X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=379eb91a3c2a1a41a9a21a862c658448171c84f7;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=e9b02470ad17b8277e60bcec4e81f87100bfabdd;hpb=1f6abafc27f8c03eb9261eb3fea054e123171743;p=jalview.git diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index e9b0247..379eb91 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -1,31 +1,40 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package MCview; -import java.util.*; - -import java.awt.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.schemes.*; +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.List; +import java.util.Vector; + public class PDBChain { /** @@ -37,16 +46,27 @@ 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; - public boolean isNa=false; + /** + * 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; + public boolean isVisible = true; public int pdbstart = 0; @@ -65,25 +85,54 @@ public class PDBChain this.id = id; } + /** + * character used to write newlines + */ + protected String newline = System.getProperty("line.separator"); + + public Mapping shadowMap; + + public void setNewlineString(String nl) + { + newline = nl; + } + + public String getNewlineString() + { + return newline; + } + 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 - + "\n"; + tmp.append(b.at1.resName).append(" ").append(b.at1.resNumber) + .append(" ").append(offset).append(newline); } - return tmp; + return tmp.toString(); } + /** + * 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(AlignSeq as, SequenceI s1) { int pdbpos = as.getSeq2Start() - 2; int alignpos = s1.getStart() + as.getSeq1Start() - 3; - + // first clear out any old alignmentMapping values: + for (Atom atom : atoms) + { + atom.alignmentMapping = -1; + } + // and now trace the alignment onto the atom set. for (int i = 0; i < as.astr1.length(); i++) { if (as.astr1.charAt(i) != '-') @@ -98,11 +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; } } @@ -146,37 +193,43 @@ 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 - .setStatus(status - + ((tx.getStatus() == null || tx.getStatus() - .length() == 0) ? "" : ":" + tx.getStatus())); + 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())); if (tx.begin != 0 && tx.end != 0) + { sq.addSequenceFeature(tx); + } } } 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; + 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; + na = false; if ((at1 == null) && (at2 == null)) { - na=true; + na = true; at1 = tmpres.findAtom("P"); - at1 = tmpres2.findAtom("P"); + at2 = tmpres2.findAtom("P"); } if ((at1 != null) && (at2 != null)) { @@ -194,41 +247,57 @@ 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() > 0 && (numNa / (residues.size() - 1) > 0.99)) { - isNa=true; + 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; for (i = 0; i <= iSize; i++) { - Atom tmp = (Atom) atoms.elementAt(i); + Atom tmp = atoms.elementAt(i); resNumber = tmp.resNumber; int res = resNumber; @@ -237,17 +306,17 @@ public class PDBChain 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())) { - resAtoms.addElement((Atom) atoms.elementAt(i)); + resAtoms.add(atoms.elementAt(i)); i++; if (i < atoms.size()) { - resNumber = ((Atom) atoms.elementAt(i)).resNumber; + resNumber = atoms.elementAt(i).resNumber; } else { @@ -261,8 +330,8 @@ public class PDBChain // 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 + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset @@ -273,8 +342,14 @@ public class PDBChain // Keep totting up the sequence if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null) { - String nucname=tmpat.resName.trim(); - if (ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1) + 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 " + @@ -284,7 +359,7 @@ public class PDBChain { // nucleotide flag nucleotide = true; - seq.append(nucname.charAt(0)); + seq.append(nucname.charAt((deoxyn ? 1 : 0))); } } else @@ -303,7 +378,7 @@ public class PDBChain { id = " "; } - isNa=nucleotide; + isNa = nucleotide; sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note: // resNumber-offset // ~= @@ -315,102 +390,97 @@ 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) - max = annots[i].value; - resAnnotation.setElementAt(null, i); + Annotation[] annots = new Annotation[resAnnotation.size()]; + float max = 0; + for (i = 0, iSize = annots.length; i < iSize; i++) + { + annots[i] = resAnnotation.elementAt(i); + if (annots[i].value > max) + { + max = annots[i].value; + } + 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; } @@ -419,67 +489,107 @@ 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((float) 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, (float) min, (float) max, - AlignmentAnnotation.LINE_GRAPH)); } } }