
<action id="2350" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="scheme" type="string">jalview</property>
</serializedBean>
</action>
<action id="2450" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="scheme" type="string">jalviews</property>
</serializedBean>
</action>
<action id="2641" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="scheme" type="string">${compiler:EXTRA_SCHEME}</property>
</serializedBean>
</action>
git://source.jalview.org / jalview.git / commitdiff
