--- /dev/null
+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.Map;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+
+
+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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff