+/* 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;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+public abstract class ChimUtils
+{
-public abstract class ChimUtils {
-
- private static Logger logger = LoggerFactory
- .getLogger(ChimUtils.class);
-
- static int MAX_SUB_MODELS = 1000;
-
- public static final HashMap<String, String> aaNames;
-
- public static String RESIDUE_ATTR = "ChimeraResidue";
- public static String RINALYZER_ATTR = "RINalyzerResidue";
- public static String DEFAULT_STRUCTURE_KEY = "pdbFileName";
-
- /**
- * Parse the model number returned by Chimera and return the int value
- */
- // invoked by the ChimeraModel constructor
- // line = model id #0 type Molecule name 1ert
- public static int[] parseModelNumber(String inputLine) {
- int hash = inputLine.indexOf('#');
- int space = inputLine.indexOf(' ', hash);
- int decimal = inputLine.substring(hash + 1, space).indexOf('.');
- // model number is between hash+1 and space
- int modelNumber = -1;
- int subModelNumber = 0;
- try {
- if (decimal > 0) {
- subModelNumber = Integer.parseInt(inputLine.substring(decimal + hash + 2, space));
- space = decimal + hash + 1;
- }
- modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
- } catch (Exception e) {
- logger.warn("Unexpected return from Chimera: " + inputLine, e);
- }
- return new int[] { modelNumber, subModelNumber };
- }
-
- /**
- * Parse the model number returned by Chimera and return the int value
- */
- // invoked by openModel in ChimeraManager
- // line: #1, chain A: hiv-1 protease
- public static int[] parseOpenedModelNumber(String inputLine) {
- int hash = inputLine.indexOf('#');
- int space = inputLine.indexOf(',', hash);
- int decimal = inputLine.substring(hash + 1, space).indexOf('.');
- // model number is between hash+1 and space
- int modelNumber = -1;
- int subModelNumber = 0;
- try {
- if (decimal > 0) {
- subModelNumber = Integer.parseInt(inputLine.substring(decimal + hash + 2, space));
- space = decimal + hash + 1;
- }
- modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
- } catch (Exception e) {
- logger.warn("Unexpected return from Chimera: " + inputLine, e);
- }
- return new int[] { modelNumber, subModelNumber };
- }
-
- /**
- * Parse the model identifier returned by Chimera and return the String value
- */
- // invoked by the ChimeraModel constructor
- // line = model id #0 type Molecule name 1ert
- public static String parseModelName(String inputLine) {
- 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)) {
- start += 6; // Skip over the first quote
- int end = inputLine.lastIndexOf('"');
- if (end >= 1) {
- return inputLine.substring(start, end);
- } else
- return inputLine.substring(start);
- } else {
- return inputLine.substring(start + 5);
- }
- }
-
- public static Color parseModelColor(String inputLine) {
- try {
- int colorStart = inputLine.indexOf("color ");
- String colorString = inputLine.substring(colorStart + 6);
- String[] rgbStrings = colorString.split(",");
- float[] rgbValues = new float[4];
- for (int i = 0; i < rgbStrings.length; i++) {
- Float f = new Float(rgbStrings[i]);
- rgbValues[i] = f.floatValue();
- }
- if (rgbStrings.length == 4) {
- return new Color(rgbValues[0], rgbValues[1], rgbValues[2], rgbValues[3]);
- } else {
- return new Color(rgbValues[0], rgbValues[1], rgbValues[2]);
- }
- } catch (Exception ex) {
- logger.warn("Unexpected return from Chimera: " + inputLine, ex);
- }
- return Color.white;
- }
-
- /**
- * Create the key to use for forming the model/submodel key into the modelHash
- *
- * @param model
- * the model number
- * @param subModel
- * the submodel number
- * @return the model key as an Integer
- */
- public static Integer makeModelKey(int model, int subModel) {
- return new Integer(model * MAX_SUB_MODELS + subModel);
- }
-
- // invoked by the getResdiue (parseConnectivityReplies in CreateStructureNetworkTask)
- // atomSpec = #0:1.A or #1:96.B@N
- public static ChimeraModel getModel(String atomSpec, ChimeraManager chimeraManager) {
- // System.out.println("getting model for "+atomSpec);
- String[] split = atomSpec.split(":");
- // No model specified....
- if (split[0].length() == 0) {
- logger.info("Unexpected return from Chimera: " + atomSpec);
- return null;
- }
- // System.out.println("model = "+split[0].substring(1));
- int model = 0;
- int submodel = 0;
- try {
- 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
- logger.warn("Unexpected return from Chimera: " + atomSpec, e);
- }
- return chimeraManager.getChimeraModel(model, submodel);
- }
-
- // invoked by the parseConnectivityReplies in CreateStructureNetworkTask
- // atomSpec = #0:1.A or #1:96.B@N
- public static ChimeraResidue getResidue(String atomSpec, ChimeraManager chimeraManager) {
- // System.out.println("Getting residue from: "+atomSpec);
- ChimeraModel model = getModel(atomSpec, chimeraManager); // Get the model
- if (model == null) {
- model = chimeraManager.getChimeraModel();
- }
- return getResidue(atomSpec, model);
- }
-
- // invoked by the getResdiue (parseConnectivityReplies in CreateStructureNetworkTask)
- // atomSpec = #0:1.A or #1:96.B@N
- public static ChimeraResidue getResidue(String atomSpec, ChimeraModel model) {
- // System.out.println("Getting residue from: "+atomSpec);
- String[] split = atomSpec.split(":|@");
-
- // Split into residue and chain
- String[] residueChain = split[1].split("\\.");
-
- if (residueChain[0].length() == 0) {
- logger.info("Unexpected return from Chimera: " + atomSpec);
- return null;
- }
-
- if (residueChain.length == 2 && residueChain[1].length() > 0) {
- ChimeraChain chain = model.getChain(residueChain[1]);
- return chain.getResidue(residueChain[0]);
- }
- return model.getResidue("_", residueChain[0]);
- }
-
- public static ChimeraChain getChain(String atomSpec, ChimeraModel model) {
- String[] split = atomSpec.split(":|@");
-
- // Split into residue and chain
- String[] residueChain = split[1].split("\\.");
- if (residueChain.length == 1) {
- logger.info("Unexpected return from Chimera: " + atomSpec);
- return null;
- }
- return model.getChain(residueChain[1]);
- }
-
- public static String getAtomName(String atomSpec) {
- String[] split = atomSpec.split("@");
- if (split.length > 1) {
- return split[1];
- }
- return atomSpec;
- }
-
- public static boolean isBackbone(String atom) {
- if (atom.equals("C") || atom.equals("CA") || atom.equals("N") || atom.equals("O")
- || atom.equals("H"))
- return true;
- return false;
- }
-
- public static String getIntSubtype(String node, String atom) {
- String[] split = node.split("#| ");
- String resType = "";
- if (split.length == 2) {
- resType = split[0].trim().toUpperCase();
- } else if (split.length == 3) {
- resType = split[1].trim().toUpperCase();
- }
- if (resType.equalsIgnoreCase("HOH") || resType.equalsIgnoreCase("WAT")) {
- return "water";
- } else if (aaNames.containsKey(resType)) {
- if (atom.equals("C") || atom.equals("CA") || atom.equals("N") || atom.equals("O")
- || atom.equals("H")) {
- return "mc";
- } else {
- return "sc";
- }
- } else {
- return "other";
- }
- }
-
-
- public static String[] getResKeyParts(String resKey) {
- // [pdbID[.modelNo]#][residueID][.chainID]
- // pdbID := 4-character code | "URL" | "path"
- String[] resKeyParts = new String[4];
- String[] split = resKey.split("#");
- String resChain = null;
- // if no "#" then it is either only a pdb id or a residue or a chain
- if (split.length == 1) {
- // pdb id without model
- if (resKey.length() == 4 && resKey.indexOf("\\.") < 0) {
- parseModelID(resKey, resKeyParts);
- }
- // pdb link or file
- else if (resKey.startsWith("\"")) {
- parseModelID(resKey, resKeyParts);
- }
- // chain and residue or model and number
- else {
- String[] splitSplit = resKey.split("\\.");
- if (splitSplit.length == 1) {
- // only a chain or a residue
- resChain = resKey;
- } else {
- try {
- // pdb with a model
- Integer.parseInt(splitSplit[1]);
- parseModelID(resKey, resKeyParts);
- } catch (NumberFormatException ex) {
- // residue and chain
- resChain = resKey;
- }
- }
- }
- } else if (split.length == 2) {
- // model and residue+chain
- parseModelID(split[0], resKeyParts);
- resChain = split[1];
- } else {
- // model string with "#"
- // TODO: [Optional] Are there more possibilities?
- parseModelID(resKey.substring(0, resKey.lastIndexOf("#")), resKeyParts);
- resChain = resKey.substring(resKey.lastIndexOf("#") + 1, resKey.length());
- }
- if (resChain != null) {
- //System.out.println(resChain);
- String[] resChainSplit = resChain.split("\\.");
- if (resChainSplit.length == 1) {
- // TODO: [Optional] Find a better way to distinguish between chain and residue
- // if only one character and not an int, probably a chain
- if (resChainSplit[0].length() == 1) {
- try {
- Integer.parseInt(resChainSplit[0]);
- resKeyParts[3] = resChainSplit[0];
- } catch (NumberFormatException ex) {
- resKeyParts[2] = resChainSplit[0];
- }
- } else {
- resKeyParts[3] = resChainSplit[0];
- }
- } else if (resChainSplit.length == 2) {
- resKeyParts[2] = resChainSplit[0];
- resKeyParts[3] = resChainSplit[1];
- } else {
- // too many dots?
- logger.info("Could not parse residue identifier: " + resKey);
- }
- }
- // String print = "";
- // for (int i = 0; i < resKeyParts.length; i++) {
- // if (resKeyParts[i] == null) {
- // print += i + ": null\t";
- // } else {
- // print += i + ": " + resKeyParts[i] + ";";
- // }
- // }
- // System.out.println(print);
- return resKeyParts;
- }
-
- public static void parseModelID(String modelID, String[] resKeyParts) {
- if (modelID.startsWith("\"")) {
- if (modelID.endsWith("\"")) {
- resKeyParts[0] = modelID.substring(1, modelID.length() - 1);
- return;
- } else {
- try {
- Integer.parseInt(modelID.substring(modelID.lastIndexOf("\"") + 2,
- modelID.length()));
- resKeyParts[0] = modelID.substring(0, modelID.lastIndexOf("\"") - 1);
- resKeyParts[1] = modelID.substring(modelID.lastIndexOf("\"") + 2,
- modelID.length());
- } catch (NumberFormatException ex) {
- resKeyParts[0] = modelID.substring(1);
- }
- }
- } else {
- String[] modelIDNo = modelID.split("\\.");
- if (modelIDNo.length == 1) {
- resKeyParts[0] = modelIDNo[0];
- } else if (modelIDNo.length == 2) {
- try {
- Integer.parseInt(modelIDNo[1]);
- resKeyParts[0] = modelIDNo[0];
- resKeyParts[1] = modelIDNo[1];
- } catch (NumberFormatException ex) {
- resKeyParts[0] = modelID;
- }
- } else {
- logger.info("Could not parse model identifier: " + modelID);
- }
- }
- }
-
- /**
- * This method takes a Cytoscape attribute specification ([structure#][residue][.chainID]) and
- * returns the lowest-level object referenced by the spec. For example, if the spec is "1tkk",
- * this method will return a ChimeraModel. If the spec is ".A", it will return a ChimeraChain,
- * etc.
- *
- * @param attrSpec
- * the specification string
- * @param chimeraManager
- * the Chimera object we're currently using
- * @return a ChimeraStructuralObject of the lowest type
- */
- public static ChimeraStructuralObject fromAttributeOld(String attrSpec,
- ChimeraManager chimeraManager) {
- if (attrSpec == null || attrSpec.indexOf(',') > 0 || attrSpec.indexOf('-') > 0) {
- // No support for either lists or ranges
- logger.warn("No support for identifier: " + attrSpec);
- return null;
- }
-
- String residue = null;
- String model = null;
- String chain = null;
-
- ChimeraModel chimeraModel = null;
- ChimeraChain chimeraChain = null;
- ChimeraResidue chimeraResidue = null;
-
- // System.out.println("Getting object from attribute: "+attrSpec);
- try {
- String[] split = attrSpec.split("#");
- String resChain = null;
- if (split.length == 1) {
- // no model
- resChain = split[0];
- } else if (split.length == 2) {
- // model and rest
- model = split[0];
- resChain = split[1];
- } else {
- // model string with "#"
- model = attrSpec.substring(0, attrSpec.lastIndexOf("#"));
- resChain = attrSpec.substring(attrSpec.lastIndexOf("#") + 1, attrSpec.length());
- }
- if (resChain != null) {
- String[] resChainSplit = resChain.split("\\.");
- if (resChainSplit.length == 1) {
- residue = resChainSplit[0];
- } else if (resChainSplit.length == 2) {
- residue = resChainSplit[0];
- chain = resChainSplit[1];
- } else {
- // too many dots?
- logger.warn("No support for identifier: " + attrSpec);
- }
- }
-
- // if (split.length == 1) {
- // // No model
- // residue = split[0];
- // } else if (split.length == 3) {
- // // We have all three
- // model = split[0];
- // residue = split[1];
- // chain = split[2];
- // } else if (split.length == 2 && attrSpec.indexOf('#') > 0) {
- // // Model and Residue
- // model = split[0];
- // residue = split[1];
- // } else {
- // // Residue and Chain
- // residue = split[0];
- // chain = split[1];
- // }
-
- // System.out.println("model = " + model + " chain = " + chain + " residue = " +
- // residue);
- if (model != null) {
- List<ChimeraModel> models = chimeraManager.getChimeraModels(model,
- ModelType.PDB_MODEL);
- if (models.size() == 1) {
- chimeraModel = models.get(0);
- } else {
- try {
- chimeraModel = chimeraManager.getChimeraModel(Integer.valueOf(model), 0);
- } catch (NumberFormatException ex) {
- // ignore
- }
- }
- }
- if (chimeraModel == null) {
- chimeraModel = chimeraManager.getChimeraModel();
- }
- // System.out.println("ChimeraModel = " + chimeraModel);
-
- if (chain != null) {
- chimeraChain = chimeraModel.getChain(chain);
- // System.out.println("ChimeraChain = " + chimeraChain);
- }
- if (residue != null) {
- if (chimeraChain != null) {
- chimeraResidue = chimeraChain.getResidue(residue);
- } else {
- chimeraResidue = chimeraModel.getResidue("_", residue);
- }
- // System.out.println("ChimeraResidue = " + chimeraResidue);
- }
-
- if (chimeraResidue != null)
- return chimeraResidue;
-
- if (chimeraChain != null)
- return chimeraChain;
-
- if (chimeraModel != null)
- return chimeraModel;
-
- } catch (Exception ex) {
- logger.warn("Could not parse residue identifier: " + attrSpec, ex);
- }
- return null;
- }
-
- public static ChimeraStructuralObject fromAttribute(String attrSpec,
- ChimeraManager chimeraManager) {
- // TODO: Make sure it is OK to remove this: || attrSpec.indexOf('-') > 0
- if (attrSpec == null || attrSpec.indexOf(',') > 0) {
- // No support for either lists or ranges
- // System.out.println("No support for identifier: " + attrSpec);
- logger.warn("No support for identifier: " + attrSpec);
- return null;
- }
- String[] modelIDNoResChain = getResKeyParts(attrSpec);
-
- ChimeraModel chimeraModel = null;
- ChimeraChain chimeraChain = null;
- ChimeraResidue chimeraResidue = null;
-
- // System.out.println("Getting object from attribute: "+attrSpec);
- try {
- if (modelIDNoResChain[0] != null) {
- String modelID = modelIDNoResChain[0];
- List<ChimeraModel> models = chimeraManager.getChimeraModels(modelID,
- ModelType.PDB_MODEL);
- if (models.size() == 1) { // usual case with only one model
- chimeraModel = models.get(0);
- } else if (models.size() > 1 && modelIDNoResChain[1] != null) {
- // there are several submodels
- try {
- int modelNo = Integer.valueOf(modelIDNoResChain[1]);
- for (ChimeraModel model : models) {
- if (model.getSubModelNumber() == modelNo) {
- chimeraModel = model;
- break;
- }
- }
- } catch (NumberFormatException ex) {
- // ignore
- }
- } else {
- // TODO: [Optional] What is this doing?
- try {
- chimeraModel = chimeraManager.getChimeraModel(Integer.valueOf(modelID), 0);
- } catch (NumberFormatException ex) {
- // ignore
- }
- }
- }
- if (chimeraModel == null) {
- // TODO: [Optional] Find a better way to handle this case
- // If no model can be matched, continue
- // System.out.println("No matching model could be find for " + attrSpec);
- return null;
- // chimeraModel = chimeraManager.getChimeraModel();
- // logger.warn("No matching model could be find for " + attrSpec + ". Trying with "
- // + chimeraModel.toSpec());
- }
- // System.out.println("ChimeraModel = " + chimeraModel);
-
- if (modelIDNoResChain[3] != null) {
- chimeraChain = chimeraModel.getChain(modelIDNoResChain[3]);
- // System.out.println("ChimeraChain = " + chimeraChain);
- }
- if (modelIDNoResChain[2] != null) {
- String residue = modelIDNoResChain[2];
- if (chimeraChain != null) {
- chimeraResidue = chimeraChain.getResidue(residue);
- } else if (chimeraModel.getChain("_") != null) {
- chimeraResidue = chimeraModel.getResidue("_", residue);
- } else if (chimeraModel.getChainCount() == 1) {
- 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) {
- // System.out.println("Could not parse chimera identifier: " +
- // attrSpec+"("+ex.getMessage()+")");
- logger.warn("Could not parse chimera identifier: " + attrSpec, ex);
- }
- return null;
- }
-
- /**
- * Search for structure references in the residue list
- *
- * @param residueList
- * the list of residues
- * @return a concatenated list of structures encoded in the list
- */
- 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++) {
- String[] components = residues[i].split("#");
- if (components.length > 1) {
- structureNameMap.put(components[0], components[1]);
- }
- }
- 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;
- }
-
- // invoked by openStructures in StructureManager
- public static List<String> parseFuncRes(List<String> residueNames, String modelName) {
- List<String> resRanges = new ArrayList<String>();
- for (int i = 0; i < residueNames.size(); i++) {
- String residue = residueNames.get(i);
- // Parse out the structure, if there is one
- String[] components = residue.split("#");
- if (components.length > 1 && !modelName.equals(components[0])) {
- continue;
- } else if (components.length > 1) {
- residue = components[1];
- } else if (components.length == 1) {
- residue = components[0];
- }
- // Check to see if we have a range-spec
- String resRange = "";
- if (residue == null || residue.equals("") || residue.length() == 0) {
- continue;
- }
- String[] range = residue.split("-", 2);
- String chain = null;
- for (int res = 0; res < range.length; res++) {
- if (res == 1) {
- 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) {
- // This is a range spec with the leading residue containing a chain spec
- String[] resChain = range[res].split("\\.");
- chain = resChain[1];
- range[res] = resChain[0];
- }
- // Fix weird SFLD syntax...
- if (range[res].indexOf('|') > 0 && Character.isDigit(range[res].charAt(0))) {
- int offset = range[res].indexOf('|');
- String str = range[res].substring(offset + 1) + range[res].substring(0, offset);
- range[res] = str;
- }
-
- // Convert to legal atom-spec
- if (Character.isDigit(range[res].charAt(0))) {
- resRange = resRange.concat(range[res]);
- } else if (Character.isDigit(range[res].charAt(1))) {
- resRange = resRange.concat(range[res].substring(1));
- } else if (range[res].charAt(0) == '.') {
- // Do we have a chain spec?
- resRange = resRange.concat(range[res]);
- } else {
- resRange = resRange.concat(range[res].substring(3));
- }
- }
- if (!resRanges.contains(resRange)) {
- resRanges.add(resRange);
- }
- }
- return resRanges;
- }
-
- static {
- aaNames = new HashMap<String, String>();
- aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
- aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
- aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
- aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
- aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
- aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
- aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
- aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
- aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
- aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
- aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
- 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("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");
- aaNames.put("TRP", "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
- aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
- aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
- aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
- aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
- aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
- aaNames.put("HOH", "HOH HOH Water [H]O[H]");
- }
-
- /**
- * Convert the amino acid type to a full name
- *
- * @param aaType
- * the residue type to convert
- * @return the full name of the residue
- */
- public static String toFullName(String aaType) {
- if (!aaNames.containsKey(aaType))
- return aaType;
- String[] ids = ((String) aaNames.get(aaType)).split(" ");
- return ids[2].replace('_', ' ');
- }
-
- /**
- * Convert the amino acid type to a single letter
- *
- * @param aaType
- * the residue type to convert
- * @return the single letter representation of the residue
- */
- public static String toSingleLetter(String aaType) {
- if (!aaNames.containsKey(aaType))
- return aaType;
- String[] ids = ((String) aaNames.get(aaType)).split(" ");
- return ids[0];
- }
-
- /**
- * Convert the amino acid type to three letters
- *
- * @param aaType
- * the residue type to convert
- * @return the three letter representation of the residue
- */
- public static String toThreeLetter(String aaType) {
- if (!aaNames.containsKey(aaType))
- return aaType;
- String[] ids = ((String) aaNames.get(aaType)).split(" ");
- return ids[1];
- }
-
- /**
- * Convert the amino acid type to its SMILES string
- *
- * @param aaType
- * the residue type to convert
- * @return the SMILES representation of the residue
- */
- public static String toSMILES(String aaType) {
- if (!aaNames.containsKey(aaType))
- return null;
- String[] ids = ((String) aaNames.get(aaType)).split(" ");
- if (ids.length < 4)
- return null;
- return ids[3];
- }
-
- public static String getAlignName(ChimeraStructuralObject chimObj) {
- String name = chimObj.getChimeraModel().toString();
- if (chimObj instanceof ChimeraChain) {
- name = ((ChimeraChain) chimObj).toString() + " [" + name + "]";
- }
- return name;
- }
+ private static Logger logger = LoggerFactory.getLogger(ChimUtils.class);
+
+ static int MAX_SUB_MODELS = 1000;
+
+ public static final HashMap<String, String> aaNames;
+
+ public static String RESIDUE_ATTR = "ChimeraResidue";
+
+ public static String RINALYZER_ATTR = "RINalyzerResidue";
+
+ public static String DEFAULT_STRUCTURE_KEY = "pdbFileName";
+
+ /**
+ * Parse the model number returned by Chimera and return the int value
+ */
+ // invoked by the ChimeraModel constructor
+ // line = model id #0 type Molecule name 1ert
+ public static int[] parseModelNumber(String inputLine)
+ {
+ int hash = inputLine.indexOf('#');
+ int space = inputLine.indexOf(' ', hash);
+ int decimal = inputLine.substring(hash + 1, space).indexOf('.');
+ // model number is between hash+1 and space
+ int modelNumber = -1;
+ int subModelNumber = 0;
+ try
+ {
+ if (decimal > 0)
+ {
+ subModelNumber = Integer
+ .parseInt(inputLine.substring(decimal + hash + 2, space));
+ space = decimal + hash + 1;
+ }
+ modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
+ } catch (Exception e)
+ {
+ logger.warn("Unexpected return from Chimera: " + inputLine, e);
+ }
+ return new int[] { modelNumber, subModelNumber };
+ }
+
+ /**
+ * Parse the model number returned by Chimera and return the int value
+ */
+ // 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 = -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;
+ int subModelNumber = 0;
+ try
+ {
+ if (decimal > 0)
+ {
+ subModelNumber = Integer
+ .parseInt(inputLine.substring(decimal + hash + 2, space));
+ space = decimal + hash + 1;
+ }
+ modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
+ } catch (Exception e)
+ {
+ logger.warn("Unexpected return from Chimera: " + inputLine, e);
+ }
+ return new int[] { modelNumber, subModelNumber };
+ }
+
+ /**
+ * Parse the model identifier returned by Chimera and return the String value
+ */
+ // invoked by the ChimeraModel constructor
+ // line = model id #0 type Molecule name 1ert
+ public static String parseModelName(String inputLine)
+ {
+ 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))
+ {
+ start += 6; // Skip over the first quote
+ int end = inputLine.lastIndexOf('"');
+ if (end >= 1)
+ {
+ return inputLine.substring(start, end);
+ }
+ else
+ {
+ return inputLine.substring(start);
+ }
+ }
+ else
+ {
+ return inputLine.substring(start + 5);
+ }
+ }
+
+ public static Color parseModelColor(String inputLine)
+ {
+ try
+ {
+ int colorStart = inputLine.indexOf("color ");
+ String colorString = inputLine.substring(colorStart + 6);
+ String[] rgbStrings = colorString.split(",");
+ float[] rgbValues = new float[4];
+ for (int i = 0; i < rgbStrings.length; i++)
+ {
+ Float f = Float.valueOf(rgbStrings[i]);
+ rgbValues[i] = f.floatValue();
+ }
+ if (rgbStrings.length == 4)
+ {
+ return new Color(rgbValues[0], rgbValues[1], rgbValues[2],
+ rgbValues[3]);
+ }
+ else
+ {
+ return new Color(rgbValues[0], rgbValues[1], rgbValues[2]);
+ }
+ } catch (Exception ex)
+ {
+ logger.warn("Unexpected return from Chimera: " + inputLine, ex);
+ }
+ return Color.white;
+ }
+
+ /**
+ * Create the key to use for forming the model/submodel key into the modelHash
+ *
+ * @param model
+ * the model number
+ * @param subModel
+ * the submodel number
+ * @return the model key as an Integer
+ */
+ public static Integer makeModelKey(int model, int subModel)
+ {
+ return Integer.valueOf(model * MAX_SUB_MODELS + subModel);
+ }
+
+ // invoked by the getResdiue (parseConnectivityReplies in
+ // CreateStructureNetworkTask)
+ // atomSpec = #0:1.A or #1:96.B@N
+ public static ChimeraModel getModel(String atomSpec,
+ ChimeraManager chimeraManager)
+ {
+ // System.out.println("getting model for "+atomSpec);
+ String[] split = atomSpec.split(":");
+ // No model specified....
+ if (split[0].length() == 0)
+ {
+ logger.info("Unexpected return from Chimera: " + atomSpec);
+ return null;
+ }
+ // System.out.println("model = "+split[0].substring(1));
+ int model = 0;
+ int submodel = 0;
+ try
+ {
+ 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
+ logger.warn("Unexpected return from Chimera: " + atomSpec, e);
+ }
+ return chimeraManager.getChimeraModel(model, submodel);
+ }
+
+ // invoked by the parseConnectivityReplies in CreateStructureNetworkTask
+ // atomSpec = #0:1.A or #1:96.B@N
+ public static ChimeraResidue getResidue(String atomSpec,
+ ChimeraManager chimeraManager)
+ {
+ // System.out.println("Getting residue from: "+atomSpec);
+ ChimeraModel model = getModel(atomSpec, chimeraManager); // Get the model
+ if (model == null)
+ {
+ model = chimeraManager.getChimeraModel();
+ }
+ return getResidue(atomSpec, model);
+ }
+
+ // invoked by the getResdiue (parseConnectivityReplies in
+ // CreateStructureNetworkTask)
+ // atomSpec = #0:1.A or #1:96.B@N
+ public static ChimeraResidue getResidue(String atomSpec,
+ ChimeraModel model)
+ {
+ // System.out.println("Getting residue from: "+atomSpec);
+ String[] split = atomSpec.split(":|@");
+
+ // Split into residue and chain
+ String[] residueChain = split[1].split("\\.");
+
+ if (residueChain[0].length() == 0)
+ {
+ logger.info("Unexpected return from Chimera: " + atomSpec);
+ return null;
+ }
+
+ if (residueChain.length == 2 && residueChain[1].length() > 0)
+ {
+ ChimeraChain chain = model.getChain(residueChain[1]);
+ return chain.getResidue(residueChain[0]);
+ }
+ return model.getResidue("_", residueChain[0]);
+ }
+
+ public static ChimeraChain getChain(String atomSpec, ChimeraModel model)
+ {
+ String[] split = atomSpec.split(":|@");
+
+ // Split into residue and chain
+ String[] residueChain = split[1].split("\\.");
+ if (residueChain.length == 1)
+ {
+ logger.info("Unexpected return from Chimera: " + atomSpec);
+ return null;
+ }
+ return model.getChain(residueChain[1]);
+ }
+
+ public static String getAtomName(String atomSpec)
+ {
+ String[] split = atomSpec.split("@");
+ if (split.length > 1)
+ {
+ return split[1];
+ }
+ return atomSpec;
+ }
+
+ public static boolean isBackbone(String atom)
+ {
+ if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
+ || atom.equals("O") || atom.equals("H"))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ public static String getIntSubtype(String node, String atom)
+ {
+ String[] split = node.split("#| ");
+ String resType = "";
+ if (split.length == 2)
+ {
+ resType = split[0].trim().toUpperCase(Locale.ROOT);
+ }
+ else if (split.length == 3)
+ {
+ resType = split[1].trim().toUpperCase(Locale.ROOT);
+ }
+ if (resType.equalsIgnoreCase("HOH") || resType.equalsIgnoreCase("WAT"))
+ {
+ return "water";
+ }
+ else if (aaNames.containsKey(resType))
+ {
+ if (atom.equals("C") || atom.equals("CA") || atom.equals("N")
+ || atom.equals("O") || atom.equals("H"))
+ {
+ return "mc";
+ }
+ else
+ {
+ return "sc";
+ }
+ }
+ else
+ {
+ return "other";
+ }
+ }
+
+ public static String[] getResKeyParts(String resKey)
+ {
+ // [pdbID[.modelNo]#][residueID][.chainID]
+ // pdbID := 4-character code | "URL" | "path"
+ String[] resKeyParts = new String[4];
+ String[] split = resKey.split("#");
+ String resChain = null;
+ // if no "#" then it is either only a pdb id or a residue or a chain
+ if (split.length == 1)
+ {
+ // pdb id without model
+ if (resKey.length() == 4 && resKey.indexOf("\\.") < 0)
+ {
+ parseModelID(resKey, resKeyParts);
+ }
+ // pdb link or file
+ else if (resKey.startsWith("\""))
+ {
+ parseModelID(resKey, resKeyParts);
+ }
+ // chain and residue or model and number
+ else
+ {
+ String[] splitSplit = resKey.split("\\.");
+ if (splitSplit.length == 1)
+ {
+ // only a chain or a residue
+ resChain = resKey;
+ }
+ else
+ {
+ try
+ {
+ // pdb with a model
+ Integer.parseInt(splitSplit[1]);
+ parseModelID(resKey, resKeyParts);
+ } catch (NumberFormatException ex)
+ {
+ // residue and chain
+ resChain = resKey;
+ }
+ }
+ }
+ }
+ else if (split.length == 2)
+ {
+ // model and residue+chain
+ parseModelID(split[0], resKeyParts);
+ resChain = split[1];
+ }
+ else
+ {
+ // model string with "#"
+ // TODO: [Optional] Are there more possibilities?
+ parseModelID(resKey.substring(0, resKey.lastIndexOf("#")),
+ resKeyParts);
+ resChain = resKey.substring(resKey.lastIndexOf("#") + 1,
+ resKey.length());
+ }
+ if (resChain != null)
+ {
+ // System.out.println(resChain);
+ String[] resChainSplit = resChain.split("\\.");
+ if (resChainSplit.length == 1)
+ {
+ // TODO: [Optional] Find a better way to distinguish between chain and
+ // residue
+ // if only one character and not an int, probably a chain
+ if (resChainSplit[0].length() == 1)
+ {
+ try
+ {
+ Integer.parseInt(resChainSplit[0]);
+ resKeyParts[3] = resChainSplit[0];
+ } catch (NumberFormatException ex)
+ {
+ resKeyParts[2] = resChainSplit[0];
+ }
+ }
+ else
+ {
+ resKeyParts[3] = resChainSplit[0];
+ }
+ }
+ else if (resChainSplit.length == 2)
+ {
+ resKeyParts[2] = resChainSplit[0];
+ resKeyParts[3] = resChainSplit[1];
+ }
+ else
+ {
+ // too many dots?
+ logger.info("Could not parse residue identifier: " + resKey);
+ }
+ }
+ // String print = "";
+ // for (int i = 0; i < resKeyParts.length; i++) {
+ // if (resKeyParts[i] == null) {
+ // print += i + ": null\t";
+ // } else {
+ // print += i + ": " + resKeyParts[i] + ";";
+ // }
+ // }
+ // System.out.println(print);
+ return resKeyParts;
+ }
+
+ public static void parseModelID(String modelID, String[] resKeyParts)
+ {
+ if (modelID.startsWith("\""))
+ {
+ if (modelID.endsWith("\""))
+ {
+ resKeyParts[0] = modelID.substring(1, modelID.length() - 1);
+ return;
+ }
+ else
+ {
+ try
+ {
+ Integer.parseInt(modelID.substring(modelID.lastIndexOf("\"") + 2,
+ modelID.length()));
+ resKeyParts[0] = modelID.substring(0,
+ modelID.lastIndexOf("\"") - 1);
+ resKeyParts[1] = modelID.substring(modelID.lastIndexOf("\"") + 2,
+ modelID.length());
+ } catch (NumberFormatException ex)
+ {
+ resKeyParts[0] = modelID.substring(1);
+ }
+ }
+ }
+ else
+ {
+ String[] modelIDNo = modelID.split("\\.");
+ if (modelIDNo.length == 1)
+ {
+ resKeyParts[0] = modelIDNo[0];
+ }
+ else if (modelIDNo.length == 2)
+ {
+ try
+ {
+ Integer.parseInt(modelIDNo[1]);
+ resKeyParts[0] = modelIDNo[0];
+ resKeyParts[1] = modelIDNo[1];
+ } catch (NumberFormatException ex)
+ {
+ resKeyParts[0] = modelID;
+ }
+ }
+ else
+ {
+ // length > 1, so we probably have a file name with "." in it
+ logger.info("Could not parse model identifier: " + modelID);
+ resKeyParts[0] = modelID;
+ }
+ }
+ }
+
+ /**
+ * This method takes a Cytoscape attribute specification
+ * ([structure#][residue][.chainID]) and returns the lowest-level object
+ * referenced by the spec. For example, if the spec is "1tkk", this method
+ * will return a ChimeraModel. If the spec is ".A", it will return a
+ * ChimeraChain, etc.
+ *
+ * @param attrSpec
+ * the specification string
+ * @param chimeraManager
+ * the Chimera object we're currently using
+ * @return a ChimeraStructuralObject of the lowest type
+ */
+ public static ChimeraStructuralObject fromAttributeOld(String attrSpec,
+ ChimeraManager chimeraManager)
+ {
+ if (attrSpec == null || attrSpec.indexOf(',') > 0
+ || attrSpec.indexOf('-') > 0)
+ {
+ // No support for either lists or ranges
+ logger.warn("No support for identifier: " + attrSpec);
+ return null;
+ }
+
+ String residue = null;
+ String model = null;
+ String chain = null;
+
+ ChimeraModel chimeraModel = null;
+ ChimeraChain chimeraChain = null;
+ ChimeraResidue chimeraResidue = null;
+
+ // System.out.println("Getting object from attribute: "+attrSpec);
+ try
+ {
+ String[] split = attrSpec.split("#");
+ String resChain = null;
+ if (split.length == 1)
+ {
+ // no model
+ resChain = split[0];
+ }
+ else if (split.length == 2)
+ {
+ // model and rest
+ model = split[0];
+ resChain = split[1];
+ }
+ else
+ {
+ // model string with "#"
+ model = attrSpec.substring(0, attrSpec.lastIndexOf("#"));
+ resChain = attrSpec.substring(attrSpec.lastIndexOf("#") + 1,
+ attrSpec.length());
+ }
+ if (resChain != null)
+ {
+ String[] resChainSplit = resChain.split("\\.");
+ if (resChainSplit.length == 1)
+ {
+ residue = resChainSplit[0];
+ }
+ else if (resChainSplit.length == 2)
+ {
+ residue = resChainSplit[0];
+ chain = resChainSplit[1];
+ }
+ else
+ {
+ // too many dots?
+ logger.warn("No support for identifier: " + attrSpec);
+ }
+ }
+
+ // if (split.length == 1) {
+ // // No model
+ // residue = split[0];
+ // } else if (split.length == 3) {
+ // // We have all three
+ // model = split[0];
+ // residue = split[1];
+ // chain = split[2];
+ // } else if (split.length == 2 && attrSpec.indexOf('#') > 0) {
+ // // Model and Residue
+ // model = split[0];
+ // residue = split[1];
+ // } else {
+ // // Residue and Chain
+ // residue = split[0];
+ // chain = split[1];
+ // }
+
+ // System.out.println("model = " + model + " chain = " + chain +
+ // " residue = " + residue);
+ if (model != null)
+ {
+ List<ChimeraModel> models = chimeraManager.getChimeraModels(model,
+ ModelType.PDB_MODEL);
+ if (models.size() == 1)
+ {
+ chimeraModel = models.get(0);
+ }
+ else
+ {
+ try
+ {
+ chimeraModel = chimeraManager
+ .getChimeraModel(Integer.valueOf(model), 0);
+ } catch (NumberFormatException ex)
+ {
+ // ignore
+ }
+ }
+ }
+ if (chimeraModel == null)
+ {
+ chimeraModel = chimeraManager.getChimeraModel();
+ }
+ // System.out.println("ChimeraModel = " + chimeraModel);
+
+ if (chain != null)
+ {
+ chimeraChain = chimeraModel.getChain(chain);
+ // System.out.println("ChimeraChain = " + chimeraChain);
+ }
+ if (residue != null)
+ {
+ if (chimeraChain != null)
+ {
+ chimeraResidue = chimeraChain.getResidue(residue);
+ }
+ else
+ {
+ chimeraResidue = chimeraModel.getResidue("_", residue);
+ }
+ // System.out.println("ChimeraResidue = " + chimeraResidue);
+ }
+
+ if (chimeraResidue != null)
+ {
+ return chimeraResidue;
+ }
+
+ if (chimeraChain != null)
+ {
+ return chimeraChain;
+ }
+
+ if (chimeraModel != null)
+ {
+ return chimeraModel;
+ }
+
+ } catch (Exception ex)
+ {
+ logger.warn("Could not parse residue identifier: " + attrSpec, ex);
+ }
+ return null;
+ }
+
+ public static ChimeraStructuralObject fromAttribute(String attrSpec,
+ ChimeraManager chimeraManager)
+ {
+ // TODO: Make sure it is OK to remove this: || attrSpec.indexOf('-') > 0
+ if (attrSpec == null || attrSpec.indexOf(',') > 0)
+ {
+ // No support for either lists or ranges
+ // System.out.println("No support for identifier: " + attrSpec);
+ logger.warn("No support for identifier: " + attrSpec);
+ return null;
+ }
+ String[] modelIDNoResChain = getResKeyParts(attrSpec);
+
+ ChimeraModel chimeraModel = null;
+ ChimeraChain chimeraChain = null;
+ ChimeraResidue chimeraResidue = null;
+
+ // System.out.println("Getting object from attribute: "+attrSpec);
+ try
+ {
+ if (modelIDNoResChain[0] != null)
+ {
+ String modelID = modelIDNoResChain[0];
+ List<ChimeraModel> models = chimeraManager.getChimeraModels(modelID,
+ ModelType.PDB_MODEL);
+ if (models.size() == 1)
+ { // usual case with only one model
+ chimeraModel = models.get(0);
+ }
+ else if (models.size() > 1 && modelIDNoResChain[1] != null)
+ {
+ // there are several submodels
+ try
+ {
+ int modelNo = Integer.valueOf(modelIDNoResChain[1]);
+ for (ChimeraModel model : models)
+ {
+ if (model.getSubModelNumber() == modelNo)
+ {
+ chimeraModel = model;
+ break;
+ }
+ }
+ } catch (NumberFormatException ex)
+ {
+ // ignore
+ }
+ }
+ else
+ {
+ // TODO: [Optional] What is this doing?
+ try
+ {
+ chimeraModel = chimeraManager
+ .getChimeraModel(Integer.valueOf(modelID), 0);
+ } catch (NumberFormatException ex)
+ {
+ // ignore
+ }
+ }
+ }
+ if (chimeraModel == null)
+ {
+ // TODO: [Optional] Find a better way to handle this case
+ // If no model can be matched, continue
+ // System.out.println("No matching model could be find for " +
+ // attrSpec);
+ return null;
+ // chimeraModel = chimeraManager.getChimeraModel();
+ // logger.warn("No matching model could be find for " + attrSpec +
+ // ". Trying with "
+ // + chimeraModel.toSpec());
+ }
+ // System.out.println("ChimeraModel = " + chimeraModel);
+
+ if (modelIDNoResChain[3] != null)
+ {
+ chimeraChain = chimeraModel.getChain(modelIDNoResChain[3]);
+ // System.out.println("ChimeraChain = " + chimeraChain);
+ }
+ if (modelIDNoResChain[2] != null)
+ {
+ String residue = modelIDNoResChain[2];
+ if (chimeraChain != null)
+ {
+ chimeraResidue = chimeraChain.getResidue(residue);
+ }
+ else if (chimeraModel.getChain("_") != null)
+ {
+ chimeraResidue = chimeraModel.getResidue("_", residue);
+ }
+ else if (chimeraModel.getChainCount() == 1)
+ {
+ 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)
+ {
+ // System.out.println("Could not parse chimera identifier: " +
+ // attrSpec+"("+ex.getMessage()+")");
+ logger.warn("Could not parse chimera identifier: " + attrSpec, ex);
+ }
+ return null;
+ }
+
+ /**
+ * Search for structure references in the residue list
+ *
+ * @param residueList
+ * the list of residues
+ * @return a concatenated list of structures encoded in the list
+ */
+ 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++)
+ {
+ String[] components = residues[i].split("#");
+ if (components.length > 1)
+ {
+ structureNameMap.put(components[0], components[1]);
+ }
+ }
+ 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;
+ }
+
+ // invoked by openStructures in StructureManager
+ public static List<String> parseFuncRes(List<String> residueNames,
+ String modelName)
+ {
+ List<String> resRanges = new ArrayList<String>();
+ for (int i = 0; i < residueNames.size(); i++)
+ {
+ String residue = residueNames.get(i);
+ // Parse out the structure, if there is one
+ String[] components = residue.split("#");
+ if (components.length > 1 && !modelName.equals(components[0]))
+ {
+ continue;
+ }
+ else if (components.length > 1)
+ {
+ residue = components[1];
+ }
+ else if (components.length == 1)
+ {
+ residue = components[0];
+ }
+ // Check to see if we have a range-spec
+ String resRange = "";
+ if (residue == null || residue.equals("") || residue.length() == 0)
+ {
+ continue;
+ }
+ String[] range = residue.split("-", 2);
+ String chain = null;
+ for (int res = 0; res < range.length; res++)
+ {
+ if (res == 1)
+ {
+ 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)
+ {
+ // This is a range spec with the leading residue containing a chain
+ // spec
+ String[] resChain = range[res].split("\\.");
+ chain = resChain[1];
+ range[res] = resChain[0];
+ }
+ // Fix weird SFLD syntax...
+ if (range[res].indexOf('|') > 0
+ && Character.isDigit(range[res].charAt(0)))
+ {
+ int offset = range[res].indexOf('|');
+ String str = range[res].substring(offset + 1)
+ + range[res].substring(0, offset);
+ range[res] = str;
+ }
+
+ // Convert to legal atom-spec
+ if (Character.isDigit(range[res].charAt(0)))
+ {
+ resRange = resRange.concat(range[res]);
+ }
+ else if (Character.isDigit(range[res].charAt(1)))
+ {
+ resRange = resRange.concat(range[res].substring(1));
+ }
+ else if (range[res].charAt(0) == '.')
+ {
+ // Do we have a chain spec?
+ resRange = resRange.concat(range[res]);
+ }
+ else
+ {
+ resRange = resRange.concat(range[res].substring(3));
+ }
+ }
+ if (!resRanges.contains(resRange))
+ {
+ resRanges.add(resRange);
+ }
+ }
+ return resRanges;
+ }
+
+ static
+ {
+ aaNames = new HashMap<String, String>();
+ aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
+ aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
+ aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
+ aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
+ aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
+ aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
+ aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
+ aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
+ aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
+ aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
+ aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
+ 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("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");
+ aaNames.put("TRP",
+ "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
+ aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
+ aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
+ aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
+ aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
+ aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
+ aaNames.put("HOH", "HOH HOH Water [H]O[H]");
+ }
+
+ /**
+ * Convert the amino acid type to a full name
+ *
+ * @param aaType
+ * the residue type to convert
+ * @return the full name of the residue
+ */
+ public static String toFullName(String aaType)
+ {
+ if (!aaNames.containsKey(aaType))
+ {
+ return aaType;
+ }
+ String[] ids = aaNames.get(aaType).split(" ");
+ return ids[2].replace('_', ' ');
+ }
+
+ /**
+ * Convert the amino acid type to a single letter
+ *
+ * @param aaType
+ * the residue type to convert
+ * @return the single letter representation of the residue
+ */
+ public static String toSingleLetter(String aaType)
+ {
+ if (!aaNames.containsKey(aaType))
+ {
+ return aaType;
+ }
+ String[] ids = aaNames.get(aaType).split(" ");
+ return ids[0];
+ }
+
+ /**
+ * Convert the amino acid type to three letters
+ *
+ * @param aaType
+ * the residue type to convert
+ * @return the three letter representation of the residue
+ */
+ public static String toThreeLetter(String aaType)
+ {
+ if (!aaNames.containsKey(aaType))
+ {
+ return aaType;
+ }
+ String[] ids = aaNames.get(aaType).split(" ");
+ return ids[1];
+ }
+
+ /**
+ * Convert the amino acid type to its SMILES string
+ *
+ * @param aaType
+ * the residue type to convert
+ * @return the SMILES representation of the residue
+ */
+ public static String toSMILES(String aaType)
+ {
+ if (!aaNames.containsKey(aaType))
+ {
+ return null;
+ }
+ String[] ids = aaNames.get(aaType).split(" ");
+ if (ids.length < 4)
+ {
+ return null;
+ }
+ return ids[3];
+ }
+
+ public static String getAlignName(ChimeraStructuralObject chimObj)
+ {
+ String name = chimObj.getChimeraModel().toString();
+ if (chimObj instanceof ChimeraChain)
+ {
+ name = ((ChimeraChain) chimObj).toString() + " [" + name + "]";
+ }
+ return name;
+ }
}
git://source.jalview.org / jalview.git / blobdiff