X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=f2dd3d09b9424d0d8f1a59909b7c977285fb0ba0;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=49d7d4a429c094db5a3ca85a8f74468b5722422f;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 49d7d4a..f2dd3d0 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 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. * @@ -27,16 +27,20 @@ import jalview.datamodel.Mapping; import jalview.datamodel.Sequence; 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.Enumeration; import java.util.List; import java.util.Vector; public class PDBChain { + public static final String RESNUM_FEATURE = "RESNUM"; + /** * SequenceFeature group for PDB File features added to sequences */ @@ -46,11 +50,11 @@ public class PDBChain 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; @@ -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; } @@ -104,16 +108,15 @@ public class PDBChain public String print() { - String tmp = ""; + StringBuilder tmp = new StringBuilder(256); - for (int i = 0; i < bonds.size(); i++) + for (Bond b : bonds) { - tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " " - + ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset - + newline; + tmp.append(b.at1.resName).append(" ").append(b.at1.resNumber) + .append(" ").append(offset).append(newline); } - return tmp; + return tmp.toString(); } /** @@ -129,7 +132,7 @@ public class PDBChain int pdbpos = as.getSeq2Start() - 2; int alignpos = s1.getStart() + as.getSeq1Start() - 3; // first clear out any old alignmentMapping values: - for (Atom atom : (Vector) atoms) + for (Atom atom : atoms) { atom.alignmentMapping = -1; } @@ -146,13 +149,17 @@ 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) { - Residue res = (Residue) residues.elementAt(pdbpos); - Enumeration en = res.atoms.elements(); - while (en.hasMoreElements()) + if (pdbpos >= residues.size()) + { + continue; + } + Residue res = residues.elementAt(pdbpos); + for (Atom atom : res.atoms) { - Atom atom = (Atom) en.nextElement(); atom.alignmentMapping = alignpos; } } @@ -191,17 +198,23 @@ 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 + ((Atom) ((Residue) residues.elementAt(tx.getBegin() - - offset)).atoms.elementAt(0)).alignmentMapping); - tx.setEnd(1 + ((Atom) ((Residue) residues.elementAt(tx.getEnd() - - offset)).atoms.elementAt(0)).alignmentMapping); + tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms + .elementAt(0).alignmentMapping); + 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) { @@ -212,14 +225,19 @@ public class PDBChain return features; } + /** + * Traverses the list of residues and constructs bonds where CA-to-CA atoms or + * P-to-P atoms are found. Also sets the 'isNa' flag if more than 99% of + * residues contain a P not a CA. + */ public void makeCaBondList() { boolean na = false; int numNa = 0; for (int i = 0; i < (residues.size() - 1); i++) { - Residue tmpres = (Residue) residues.elementAt(i); - Residue tmpres2 = (Residue) residues.elementAt(i + 1); + Residue tmpres = residues.elementAt(i); + Residue tmpres2 = residues.elementAt(i + 1); Atom at1 = tmpres.findAtom("CA"); Atom at2 = tmpres2.findAtom("CA"); na = false; @@ -245,61 +263,81 @@ public class PDBChain System.out.println("not found " + i); } } - if (numNa > 0 && ((numNa / residues.size()) > 0.99)) + + /* + * If > 99% 'P', flag as nucleotide; note the count doesn't include the last + * residue + */ + if (residues.size() > 1 && (numNa / (residues.size() - 1) > 0.99)) { isNa = true; } } + /** + * Construct a bond from atom1 to atom2 and add it to the list of bonds for + * this chain + * + * @param at1 + * @param at2 + */ public void makeBond(Atom at1, Atom at2) { - float[] start = new float[3]; - float[] end = new float[3]; - - start[0] = at1.x; - start[1] = at1.y; - start[2] = at1.z; - - end[0] = at2.x; - end[1] = at2.y; - end[2] = at2.z; - - bonds.addElement(new Bond(start, end, at1, at2)); + bonds.addElement(new Bond(at1, at2)); } + /** + * Traverses the list of atoms and + *
    + *
  • constructs a list of Residues, each containing all the atoms that share + * the same residue number
    • + *
  • adds a RESNUM sequence feature for each position
    • + *
  • creates the sequence string
    • + *
  • determines if nucleotide
    • + *
  • saves the residue number of the first atom as 'offset'
    • + *
  • adds temp factor annotation if the flag is set to do so
    • + *
+ * + * @param visibleChainAnnotation + */ public void makeResidueList(boolean visibleChainAnnotation) { int count = 0; Object symbol; boolean deoxyn = false; boolean nucleotide = false; - StringBuffer seq = new StringBuffer(); - Vector resFeatures = new Vector(); - Vector resAnnotation = new Vector(); + StringBuilder seq = new StringBuilder(256); + Vector resFeatures = new Vector(); + Vector resAnnotation = new Vector(); int i, iSize = atoms.size() - 1; int resNumber = -1; + char insCode = ' '; for (i = 0; i <= iSize; i++) { - Atom tmp = (Atom) atoms.elementAt(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.addElement(atoms.elementAt(i)); + resAtoms.add(atoms.elementAt(i)); i++; if (i < atoms.size()) { - resNumber = ((Atom) atoms.elementAt(i)).resNumber; + resNumber = atoms.elementAt(i).resNumber; + insCode = atoms.elementAt(i).insCode; } else { @@ -310,51 +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 = (Residue) residues.lastElement(); - Atom tmpat = (Atom) tmpres.atoms.elementAt(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))); + } } - seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]); + 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()]); + } + count++; } - count++; } if (id.length() < 1) @@ -371,11 +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((SequenceFeature) 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) { @@ -383,7 +445,7 @@ public class PDBChain float max = 0; for (i = 0, iSize = annots.length; i < iSize; i++) { - annots[i] = (Annotation) resAnnotation.elementAt(i); + annots[i] = resAnnotation.elementAt(i); if (annots[i].value > max) { max = annots[i].value; @@ -393,88 +455,80 @@ public class PDBChain AlignmentAnnotation tfactorann = new AlignmentAnnotation( "Temperature Factor", "Temperature Factor for " + pdbid + id, - annots, 0, max, - AlignmentAnnotation.LINE_GRAPH); + annots, 0, max, AlignmentAnnotation.LINE_GRAPH); tfactorann.setSequenceRef(sequence); sequence.addAlignmentAnnotation(tfactorann); } } + /** + * Colour start/end of bonds by charge + *
    + *
  • ASP and GLU red
    • + *
  • LYS and ARG blue
    • + *
  • CYS yellow
    • + *
  • others light gray
    • + *
+ */ public void setChargeColours() { - for (int i = 0; i < bonds.size(); i++) + for (Bond b : bonds) { - try + if (b.at1 != null && b.at2 != null) { - Bond b = (Bond) bonds.elementAt(i); - - if (b.at1.resName.equalsIgnoreCase("ASP") - || b.at1.resName.equalsIgnoreCase("GLU")) - { - b.startCol = Color.red; - } - else if (b.at1.resName.equalsIgnoreCase("LYS") - || b.at1.resName.equalsIgnoreCase("ARG")) - { - b.startCol = Color.blue; - } - else if (b.at1.resName.equalsIgnoreCase("CYS")) - { - b.startCol = Color.yellow; - } - else - { - b.startCol = Color.lightGray; - } - - if (b.at2.resName.equalsIgnoreCase("ASP") - || b.at2.resName.equalsIgnoreCase("GLU")) - { - b.endCol = Color.red; - } - else if (b.at2.resName.equalsIgnoreCase("LYS") - || b.at2.resName.equalsIgnoreCase("ARG")) - { - b.endCol = Color.blue; - } - else if (b.at2.resName.equalsIgnoreCase("CYS")) - { - b.endCol = Color.yellow; - } - else - { - b.endCol = Color.lightGray; - } - } catch (Exception e) + b.startCol = getChargeColour(b.at1.resName); + b.endCol = getChargeColour(b.at2.resName); + } + else { - Bond b = (Bond) bonds.elementAt(i); b.startCol = Color.gray; b.endCol = Color.gray; } } } - public void setChainColours(jalview.schemes.ColourSchemeI cs) + public static Color getChargeColour(String resName) + { + Color result = Color.lightGray; + if ("ASP".equals(resName) || "GLU".equals(resName)) + { + result = Color.red; + } + else if ("LYS".equals(resName) || "ARG".equals(resName)) + { + result = Color.blue; + } + else if ("CYS".equals(resName)) + { + result = Color.yellow; + } + return result; + } + + /** + * Sets the start/end colours of bonds to those of the start/end atoms + * according to the specified colour scheme. Note: currently only works for + * peptide residues. + * + * @param cs + */ + public void setChainColours(ColourSchemeI cs) { - Bond b; int index; - for (int i = 0; i < bonds.size(); i++) + for (Bond b : bonds) { try { - b = (Bond) bonds.elementAt(i); - - index = ((Integer) ResidueProperties.aa3Hash.get(b.at1.resName)) - .intValue(); - b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); + index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue(); + b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0, + null, null, 0f); - index = ((Integer) ResidueProperties.aa3Hash.get(b.at2.resName)) - .intValue(); - b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); + index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue(); + b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0, + null, null, 0f); } catch (Exception e) { - b = (Bond) bonds.elementAt(i); b.startCol = Color.gray; b.endCol = Color.gray; } @@ -483,11 +537,10 @@ public class PDBChain public void setChainColours(Color col) { - for (int i = 0; i < bonds.size(); i++) + for (Bond b : bonds) { - Bond tmp = (Bond) bonds.elementAt(i); - tmp.startCol = col; - tmp.endCol = col; + b.startCol = col; + b.endCol = col; } } @@ -500,8 +553,8 @@ public class PDBChain * @param sqmpping * - mapping between destination sequence and local chain */ - public void transferResidueAnnotation( - StructureMapping mapping, jalview.datamodel.Mapping sqmpping) + public void transferResidueAnnotation(StructureMapping mapping, + jalview.datamodel.Mapping sqmpping) { SequenceI sq = mapping.getSequence(); SequenceI dsq = sq; @@ -518,8 +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); @@ -539,12 +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 @@ -559,7 +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);