/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ext.rbvi.chimera;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.Comparison;
-
import java.awt.Color;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
import java.util.ArrayList;
-import java.util.LinkedHashMap;
+import java.util.Arrays;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsBase;
+import jalview.util.ColorUtils;
+
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
*
* @author JimP
*
*/
-public class ChimeraCommands
+public class ChimeraCommands extends StructureCommandsBase
{
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+ "focus");
+
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr
+ private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
+ "list resattr");
+
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
+ private static final StructureCommand CLOSE_CHIMERA = new StructureCommand(
+ "stop really");
+
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
+ private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
+ "listen stop selection");
+
+ private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
+ "listen stop models");
+
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection
+ private static final StructureCommand GET_SELECTION = new StructureCommand(
+ "list selection level residue");
+
+ private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
+ "~display all;~ribbon;chain @CA|P");
+
+ private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
+ "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
+
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rainbow.html
+ private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
+ "rainbow chain");
+
+ // Chimera clause to exclude alternate locations in atom selection
+ private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
+
+ @Override
+ public StructureCommandI colourResidues(String atomSpec, Color colour)
+ {
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html
+ String colourCode = getColourString(colour);
+ return new StructureCommand("color " + colourCode + " " + atomSpec);
+ }
/**
- * utility to construct the commands to colour chains by the given alignment
- * for passing to Chimera
+ * Returns a colour formatted suitable for use in viewer command syntax
*
- * @returns Object[] { Object[] { <model being coloured>,
+ * @param colour
+ * @return
+ */
+ protected String getColourString(Color colour)
+ {
+ return ColorUtils.toTkCode(colour);
+ }
+
+ /**
+ * Traverse the map of features/values/models/chains/positions to construct a
+ * list of 'setattr' commands (one per distinct feature type and value).
+ * <p>
+ * The format of each command is
+ *
+ * <pre>
+ * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
+ * e.g. setattr r jv_chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+ * </blockquote>
+ * </pre>
*
+ * @param featureMap
+ * @return
*/
- public static StructureMappingcommandSet[] getColourBySequenceCommand(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ @Override
+ public List<StructureCommandI> setAttributes(
+ Map<String, Map<Object, AtomSpecModel>> featureMap)
{
- String defAttrPath = null;
- FileOutputStream fos = null;
- try
- {
- File outFile = File.createTempFile("jalviewdefattr", ".xml");
- outFile.deleteOnExit();
- defAttrPath = outFile.getPath();
- fos = new FileOutputStream(outFile);
- fos.write("attribute: jalviewclr\n".getBytes());
- } catch (IOException e1)
+ List<StructureCommandI> commands = new ArrayList<>();
+ for (String featureType : featureMap.keySet())
{
- e1.printStackTrace();
+ String attributeName = makeAttributeName(featureType);
+
+ /*
+ * clear down existing attributes for this feature
+ */
+ // 'problem' - sets attribute to None on all residues - overkill?
+ // commands.add("~setattr r " + attributeName + " :*");
+
+ Map<Object, AtomSpecModel> values = featureMap.get(featureType);
+ for (Object value : values.keySet())
+ {
+ /*
+ * for each distinct value recorded for this feature type,
+ * add a command to set the attribute on the mapped residues
+ * Put values in single quotes, encoding any embedded single quotes
+ */
+ AtomSpecModel atomSpecModel = values.get(value);
+ String featureValue = value.toString();
+ featureValue = featureValue.replaceAll("\\'", "'");
+ StructureCommandI cmd = setAttribute(attributeName, featureValue,
+ atomSpecModel);
+ commands.add(cmd);
+ }
}
- List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+
+ return commands;
+ }
+
+ /**
+ * Returns a viewer command to set the given residue attribute value on
+ * residues specified by the AtomSpecModel, for example
+ *
+ * <pre>
+ * setatr res jv_chain 'primary' #1:12-34,48-55.B
+ * </pre>
+ *
+ * @param attributeName
+ * @param attributeValue
+ * @param atomSpecModel
+ * @return
+ */
+ protected StructureCommandI setAttribute(String attributeName,
+ String attributeValue, AtomSpecModel atomSpecModel)
+ {
+ StringBuilder sb = new StringBuilder(128);
+ sb.append("setattr res ").append(attributeName).append(" '")
+ .append(attributeValue).append("' ");
+ sb.append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
+ return new StructureCommand(sb.toString());
+ }
+
+ /**
+ * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
+ * for a 'Jalview' namespace, and any non-alphanumeric character is converted
+ * to an underscore.
+ *
+ * @param featureType
+ * @return
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+ */
+ @Override
+ protected String makeAttributeName(String featureType)
+ {
+ String attName = super.makeAttributeName(featureType);
/*
- * Map of { colour, positionSpecs}
+ * Chimera treats an attribute name ending in 'color' as colour-valued;
+ * Jalview doesn't, so prevent this by appending an underscore
*/
- Map<String, StringBuilder> colranges = new LinkedHashMap<String, StringBuilder>();
- StringBuilder setAttributes = new StringBuilder(256);
- String lastColour = "none";
- Color lastCol = null;
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR"))
{
- boolean startModel = true;
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+ attName += "_";
+ }
- if (mapping == null || mapping.length < 1)
- {
- continue;
- }
+ return attName;
+ }
+
+ @Override
+ public StructureCommandI colourByChain()
+ {
+ return COLOUR_BY_CHAIN;
+ }
+
+ @Override
+ public List<StructureCommandI> colourByCharge()
+ {
+ return Arrays.asList(COLOUR_BY_CHARGE);
+ }
- int startPos = -1, lastPos = -1;
- String lastChain = "";
- for (int s = 0; s < sequence[pdbfnum].length; s++)
+ @Override
+ public String getResidueSpec(String residue)
+ {
+ return "::" + residue;
+ }
+
+ @Override
+ public StructureCommandI setBackgroundColour(Color col)
+ {
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/set.html#bgcolor
+ return new StructureCommand("set bgColor " + ColorUtils.toTkCode(col));
+ }
+
+ @Override
+ public StructureCommandI focusView()
+ {
+ return FOCUS_VIEW;
+ }
+
+ @Override
+ public List<StructureCommandI> showChains(List<String> toShow)
+ {
+ /*
+ * Construct a chimera command like
+ *
+ * ~display #*;~ribbon #*;ribbon :.A,:.B
+ */
+ StringBuilder cmd = new StringBuilder(64);
+ boolean first = true;
+ for (String chain : toShow)
+ {
+ String[] tokens = chain.split(":");
+ if (tokens.length == 2)
{
- for (int sp, m = 0; m < mapping.length; m++)
+ String showChainCmd = tokens[0] + ":." + tokens[1];
+ if (!first)
{
- final SequenceI seq = sequence[pdbfnum][s];
- if (mapping[m].getSequence() == seq
- && (sp = alignment.findIndex(seq)) > -1)
- {
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- {
- continue;
- }
-
- Color col = getResidueColour(seq, r, sr, fr);
- /*
- * Just keep incrementing the end position for this colour range
- * _unless_ colour, PDB model or chain has changed, or there is a
- * gap in the mapped residue sequence
- */
- final boolean newColour = !col.equals(lastCol);
- final boolean nonContig = lastPos + 1 != pos;
- final boolean newChain = !mapping[m].getChain().equals(lastChain);
- if (newColour || nonContig || startModel || newChain)
- {
- if (/* lastCol != null */startPos != -1)
- {
- addColourRange(colranges, lastCol, pdbfnum, startPos,
- lastPos, lastChain, startModel);
- startModel = false;
- }
- // lastCol = null;
- startPos = pos;
- }
- lastCol = col;
- lastPos = pos;
- // lastModel = pdbfnum;
- lastChain = mapping[m].getChain();
- }
- // final colour range
- if (lastCol != null)
- {
- addColourRange(colranges, lastCol, pdbfnum, startPos,
- lastPos, lastChain, false);
- }
- break;
- }
+ cmd.append(",");
}
+ cmd.append(showChainCmd);
+ first = false;
}
}
- try
- {
- lastColour = buildColourCommands(cset, colranges,
- fos, setAttributes);
- } catch (IOException e)
- {
- e.printStackTrace();
- }
- try
- {
- fos.close();
- } catch (IOException e)
- {
- e.printStackTrace();
- }
+ /*
+ * could append ";focus" to this command to resize the display to fill the
+ * window, but it looks more helpful not to (easier to relate chains to the
+ * whole)
+ */
+ final String command = "~display #*; ~ribbon #*; ribbon :"
+ + cmd.toString();
+ return Arrays.asList(new StructureCommand(command));
+ }
+ @Override
+ public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
+ AtomSpecModel spec, AtomSpecType backbone)
+ {
/*
- * Send a rangeColor command, preceded by either defattr or setattr,
- * whichever we end up preferring!
+ * Form Chimera match command to match spec to ref
+ * (the first set of atoms are moved on to the second)
+ *
+ * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
*
- * rangecolor requires a minimum of two attribute values to operate on
+ * @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
*/
- StringBuilder rangeColor = new StringBuilder(256);
- rangeColor.append("rangecolor jalviewclr");
- int colourId = 0;
- for (String colour : colranges.keySet())
- {
- colourId++;
- rangeColor.append(" " + colourId + " " + colour);
- }
- String rangeColorCommand = rangeColor.toString();
- if (rangeColorCommand.split(" ").length < 5)
- {
- rangeColorCommand += " max " + lastColour;
- }
- final String defAttrCommand = "defattr " + defAttrPath
- + " raiseTool false";
- final String setAttrCommand = setAttributes.toString();
- final String attrCommand = false ? defAttrCommand : setAttrCommand;
- cset.add(new StructureMappingcommandSet(ChimeraCommands.class, null,
- new String[]
- { attrCommand /* , rangeColorCommand */}));
-
- return cset.toArray(new StructureMappingcommandSet[cset.size()]);
+ StringBuilder cmd = new StringBuilder();
+ String atomSpecAlphaOnly = getAtomSpec(spec, backbone);
+ String refSpecAlphaOnly = getAtomSpec(ref, backbone);
+ cmd.append("match ").append(atomSpecAlphaOnly).append(" ")
+ .append(refSpecAlphaOnly);
+
+ /*
+ * show superposed residues as ribbon
+ */
+ String atomSpec = getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY);
+ String refSpec = getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY);
+ cmd.append("; ribbon ");
+ cmd.append(atomSpec).append("|").append(refSpec).append("; focus");
+
+ return Arrays.asList(new StructureCommand(cmd.toString()));
}
- /**
- * Get the residue colour at the given sequence position - as determined by
- * the sequence group colour (if any), else the colour scheme, possibly
- * overridden by a feature colour.
- *
- * @param seq
- * @param position
- * @param sr
- * @param fr
- * @return
- */
- protected static Color getResidueColour(final SequenceI seq,
- int position, SequenceRenderer sr, FeatureRenderer fr)
+ @Override
+ public StructureCommandI openCommandFile(String path)
{
- Color col = sr.getResidueBoxColour(seq, position);
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
+ return new StructureCommand("open cmd:" + path);
+ }
- if (fr != null)
- {
- col = fr.findFeatureColour(col, seq, position);
- }
- return col;
+ @Override
+ public StructureCommandI saveSession(String filepath)
+ {
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html
+ return new StructureCommand("save " + filepath);
}
/**
- * Helper method to build the colour commands for one PDBfile.
+ * Returns the range(s) modelled by {@code atomSpec} formatted as a Chimera
+ * atomspec string, e.g.
+ *
+ * <pre>
+ * #0:15.A,28.A,54.A,70-72.A|#1:2.A,6.A,11.A,13-14.A
+ * </pre>
*
- * @param cset
- * the list of commands to be added to
- * @param colranges
- * the map of colours to residue positions already determined
- * @param fos
- * file to write 'defattr' commands to
- * @param setAttributes
- * @throws IOException
+ * where
+ * <ul>
+ * <li>#0 is a model number</li>
+ * <li>15 or 70-72 is a residue number, or range of residue numbers</li>
+ * <li>.A is a chain identifier</li>
+ * <li>residue ranges are separated by comma</li>
+ * <li>atomspecs for distinct models are separated by | (or)</li>
+ * </ul>
+ *
+ * <pre>
+ *
+ * @param model
+ * @param specType
+ * @return
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
*/
- protected static String buildColourCommands(
- List<StructureMappingcommandSet> cset,
- Map<String, StringBuilder> colranges,
- FileOutputStream fos, StringBuilder setAttributes)
- throws IOException
+ @Override
+ public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
{
- int colourId = 0;
- String lastColour = null;
- for (String colour : colranges.keySet())
+ StringBuilder sb = new StringBuilder(128);
+ boolean firstModel = true;
+ for (String model : atomSpec.getModels())
{
- lastColour = colour;
- colourId++;
- /*
- * Using color command directly is slow for larger structures.
- * setAttributes.append("color #" + colour + " " + colranges.get(colour)+
- * ";");
- */
- setAttributes.append("color " + colour + " " + colranges.get(colour)
- + ";");
- final String atomSpec = new String(colranges.get(colour));
- // setAttributes.append("setattr r jalviewclr " + colourId + " "
- // + atomSpec + ";");
- fos.write(("\t" + atomSpec + "\t" + colourId + "\n").getBytes());
+ if (!firstModel)
+ {
+ sb.append("|");
+ }
+ firstModel = false;
+ appendModel(sb, model, atomSpec, specType);
}
- return lastColour;
+ return sb.toString();
}
/**
- * Helper method to record a range of positions of the same colour.
+ * A helper method to append an atomSpec string for atoms in the given model
*
- * @param colranges
- * @param colour
+ * @param sb
* @param model
- * @param startPos
- * @param endPos
- * @param chain
- * @param changeModel
+ * @param atomSpec
+ * @param alphaOnly
*/
- private static void addColourRange(Map<String, StringBuilder> colranges,
- Color colour, int model, int startPos, int endPos, String chain,
- boolean startModel)
+ protected void appendModel(StringBuilder sb, String model,
+ AtomSpecModel atomSpec, AtomSpecType specType)
{
- String colstring = "#" + ((colour.getRed() < 16) ? "0" : "")
- + Integer.toHexString(colour.getRed())
- + ((colour.getGreen()< 16) ? "0":"")+Integer.toHexString(colour.getGreen())
- + ((colour.getBlue()< 16) ? "0":"")+Integer.toHexString(colour.getBlue());
- StringBuilder currange = colranges.get(colstring);
- if (currange == null)
- {
- colranges.put(colstring, currange = new StringBuilder(256));
- }
- /*
- * Format as (e.g.) #0:1-3.A,5.A,7-10.A,...#1:1-4.B,..etc
- */
- // if (currange.length() > 0)
- // {
- // currange.append("|");
- // }
- // currange.append("#" + model + ":" + ((startPos==endPos) ? startPos :
- // startPos + "-"
- // + endPos) + "." + chain);
- if (currange.length() == 0)
+ sb.append("#").append(model).append(":");
+
+ boolean firstPositionForModel = true;
+
+ for (String chain : atomSpec.getChains(model))
{
- currange.append("#" + model + ":");
+ chain = " ".equals(chain) ? chain : chain.trim();
+
+ List<int[]> rangeList = atomSpec.getRanges(model, chain);
+ for (int[] range : rangeList)
+ {
+ appendRange(sb, range[0], range[1], chain, firstPositionForModel,
+ false);
+ firstPositionForModel = false;
+ }
}
- else if (startModel)
+ if (specType == AtomSpecType.ALPHA)
{
- currange.append(",#" + model + ":");
+ /*
+ * restrict to alpha carbon, no alternative locations
+ * (needed to ensuring matching atom counts for superposition)
+ */
+ sb.append("@CA").append(NO_ALTLOCS);
}
- else
+ if (specType == AtomSpecType.PHOSPHATE)
{
- currange.append(",");
+ sb.append("@P").append(NO_ALTLOCS);
}
- final String rangeSpec = (startPos == endPos) ? Integer
- .toString(startPos) : (startPos + "-" + endPos);
- currange.append(rangeSpec + "." + chain);
+ }
+
+ @Override
+ public List<StructureCommandI> showBackbone()
+ {
+ return Arrays.asList(SHOW_BACKBONE);
+ }
+
+ @Override
+ public StructureCommandI loadFile(String file)
+ {
+ return new StructureCommand("open " + file);
+ }
+
+ @Override
+ public StructureCommandI openSession(String filepath)
+ {
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
+ // this version of the command has no dependency on file extension
+ return new StructureCommand("open chimera:" + filepath);
+ }
+
+ @Override
+ public StructureCommandI closeViewer()
+ {
+ return CLOSE_CHIMERA;
+ }
+
+ @Override
+ public List<StructureCommandI> startNotifications(String uri)
+ {
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
+ List<StructureCommandI> cmds = new ArrayList<>();
+ cmds.add(new StructureCommand("listen start models url " + uri));
+ cmds.add(new StructureCommand(
+ "listen start select prefix SelectionChanged url " + uri));
+ return cmds;
+ }
+
+ @Override
+ public List<StructureCommandI> stopNotifications()
+ {
+ List<StructureCommandI> cmds = new ArrayList<>();
+ cmds.add(STOP_NOTIFY_MODELS);
+ cmds.add(STOP_NOTIFY_SELECTION);
+ return cmds;
+ }
+
+ @Override
+ public StructureCommandI getSelectedResidues()
+ {
+ return GET_SELECTION;
+ }
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return LIST_RESIDUE_ATTRIBUTES;
+ }
+
+ @Override
+ public StructureCommandI getResidueAttributes(String attName)
+ {
+ // this alternative command
+ // list residues spec ':*/attName' attr attName
+ // doesn't report 'None' values (which is good), but
+ // fails for 'average.bfactor' (which is bad):
+ return new StructureCommand("list residues attr '" + attName + "'");
+ }
+
+ @Override
+ public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues)
+ {
+ // TODO Auto-generated method stub
+ return null;
}
}