X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=65b4b9627c1b09a30ed2af0149b15460db0f6fc3;hb=ab889432b2f2ebea75aca36e814efc42ab50b9ac;hp=a339c6b159778124862fd497e31096e6c5a2e372;hpb=8a693367d8a0f6113d21248993ca4e0355b32659;p=jalview.git diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index a339c6b..65b4b96 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -22,14 +22,18 @@ package jalview.ext.jmol; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; +import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.io.FileParse; import jalview.io.StructureFile; import jalview.schemes.ResidueProperties; +import jalview.structure.StructureImportSettings; +import jalview.util.Format; import jalview.util.MessageManager; import java.io.IOException; import java.util.ArrayList; +import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.Vector; @@ -57,24 +61,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener { Viewer viewer = null; - public JmolParser(boolean addAlignmentAnnotations, - boolean predictSecondaryStructure, boolean externalSecStr, - String inFile, String type) throws IOException + public JmolParser(String inFile, String type) + throws IOException { super(inFile, type); - this.visibleChainAnnotation = addAlignmentAnnotations; - this.predictSecondaryStructure = predictSecondaryStructure; - this.externalSecondaryStructure = externalSecStr; - } - - public JmolParser(boolean addAlignmentAnnotations, - boolean predictSecondaryStructure, boolean externalSecStr, - FileParse fp) throws IOException - { - super(fp); - this.visibleChainAnnotation = addAlignmentAnnotations; - this.predictSecondaryStructure = predictSecondaryStructure; - this.externalSecondaryStructure = externalSecStr; } public JmolParser(FileParse fp) throws IOException @@ -82,11 +72,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener super(fp); } - public JmolParser(String inFile, String type) throws IOException - { - super(inFile, type); - } - public JmolParser() { } @@ -102,7 +87,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener @Override public void parse() throws IOException { - setChains(new Vector()); Viewer jmolModel = getJmolData(); jmolModel.openReader(getDataName(), getDataName(), getReader()); @@ -113,6 +97,18 @@ public class JmolParser extends StructureFile implements JmolStatusListener */ if (jmolModel.ms.mc > 0) { + // ideally we do this + // try + // { + // setStructureFileType(jmolModel.evalString("show _fileType")); + // } catch (Exception q) + // { + // } + // ; + // instead, we distinguish .cif from non-.cif by filename + setStructureFileType(getDataName().toLowerCase().endsWith(".cif") ? PDBEntry.Type.MMCIF + .toString() : "PDB"); + transformJmolModelToJalview(jmolModel.ms); } } @@ -128,8 +124,13 @@ public class JmolParser extends StructureFile implements JmolStatusListener { try { + /* + * params -o (output to sysout) -i (no info logging, less verbose) + * -n (nodisplay) -x (exit when finished) + * see http://wiki.jmol.org/index.php/Jmol_Application + */ viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null, - null, "-x -o -n", this); + null, "-x -o -n -i", this); // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used viewer.setBooleanProperty("defaultStructureDSSP", true); } catch (ClassCastException x) @@ -172,17 +173,18 @@ public class JmolParser extends StructureFile implements JmolStatusListener } lastID = tmpatom.resNumIns.trim(); } + xferSettings(); + makeResidueList(); makeCaBondList(); if (getId() == null) { - setId(inFile.getName()); + setId(safeName(getDataName())); } for (PDBChain chain : getChains()) { SequenceI chainseq = postProcessChain(chain); - createAnnotation(chainseq, chain, ms.at); if (isRNA(chainseq)) { rna.add(chainseq); @@ -191,6 +193,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener { prot.add(chainseq); } + + if (StructureImportSettings.isProcessSecondaryStructure()) + { + createAnnotation(chainseq, chain, ms.at); + } } } catch (OutOfMemoryError er) { @@ -205,30 +212,99 @@ public class JmolParser extends StructureFile implements JmolStatusListener private List convertSignificantAtoms(ModelSet ms) { List significantAtoms = new ArrayList(); + HashMap chainTerMap = new HashMap(); + org.jmol.modelset.Atom prevAtom = null; for (org.jmol.modelset.Atom atom : ms.at) { if (atom.getAtomName().equalsIgnoreCase("CA") || atom.getAtomName().equalsIgnoreCase("P")) { + if (!atomValidated(atom, prevAtom, chainTerMap)) + { + continue; + } Atom curAtom = new Atom(atom.x, atom.y, atom.z); curAtom.atomIndex = atom.getIndex(); curAtom.chain = atom.getChainIDStr(); - curAtom.insCode = atom.group.getInsertionCode(); + curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' ' + : atom.group.getInsertionCode(); curAtom.name = atom.getAtomName(); curAtom.number = atom.getAtomNumber(); curAtom.resName = atom.getGroup3(true); curAtom.resNumber = atom.getResno(); curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom .getIndex()] : Float.valueOf(atom.getOccupancy100()); - curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode; - // curAtom.tfactor = atom.group.; + String fmt = new Format("%4i").form(curAtom.resNumber); + curAtom.resNumIns = (fmt + curAtom.insCode); + curAtom.tfactor = atom.getBfactor100() / 100f; curAtom.type = 0; - significantAtoms.add(curAtom); + // significantAtoms.add(curAtom); + // ignore atoms from subsequent models + if (!significantAtoms.contains(curAtom)) + { + significantAtoms.add(curAtom); + } + prevAtom = atom; } } return significantAtoms; } + private boolean atomValidated(org.jmol.modelset.Atom curAtom, + org.jmol.modelset.Atom prevAtom, + HashMap chainTerMap) + { + // System.out.println("Atom: " + curAtom.getAtomNumber() + // + " Last atom index " + curAtom.group.lastAtomIndex); + if (chainTerMap == null || prevAtom == null) + { + return true; + } + String curAtomChId = curAtom.getChainIDStr(); + String prevAtomChId = prevAtom.getChainIDStr(); + // new chain encoutered + if (!prevAtomChId.equals(curAtomChId)) + { + // On chain switch add previous chain termination to xTerMap if not exists + if (!chainTerMap.containsKey(prevAtomChId)) + { + chainTerMap.put(prevAtomChId, prevAtom); + } + // if current atom belongs to an already terminated chain and the resNum + // diff < 5 then mark as valid and update termination Atom + if (chainTerMap.containsKey(curAtomChId)) + { + if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno()) + { + return false; + } + if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5) + { + chainTerMap.put(curAtomChId, curAtom); + return true; + } + return false; + } + } + // atom with previously terminated chain encountered + else if (chainTerMap.containsKey(curAtomChId)) + { + if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno()) + { + return false; + } + if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5) + { + chainTerMap.put(curAtomChId, curAtom); + return true; + } + return false; + } + // HETATM with resNum jump > 2 + return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom + .getResno()) > 2)); + } + private void createAnnotation(SequenceI sequence, PDBChain chain, org.jmol.modelset.Atom[] jmolAtoms) { @@ -278,9 +354,15 @@ public class JmolParser extends StructureFile implements JmolStatusListener { if (secstr[p] >= 'A' && secstr[p] <= 'z') { + try + { asecstr[p] = new Annotation(String.valueOf(secstr[p]), null, secstrcode[p], Float.NaN); ssFound = true; + } catch (Exception e) + { + // e.printStackTrace(); + } } } @@ -561,4 +643,14 @@ public class JmolParser extends StructureFile implements JmolStatusListener this.predictSecondaryStructure = predictSecondaryStructure; } + public boolean isVisibleChainAnnotation() + { + return visibleChainAnnotation; + } + + public void setVisibleChainAnnotation(boolean visibleChainAnnotation) + { + this.visibleChainAnnotation = visibleChainAnnotation; + } + }