X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=904a8601f18865002dc0a43cc4870b80475fe1bb;hb=68b236e066089eaa850813edb5294a23d19798bb;hp=a3505c70c981271351d7915b411aaf87cbf90682;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index a3505c7..904a860 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -29,7 +29,9 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; +import jalview.structure.StructureImportSettings; import jalview.structure.StructureMapping; +import jalview.util.Comparison; import java.awt.Color; import java.util.List; @@ -37,20 +39,17 @@ import java.util.Vector; public class PDBChain { - /** - * SequenceFeature group for PDB File features added to sequences - */ - private static final String PDBFILEFEATURE = "PDBFile"; + public static final String RESNUM_FEATURE = "RESNUM"; private static final String IEASTATUS = "IEA:jalview"; public String id; - public Vector bonds = new Vector(); + public Vector bonds = new Vector<>(); - public Vector atoms = new Vector(); + public Vector atoms = new Vector<>(); - public Vector residues = new Vector(); + public Vector residues = new Vector<>(); public int offset; @@ -79,10 +78,10 @@ public class PDBChain public String pdbid = ""; - public PDBChain(String pdbid, String id) + public PDBChain(String thePdbid, String theId) { - this.pdbid = pdbid.toLowerCase(); - this.id = id; + this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase(); + this.id = theId; } /** @@ -145,8 +144,14 @@ public class PDBChain pdbpos++; } - if (as.astr1.charAt(i) == as.astr2.charAt(i)) + boolean sameResidue = Comparison.isSameResidue(as.astr1.charAt(i), + as.astr2.charAt(i), false); + if (sameResidue) { + if (pdbpos >= residues.size()) + { + continue; + } Residue res = residues.elementAt(pdbpos); for (Atom atom : res.atoms) { @@ -157,15 +162,58 @@ public class PDBChain } /** - * copy over the RESNUM seqfeatures from the internal chain sequence to the + * Annotate the residues with their corresponding positions in s1 using the + * alignment in as NOTE: This clears all atom.alignmentMapping values on the + * structure. + * + * @param as + * @param s1 + */ + public void makeExactMapping(StructureMapping mapping, SequenceI s1) + { + // first clear out any old alignmentMapping values: + for (Atom atom : atoms) + { + atom.alignmentMapping = -1; + } + SequenceI ds = s1; + while (ds.getDatasetSequence() != null) + { + ds = ds.getDatasetSequence(); + } + int pdboffset = 0; + for (Residue res : residues) + { + // res.number isn't set correctly for discontinuous/mismapped residues + int seqpos = mapping.getSeqPos(res.atoms.get(0).resNumber); + char strchar = sequence.getCharAt(pdboffset++); + if (seqpos == StructureMapping.UNASSIGNED_VALUE) + { + continue; + } + char seqchar = ds.getCharAt(seqpos - ds.getStart()); + + boolean sameResidue = Comparison.isSameResidue( + seqchar, strchar, false); + if (sameResidue) + { + for (Atom atom : res.atoms) + { + atom.alignmentMapping = seqpos - 1; + } + } + } + } + + /** + * Copies over the RESNUM seqfeatures from the internal chain sequence to the * mapped sequence * * @param seq * @param status * The Status of the transferred annotation - * @return the features added to sq (or its dataset) */ - public SequenceFeature[] transferRESNUMFeatures(SequenceI seq, + public void transferRESNUMFeatures(SequenceI seq, String status) { SequenceI sq = seq; @@ -174,10 +222,11 @@ public class PDBChain sq = sq.getDatasetSequence(); if (sq == sequence) { - return null; + return; } } - /** + + /* * Remove any existing features for this chain if they exist ? * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int * totfeat=seqsfeatures.length; // Remove any features for this exact chain @@ -187,18 +236,22 @@ public class PDBChain { status = PDBChain.IEASTATUS; } - SequenceFeature[] features = sequence.getSequenceFeatures(); - for (int i = 0; i < features.length; i++) + + List features = sequence.getSequenceFeatures(); + for (SequenceFeature feature : features) { - if (features[i].getFeatureGroup().equals(pdbid)) + if (feature.getFeatureGroup() != null + && feature.getFeatureGroup().equals(pdbid)) { - SequenceFeature tx = new SequenceFeature(features[i]); - tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms - .elementAt(0).alignmentMapping); - tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms - .elementAt(0).alignmentMapping); + int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms + .elementAt(0).alignmentMapping; + int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms + .elementAt(0).alignmentMapping; + SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd, + feature.getFeatureGroup(), feature.getScore()); tx.setStatus(status - + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? "" + + ((tx.getStatus() == null || tx.getStatus().length() == 0) + ? "" : ":" + tx.getStatus())); if (tx.begin != 0 && tx.end != 0) { @@ -206,7 +259,6 @@ public class PDBChain } } } - return features; } /** @@ -252,7 +304,7 @@ public class PDBChain * If > 99% 'P', flag as nucleotide; note the count doesn't include the last * residue */ - if (residues.size() > 0 && (numNa / (residues.size() - 1) > 0.99)) + if (residues.size() > 1 && (numNa / (residues.size() - 1) > 0.99)) { isNa = true; } @@ -291,25 +343,30 @@ public class PDBChain boolean deoxyn = false; boolean nucleotide = false; StringBuilder seq = new StringBuilder(256); - Vector resFeatures = new Vector(); - Vector resAnnotation = new Vector(); - int i, iSize = atoms.size() - 1; + Vector resFeatures = new Vector<>(); + Vector resAnnotation = new Vector<>(); + int iSize = atoms.size() - 1; int resNumber = -1; - for (i = 0; i <= iSize; i++) + char insCode = ' '; + + for (int i = 0; i <= iSize; i++) { Atom tmp = atoms.elementAt(i); resNumber = tmp.resNumber; + insCode = tmp.insCode; + int res = resNumber; + char ins = insCode; if (i == 0) { offset = resNumber; } - Vector resAtoms = new Vector(); + Vector resAtoms = new Vector<>(); // Add atoms to a vector while the residue number // remains the same as the first atom's resNumber (res) - while ((resNumber == res) && (i < atoms.size())) + while ((resNumber == res) && (ins == insCode) && (i < atoms.size())) { resAtoms.add(atoms.elementAt(i)); i++; @@ -317,6 +374,7 @@ public class PDBChain if (i < atoms.size()) { resNumber = atoms.elementAt(i).resNumber; + insCode = atoms.elementAt(i).insCode; } else { @@ -327,51 +385,72 @@ public class PDBChain // We need this to keep in step with the outer for i = loop i--; - // Make a new Residue object with the new atoms vector - residues.addElement(new Residue(resAtoms, resNumber - 1, count)); - - Residue tmpres = residues.lastElement(); - Atom tmpat = tmpres.atoms.get(0); - // Make A new SequenceFeature for the current residue numbering - SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName - + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset - + count, offset + count, pdbid); - // MCview.PDBChain.PDBFILEFEATURE); - resFeatures.addElement(sf); - resAnnotation.addElement(new Annotation(tmpat.tfactor)); - // Keep totting up the sequence - if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null) + // Add inserted residues as features to the base residue + Atom currAtom = resAtoms.get(0); + if (currAtom.insCode != ' ' && !residues.isEmpty() + && residues.lastElement().atoms + .get(0).resNumber == currAtom.resNumber) { - String nucname = tmpat.resName.trim(); - // use the aaIndex rather than call 'toLower' - which would take a bit - // more time. - deoxyn = nucname.length() == 2 - && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D']; - if (tmpat.name.equalsIgnoreCase("CA") - || ResidueProperties.nucleotideIndex[nucname - .charAt((deoxyn ? 1 : 0))] == -1) - { - seq.append("X"); - // System.err.println("PDBReader:Null aa3Hash for " + - // tmpat.resName); - } - else - { - // nucleotide flag - nucleotide = true; - seq.append(nucname.charAt((deoxyn ? 1 : 0))); - } + String desc = currAtom.resName + ":" + currAtom.resNumIns + " " + + pdbid + id; + SequenceFeature sf = new SequenceFeature("INSERTION", desc, offset + + count - 1, offset + count - 1, "PDB_INS"); + resFeatures.addElement(sf); + residues.lastElement().atoms.addAll(resAtoms); } else { - if (nucleotide) + // Make a new Residue object with the new atoms vector + residues.addElement(new Residue(resAtoms, resNumber - 1, count)); + + Residue tmpres = residues.lastElement(); + Atom tmpat = tmpres.atoms.get(0); + // Make A new SequenceFeature for the current residue numbering + String desc = tmpat.resName + + ":" + tmpat.resNumIns + " " + pdbid + id; + SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc, + offset + count, offset + count, pdbid); + resFeatures.addElement(sf); + resAnnotation.addElement(new Annotation(tmpat.tfactor)); + // Keep totting up the sequence + + if ((symbol = ResidueProperties.getAA3Hash() + .get(tmpat.resName)) == null) + { + String nucname = tmpat.resName.trim(); + // use the aaIndex rather than call 'toLower' - which would take a bit + // more time. + deoxyn = nucname.length() == 2 + && ResidueProperties.aaIndex[nucname + .charAt(0)] == ResidueProperties.aaIndex['D']; + if (tmpat.name.equalsIgnoreCase("CA") + || ResidueProperties.nucleotideIndex[nucname + .charAt((deoxyn ? 1 : 0))] == -1) + { + char r = ResidueProperties.getSingleCharacterCode( + ResidueProperties.getCanonicalAminoAcid(tmpat.resName)); + seq.append(r == '0' ? 'X' : r); + // System.err.println("PDBReader:Null aa3Hash for " + + // tmpat.resName); + } + else + { + // nucleotide flag + nucleotide = true; + seq.append(nucname.charAt((deoxyn ? 1 : 0))); + } + } + else { - System.err - .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!"); + if (nucleotide) + { + System.err.println( + "Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!"); + } + seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]); } - seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]); + count++; } - count++; } if (id.length() < 1) @@ -388,28 +467,33 @@ public class PDBChain // System.out.println("PDB Sequence is :\nSequence = " + seq); // System.out.println("No of residues = " + residues.size()); - for (i = 0, iSize = resFeatures.size(); i < iSize; i++) + + if (StructureImportSettings.isShowSeqFeatures()) { - sequence.addSequenceFeature(resFeatures.elementAt(i)); - resFeatures.setElementAt(null, i); + iSize = resFeatures.size(); + for (int i = 0; i < iSize; i++) + { + sequence.addSequenceFeature(resFeatures.elementAt(i)); + resFeatures.setElementAt(null, i); + } } if (visibleChainAnnotation) { Annotation[] annots = new Annotation[resAnnotation.size()]; - float max = 0; - for (i = 0, iSize = annots.length; i < iSize; i++) + float max = 0f; + float min = 0f; + iSize = annots.length; + for (int i = 0; i < iSize; i++) { annots[i] = resAnnotation.elementAt(i); - if (annots[i].value > max) - { - max = annots[i].value; - } + max = Math.max(max, annots[i].value); + min = Math.min(min, annots[i].value); resAnnotation.setElementAt(null, i); } AlignmentAnnotation tfactorann = new AlignmentAnnotation( "Temperature Factor", "Temperature Factor for " + pdbid + id, - annots, 0, max, AlignmentAnnotation.LINE_GRAPH); + annots, min, max, AlignmentAnnotation.LINE_GRAPH); tfactorann.setSequenceRef(sequence); sequence.addAlignmentAnnotation(tfactorann); } @@ -474,10 +558,12 @@ public class PDBChain try { index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue(); - b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); + b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0, + null, null, 0f); index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue(); - b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); + b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0, + null, null, 0f); } catch (Exception e) { @@ -510,6 +596,12 @@ public class PDBChain { SequenceI sq = mapping.getSequence(); SequenceI dsq = sq; + if (sqmpping == null) + { + // SIFTS mappings are recorded in the StructureMapping object... + + sqmpping = mapping.getSeqToPdbMapping(); + } if (sq != null) { while (dsq.getDatasetSequence() != null) @@ -523,8 +615,8 @@ public class PDBChain for (AlignmentAnnotation ana : shadow.getAnnotation()) { - List transfer = sq.getAlignmentAnnotations( - ana.getCalcId(), ana.label); + List transfer = sq + .getAlignmentAnnotations(ana.getCalcId(), ana.label); if (transfer == null || transfer.size() == 0) { ana = new AlignmentAnnotation(ana); @@ -544,12 +636,13 @@ public class PDBChain { for (AlignmentAnnotation ana : sequence.getAnnotation()) { - List transfer = sq + List transfer = dsq .getAlignmentAnnotations(ana.getCalcId(), ana.label); if (transfer == null || transfer.size() == 0) { ana = new AlignmentAnnotation(ana); ana.liftOver(dsq, sqmpping); + dsq.addAlignmentAnnotation(ana); // mapping.transfer(ana); } else @@ -564,7 +657,8 @@ public class PDBChain // Useful for debugging mappings - adds annotation for mapped position float min = -1, max = 0; Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1]; - for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++) + for (int i = sq.getStart(), j = sq + .getEnd(), k = 0; i <= j; i++, k++) { int prn = mapping.getPDBResNum(k + 1);