X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=beaaf79217f4f841f35a3c3745421c0a2c2ce638;hb=ff450fad8709ae81919af7a15ea382af7292794c;hp=ca412d0c51d1b86cf1cbd7d39e1778c4bf140040;hpb=4e3166c6b7348b10af5ee6526a83eaa78191b1b6;p=jalview.git diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index ca412d0..beaaf79 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -22,11 +22,14 @@ package jalview.ext.jmol; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; +import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; 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; @@ -36,8 +39,6 @@ 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 +60,13 @@ public class JmolParser extends StructureFile implements JmolStatusListener { Viewer viewer = null; - public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr, - boolean externalSecStr, String inFile, String type) + public JmolParser(String inFile, DataSourceType sourceType) throws IOException { - super(inFile, type); + super(inFile, sourceType); } - public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr, - boolean externalSecStr, FileParse fp) throws IOException + public JmolParser(FileParse fp) throws IOException { super(fp); } @@ -97,6 +96,18 @@ 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); } } @@ -112,6 +123,10 @@ 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 @@ -135,7 +150,17 @@ 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) { @@ -150,7 +175,7 @@ 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); } @@ -161,10 +186,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener makeResidueList(); makeCaBondList(); - if (getId() == null) - { - setId(safeName(getDataName())); - } for (PDBChain chain : getChains()) { SequenceI chainseq = postProcessChain(chain); @@ -177,7 +198,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener prot.add(chainseq); } - if (StructureImportSettings.isPredictSecondaryStructure()) + if (StructureImportSettings.isProcessSecondaryStructure()) { createAnnotation(chainseq, chain, ms.at); } @@ -209,17 +230,24 @@ public class JmolParser extends StructureFile implements JmolStatusListener 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; } } @@ -230,6 +258,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener 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; @@ -248,6 +278,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener // 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); @@ -259,6 +293,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener // 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); @@ -313,18 +351,18 @@ public class JmolParser extends StructureFile implements JmolStatusListener SequenceI sq, char[] secstr, char[] secstrcode, String chainId, int firstResNum) { - char[] seq = sq.getSequence(); + int length = sq.getLength(); boolean ssFound = false; - Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1]; - for (int p = 0; p < seq.length; p++) + Annotation asecstr[] = new Annotation[length + firstResNum - 1]; + for (int p = 0; p < length; p++) { if (secstr[p] >= 'A' && secstr[p] <= 'z') { 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(); @@ -434,7 +472,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener * Not implemented - returns null */ @Override - public String print() + public String print(SequenceI[] seqs, boolean jvSuffix) { return null; } @@ -588,7 +626,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener * Not implemented - returns null */ @Override - public Dimension resizeInnerPanel(String data) + public int[] resizeInnerPanel(String data) { return null; }