+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
package ext.edu.ucsf.rbvi.strucviz2;
import java.awt.Color;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import org.slf4j.Logger;
{
if (decimal > 0)
{
- subModelNumber = Integer.parseInt(inputLine.substring(decimal
- + hash + 2, space));
+ subModelNumber = Integer
+ .parseInt(inputLine.substring(decimal + hash + 2, space));
space = decimal + hash + 1;
}
modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
*/
// invoked by openModel in ChimeraManager
// line: #1, chain A: hiv-1 protease
+ // line: Model 0 (filename)
public static int[] parseOpenedModelNumber(String inputLine)
{
int hash = inputLine.indexOf('#');
- int space = inputLine.indexOf(',', hash);
+ int space = -1;
+ if (hash == (-1))
+ {
+ hash = inputLine.indexOf("Model");
+ if (hash >= 0)
+ {
+ hash = hash + 5;
+ }
+ space = inputLine.indexOf(' ', hash + 1);
+ }
+ else
+ {
+ space = inputLine.indexOf(',', hash);
+ }
+
int decimal = inputLine.substring(hash + 1, space).indexOf('.');
// model number is between hash+1 and space
int modelNumber = -1;
{
if (decimal > 0)
{
- subModelNumber = Integer.parseInt(inputLine.substring(decimal
- + hash + 2, space));
+ subModelNumber = Integer
+ .parseInt(inputLine.substring(decimal + hash + 2, space));
space = decimal + hash + 1;
}
modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
{
int start = inputLine.indexOf("name ");
if (start < 0)
+ {
return null;
+ }
// Might get a quoted string (don't understand why, but there you have it)
if (inputLine.startsWith("\"", start + 5))
{
return inputLine.substring(start, end);
}
else
+ {
return inputLine.substring(start);
+ }
}
else
{
float[] rgbValues = new float[4];
for (int i = 0; i < rgbStrings.length; i++)
{
- Float f = new Float(rgbStrings[i]);
+ Float f = Float.valueOf(rgbStrings[i]);
rgbValues[i] = f.floatValue();
}
if (rgbStrings.length == 4)
*/
public static Integer makeModelKey(int model, int subModel)
{
- return new Integer(model * MAX_SUB_MODELS + subModel);
+ return Integer.valueOf(model * MAX_SUB_MODELS + subModel);
}
// invoked by the getResdiue (parseConnectivityReplies in
{
String[] subSplit = split[0].substring(1).split("\\.");
if (subSplit.length > 0)
+ {
model = Integer.parseInt(subSplit[0]);
+ }
else
+ {
model = Integer.parseInt(split[0].substring(1));
+ }
if (subSplit.length > 1)
+ {
submodel = Integer.parseInt(subSplit[1]);
+ }
} catch (Exception e)
{
// ignore
{
if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
|| atom.equals("O") || atom.equals("H"))
+ {
return true;
+ }
return false;
}
String resType = "";
if (split.length == 2)
{
- resType = split[0].trim().toUpperCase();
+ resType = split[0].trim().toUpperCase(Locale.ROOT);
}
else if (split.length == 3)
{
- resType = split[1].trim().toUpperCase();
+ resType = split[1].trim().toUpperCase(Locale.ROOT);
}
if (resType.equalsIgnoreCase("HOH") || resType.equalsIgnoreCase("WAT"))
{
}
else
{
+ // length > 1, so we probably have a file name with "." in it
logger.info("Could not parse model identifier: " + modelID);
+ resKeyParts[0] = modelID;
}
}
}
// }
// System.out.println("model = " + model + " chain = " + chain +
- // " residue = " +
- // residue);
+ // " residue = " + residue);
if (model != null)
{
List<ChimeraModel> models = chimeraManager.getChimeraModels(model,
{
try
{
- chimeraModel = chimeraManager.getChimeraModel(
- Integer.valueOf(model), 0);
+ chimeraModel = chimeraManager
+ .getChimeraModel(Integer.valueOf(model), 0);
} catch (NumberFormatException ex)
{
// ignore
}
if (chimeraResidue != null)
+ {
return chimeraResidue;
+ }
if (chimeraChain != null)
+ {
return chimeraChain;
+ }
if (chimeraModel != null)
+ {
return chimeraModel;
+ }
} catch (Exception ex)
{
if (modelIDNoResChain[0] != null)
{
String modelID = modelIDNoResChain[0];
- List<ChimeraModel> models = chimeraManager.getChimeraModels(
- modelID, ModelType.PDB_MODEL);
+ List<ChimeraModel> models = chimeraManager.getChimeraModels(modelID,
+ ModelType.PDB_MODEL);
if (models.size() == 1)
{ // usual case with only one model
chimeraModel = models.get(0);
// TODO: [Optional] What is this doing?
try
{
- chimeraModel = chimeraManager.getChimeraModel(
- Integer.valueOf(modelID), 0);
+ chimeraModel = chimeraManager
+ .getChimeraModel(Integer.valueOf(modelID), 0);
} catch (NumberFormatException ex)
{
// ignore
}
else if (chimeraModel.getChainCount() == 1)
{
- chimeraResidue = chimeraModel.getResidue(chimeraModel
- .getChainNames().iterator().next(), residue);
+ chimeraResidue = chimeraModel.getResidue(
+ chimeraModel.getChainNames().iterator().next(), residue);
}
// System.out.println("ChimeraResidue = " + chimeraResidue);
}
if (chimeraResidue != null)
+ {
return chimeraResidue;
+ }
if (chimeraChain != null)
+ {
return chimeraChain;
+ }
if (chimeraModel != null)
+ {
return chimeraModel;
+ }
} catch (Exception ex)
{
public static String findStructures(String residueList)
{
if (residueList == null)
+ {
return null;
+ }
String[] residues = residueList.split(",");
Map<String, String> structureNameMap = new HashMap<String, String>();
for (int i = 0; i < residues.length; i++)
}
}
if (structureNameMap.isEmpty())
+ {
return null;
+ }
String structure = null;
for (String struct : structureNameMap.keySet())
{
if (structure == null)
+ {
structure = new String();
+ }
else
+ {
structure = structure.concat(",");
+ }
structure = structure.concat(struct);
}
return structure;
{
resRange = resRange.concat("-");
if (chain != null && range[res].indexOf('.') == -1)
+ {
range[res] = range[res].concat("." + chain);
+ }
}
if (res == 0 && range.length >= 2 && range[res].indexOf('.') > 0)
aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
- aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
+ aaNames.put("PHE",
+ "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
public static String toFullName(String aaType)
{
if (!aaNames.containsKey(aaType))
+ {
return aaType;
- String[] ids = ((String) aaNames.get(aaType)).split(" ");
+ }
+ String[] ids = aaNames.get(aaType).split(" ");
return ids[2].replace('_', ' ');
}
public static String toSingleLetter(String aaType)
{
if (!aaNames.containsKey(aaType))
+ {
return aaType;
- String[] ids = ((String) aaNames.get(aaType)).split(" ");
+ }
+ String[] ids = aaNames.get(aaType).split(" ");
return ids[0];
}
public static String toThreeLetter(String aaType)
{
if (!aaNames.containsKey(aaType))
+ {
return aaType;
- String[] ids = ((String) aaNames.get(aaType)).split(" ");
+ }
+ String[] ids = aaNames.get(aaType).split(" ");
return ids[1];
}
public static String toSMILES(String aaType)
{
if (!aaNames.containsKey(aaType))
+ {
return null;
- String[] ids = ((String) aaNames.get(aaType)).split(" ");
+ }
+ String[] ids = aaNames.get(aaType).split(" ");
if (ids.length < 4)
+ {
return null;
+ }
return ids[3];
}
git://source.jalview.org / jalview.git / blobdiff