X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=f2dd3d09b9424d0d8f1a59909b7c977285fb0ba0;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=379eb91a3c2a1a41a9a21a862c658448171c84f7;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 379eb91..f2dd3d0 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) - * 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; @@ -37,6 +39,8 @@ import java.util.Vector; public class PDBChain { + public static final String RESNUM_FEATURE = "RESNUM"; + /** * SequenceFeature group for PDB File features added to sequences */ @@ -81,7 +85,7 @@ public class PDBChain public PDBChain(String pdbid, String id) { - this.pdbid = pdbid.toLowerCase(); + this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase(); this.id = id; } @@ -145,8 +149,14 @@ 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) { @@ -188,9 +198,14 @@ public class PDBChain status = PDBChain.IEASTATUS; } SequenceFeature[] features = sequence.getSequenceFeatures(); + if (features == null) + { + return null; + } for (int i = 0; i < features.length; i++) { - if (features[i].getFeatureGroup().equals(pdbid)) + if (features[i].getFeatureGroup() != null + && features[i].getFeatureGroup().equals(pdbid)) { SequenceFeature tx = new SequenceFeature(features[i]); tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms @@ -198,7 +213,8 @@ public class PDBChain tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms .elementAt(0).alignmentMapping); 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) { @@ -252,7 +268,7 @@ 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; } @@ -295,11 +311,15 @@ public class PDBChain Vector resAnnotation = new Vector(); int i, iSize = atoms.size() - 1; int resNumber = -1; + char insCode = ' '; for (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) { @@ -309,7 +329,7 @@ public class PDBChain 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 +337,7 @@ public class PDBChain if (i < atoms.size()) { resNumber = atoms.elementAt(i).resNumber; + insCode = atoms.elementAt(i).insCode; } else { @@ -327,51 +348,72 @@ 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))); - } + SequenceFeature sf = new SequenceFeature("INSERTION", + currAtom.resName + ":" + currAtom.resNumIns + " " + pdbid + + id, + "", 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 + SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, + tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid + id, + "", 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) { - System.err - .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!"); + 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 + { + 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) @@ -388,10 +430,14 @@ 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); + for (i = 0, iSize = resFeatures.size(); i < iSize; i++) + { + sequence.addSequenceFeature(resFeatures.elementAt(i)); + resFeatures.setElementAt(null, i); + } } if (visibleChainAnnotation) { @@ -474,10 +520,12 @@ 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) { @@ -523,8 +571,8 @@ 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 +592,13 @@ 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 +613,8 @@ 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);