X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=180da8f449f8044e4f522fb5f758a5dc1b4fd277;hb=2681593fa6810815547b688b89424c837cac1240;hp=0cbd620bf11a251593294095090106b475ce12f7;hpb=d8953149cfddc56c08aecac475e5154a49f4c2f7;p=jalview.git diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index 0cbd620..180da8f 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -22,22 +22,22 @@ package jalview.ext.jmol; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; -import jalview.datamodel.DBRefSource; +import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.io.FileParse; import jalview.io.StructureFile; import jalview.schemes.ResidueProperties; -import jalview.structure.StructureViewSettings; +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; -import javajs.awt.Dimension; - import org.jmol.api.JmolStatusListener; import org.jmol.api.JmolViewer; import org.jmol.c.CBK; @@ -59,15 +59,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener { Viewer viewer = null; - public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr, - boolean externalSecStr, String inFile, String type) - throws IOException + public JmolParser(String inFile, String type) throws IOException { super(inFile, type); } - public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr, - boolean externalSecStr, FileParse fp) throws IOException + public JmolParser(FileParse fp) throws IOException { super(fp); } @@ -87,15 +84,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener @Override public void parse() throws IOException { - String dataName = getDataName(); - if (dataName.endsWith(".cif")) - { - setDbRefType(DBRefSource.MMCIF); - } - else - { - setDbRefType(DBRefSource.PDB); - } setChains(new Vector()); Viewer jmolModel = getJmolData(); jmolModel.openReader(getDataName(), getDataName(), getReader()); @@ -106,6 +94,18 @@ 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); } } @@ -121,6 +121,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener { try { + /* + * params -o (output to sysout) -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); // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used @@ -144,7 +148,17 @@ public class JmolParser extends StructureFile implements JmolStatusListener List prot = new ArrayList(); PDBChain tmpchain; String pdbId = (String) ms.getInfo(0, "title"); - setId(pdbId); + + if (pdbId == null) + { + setId(safeName(getDataName())); + setPDBIdAvailable(false); + } + else + { + setId(pdbId); + setPDBIdAvailable(true); + } List significantAtoms = convertSignificantAtoms(ms); for (Atom tmpatom : significantAtoms) { @@ -159,7 +173,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener tmpchain.atoms.addElement(tmpatom); } catch (Exception e) { - tmpchain = new PDBChain(pdbId, tmpatom.chain); + tmpchain = new PDBChain(getId(), tmpatom.chain); getChains().add(tmpchain); tmpchain.atoms.addElement(tmpatom); } @@ -170,10 +184,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener makeResidueList(); makeCaBondList(); - if (getId() == null) - { - setId(inFile.getName()); - } for (PDBChain chain : getChains()) { SequenceI chainseq = postProcessChain(chain); @@ -186,7 +196,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener prot.add(chainseq); } - if (StructureViewSettings.isPredictSecondaryStructure()) + if (StructureImportSettings.isProcessSecondaryStructure()) { createAnnotation(chainseq, chain, ms.at); } @@ -204,30 +214,99 @@ 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; + 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) { @@ -279,9 +358,9 @@ public class JmolParser extends StructureFile implements JmolStatusListener { try { - asecstr[p] = new Annotation(String.valueOf(secstr[p]), null, - secstrcode[p], Float.NaN); - ssFound = true; + asecstr[p] = new Annotation(String.valueOf(secstr[p]), null, + secstrcode[p], Float.NaN); + ssFound = true; } catch (Exception e) { // e.printStackTrace(); @@ -545,7 +624,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener * Not implemented - returns null */ @Override - public Dimension resizeInnerPanel(String data) + public int[] resizeInnerPanel(String data) { return null; }