X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=e4e619c577052c6a7a0803760c994c33af058f92;hb=77ac7f545e96bd4bde47991f77291a71eb5b90e6;hp=6055a5b0fc8f48e90ab5c26ad507aac1b9e1e8b4;hpb=fe14748825261a337ae83b2a070c44aac996c666;p=jalview.git diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 6055a5b..e4e619c 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. * @@ -23,14 +23,15 @@ package MCview; import jalview.analysis.AlignSeq; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; +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.StructureMapping; import java.awt.Color; -import java.util.Enumeration; import java.util.List; import java.util.Vector; @@ -45,15 +46,24 @@ 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; - public Sequence sequence; + /** + * sequence is the sequence extracted by the chain parsing code + */ + public SequenceI sequence; + + /** + * shadow is the sequence created by any other parsing processes (e.g. Jmol, + * RNAview) + */ + public SequenceI shadow = null; public boolean isNa = false; @@ -80,6 +90,8 @@ public class PDBChain */ protected String newline = System.getProperty("line.separator"); + public Mapping shadowMap; + public void setNewlineString(String nl) { newline = nl; @@ -92,16 +104,15 @@ 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(); } /** @@ -117,7 +128,7 @@ 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; } @@ -136,11 +147,9 @@ public class PDBChain if (as.astr1.charAt(i) == as.astr2.charAt(i)) { - Residue res = (Residue) residues.elementAt(pdbpos); - Enumeration en = res.atoms.elements(); - while (en.hasMoreElements()) + Residue res = residues.elementAt(pdbpos); + for (Atom atom : res.atoms) { - Atom atom = (Atom) en.nextElement(); atom.alignmentMapping = alignpos; } } @@ -184,10 +193,10 @@ public class PDBChain if (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())); @@ -200,14 +209,19 @@ 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; @@ -233,61 +247,81 @@ 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)); } - public void makeResidueList() + /** + * 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 { @@ -298,13 +332,28 @@ public class PDBChain // We need this to keep in step with the outer for i = loop i--; + // Add inserted residues as features to the base residue + Atom currAtom = resAtoms.get(0); + if (currAtom.insCode != ' ' + && residues.lastElement().atoms.get(0).resNumber == currAtom.resNumber) + { + 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 + { + // 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); + 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 + SequenceFeature sf = new SequenceFeature("RES NUM", tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset + count, offset + count, pdbid); // MCview.PDBChain.PDBFILEFEATURE); @@ -342,7 +391,8 @@ public class PDBChain } seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]); } - count++; + count++; + } } if (id.length() < 1) @@ -361,104 +411,97 @@ public class PDBChain // System.out.println("No of residues = " + residues.size()); for (i = 0, iSize = resFeatures.size(); i < iSize; i++) { - sequence.addSequenceFeature((SequenceFeature) resFeatures - .elementAt(i)); + sequence.addSequenceFeature(resFeatures.elementAt(i)); resFeatures.setElementAt(null, i); } - Annotation[] annots = new Annotation[resAnnotation.size()]; - float max = 0; - for (i = 0, iSize = annots.length; i < iSize; i++) + if (visibleChainAnnotation) { - annots[i] = (Annotation) resAnnotation.elementAt(i); - if (annots[i].value > max) + Annotation[] annots = new Annotation[resAnnotation.size()]; + float max = 0; + for (i = 0, iSize = annots.length; i < iSize; i++) { - max = annots[i].value; + annots[i] = resAnnotation.elementAt(i); + if (annots[i].value > max) + { + max = annots[i].value; + } + resAnnotation.setElementAt(null, i); } - resAnnotation.setElementAt(null, i); + + AlignmentAnnotation tfactorann = new AlignmentAnnotation( + "Temperature Factor", "Temperature Factor for " + pdbid + id, + annots, 0, max, AlignmentAnnotation.LINE_GRAPH); + tfactorann.setSequenceRef(sequence); + sequence.addAlignmentAnnotation(tfactorann); } - AlignmentAnnotation tfactorann = new AlignmentAnnotation( - "PDB.TempFactor", "Temperature Factor for " - + sequence.getName(), 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(); + index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue(); b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); - index = ((Integer) ResidueProperties.aa3Hash.get(b.at2.resName)) - .intValue(); + index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue(); b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); } catch (Exception e) { - b = (Bond) bonds.elementAt(i); b.startCol = Color.gray; b.endCol = Color.gray; } @@ -467,66 +510,107 @@ 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; } } - public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq, - String status) - { - AlignmentAnnotation[] transferred = null; - - return transferred; - - } - /** * copy any sequence annotation onto the sequence mapped using the provided * StructureMapping * * @param mapping + * - positional mapping between destination sequence and pdb resnum + * @param sqmpping + * - mapping between destination sequence and local chain */ - public void transferResidueAnnotation(StructureMapping mapping) + public void transferResidueAnnotation(StructureMapping mapping, + jalview.datamodel.Mapping sqmpping) { SequenceI sq = mapping.getSequence(); + SequenceI dsq = sq; if (sq != null) { - if (sequence != null && sequence.getAnnotation() != null) + while (dsq.getDatasetSequence() != null) { - + dsq = dsq.getDatasetSequence(); } - 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++) + // any annotation will be transferred onto the dataset sequence + + if (shadow != null && shadow.getAnnotation() != null) { - int prn = mapping.getPDBResNum(k + 1); - an[k] = new Annotation(prn); - if (min == -1) + for (AlignmentAnnotation ana : shadow.getAnnotation()) { - min = k; - max = k; + List transfer = sq.getAlignmentAnnotations( + ana.getCalcId(), ana.label); + if (transfer == null || transfer.size() == 0) + { + ana = new AlignmentAnnotation(ana); + ana.liftOver(sequence, shadowMap); + ana.liftOver(dsq, sqmpping); + dsq.addAlignmentAnnotation(ana); + } + else + { + continue; + } } - else + } + else + { + if (sequence != null && sequence.getAnnotation() != null) { - if (min > k) + for (AlignmentAnnotation ana : sequence.getAnnotation()) { - min = k; + List transfer = sq + .getAlignmentAnnotations(ana.getCalcId(), ana.label); + if (transfer == null || transfer.size() == 0) + { + ana = new AlignmentAnnotation(ana); + ana.liftOver(dsq, sqmpping); + // mapping.transfer(ana); + } + else + { + continue; + } } - else if (max < k) + } + } + if (false) + { + // 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++) + { + int prn = mapping.getPDBResNum(k + 1); + + an[k] = new Annotation(prn); + if (min == -1) { + min = k; max = k; } + else + { + if (min > k) + { + min = k; + } + else if (max < k) + { + max = k; + } + } } + sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM", + "PDB Residue Numbering for " + this.pdbid + ":" + this.id, + an, min, max, AlignmentAnnotation.LINE_GRAPH)); } - sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM", - "PDB Residue Numbering for " + this.pdbid + ":" + this.id, - an, min, max, AlignmentAnnotation.LINE_GRAPH)); - } } }