X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=a3505c70c981271351d7915b411aaf87cbf90682;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=0715b6abd2e8ac892fbd166856e9256b31631e2f;hpb=dbbe146185027d9cb041a83645985a6b1a26cb75;p=jalview.git diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 0715b6a..a3505c7 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -1,286 +1,595 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program 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 2 -* of the License, or (at your option) any later version. -* -* This program 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 this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package MCview; - -import jalview.datamodel.*; - -import jalview.schemes.ResidueProperties; - -import java.awt.*; - -import java.util.*; -import jalview.analysis.AlignSeq; - - -public class PDBChain { - public String id; - public Vector bonds = new Vector(); - public Vector atoms = new Vector(); - public Vector residues = new Vector(); - public int offset; - public Sequence sequence; - public boolean isVisible = true; - public int pdbstart = 0; - public int pdbend = 0; - public int seqstart = 0; - public int seqend = 0; - - public PDBChain(String id) { - this.id = id; - } - - public String print() { - String tmp = ""; - - for (int i = 0; i < bonds.size(); i++) { - tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " " + - ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset + - "\n"; - } - - return tmp; - } - - void makeExactMapping(AlignSeq as, Sequence s1) - { - int pdbpos = as.getSeq2Start()-2; - int alignpos = s1.getStart() + as.getSeq1Start()-3; - - for(int i=0; i (float) 1.0) { - red = (float) 1.0; - } - - if (red < (float) 0.0) { - red = (float) 0.0; - } - - b.startCol = new Color(red, (float) 0.0, (float) 1.0 - red); - atno = ((Integer) AA3Hash.get(b.at2.resName.toUpperCase())).intValue(); - - red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin); - - if (red > (float) 1.0) { - red = (float) 1.0; - } - - if (red < (float) 0.0) { - red = (float) 0.0; - } - - b.endCol = new Color(red, (float) 0.2, (float) 1.0 - red); - } catch (Exception e) { - Bond b = (Bond) bonds.elementAt(i); - b.startCol = Color.gray; - b.endCol = Color.gray; - } - } - } - - - - public void setChainColours(Color col) - { - for (int i = 0; i < bonds.size(); i++) - { - Bond tmp = (Bond) bonds.elementAt(i); - tmp.startCol = col; - tmp.endCol = col; - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +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.List; +import java.util.Vector; + +public class PDBChain +{ + /** + * SequenceFeature group for PDB File features added to sequences + */ + private static final String PDBFILEFEATURE = "PDBFile"; + + private static final String IEASTATUS = "IEA:jalview"; + + public String id; + + public Vector bonds = new Vector(); + + public Vector atoms = new Vector(); + + public Vector residues = new Vector(); + + public int offset; + + /** + * 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; + + public int pdbend = 0; + + public int seqstart = 0; + + public int seqend = 0; + + public String pdbid = ""; + + public PDBChain(String pdbid, String id) + { + this.pdbid = pdbid.toLowerCase(); + 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() + { + StringBuilder tmp = new StringBuilder(256); + + for (Bond b : bonds) + { + tmp.append(b.at1.resName).append(" ").append(b.at1.resNumber) + .append(" ").append(offset).append(newline); + } + + 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) != '-') + { + alignpos++; + } + + if (as.astr2.charAt(i) != '-') + { + pdbpos++; + } + + if (as.astr1.charAt(i) == as.astr2.charAt(i)) + { + Residue res = residues.elementAt(pdbpos); + for (Atom atom : res.atoms) + { + atom.alignmentMapping = alignpos; + } + } + } + } + + /** + * copy 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, + String status) + { + SequenceI sq = seq; + while (sq != null && sq.getDatasetSequence() != null) + { + sq = sq.getDatasetSequence(); + if (sq == sequence) + { + return null; + } + } + /** + * 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 + * ? for (int i=0; i 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; + } + } + + /** + * 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) + { + 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; + 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 = atoms.elementAt(i); + resNumber = tmp.resNumber; + int res = resNumber; + + if (i == 0) + { + offset = resNumber; + } + + 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.add(atoms.elementAt(i)); + i++; + + if (i < atoms.size()) + { + resNumber = atoms.elementAt(i).resNumber; + } + else + { + resNumber++; + } + } + + // 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) + { + 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))); + } + } + 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++; + } + + if (id.length() < 1) + { + id = " "; + } + isNa = nucleotide; + sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note: + // resNumber-offset + // ~= + // seq.size() + // Add normalised feature scores to RESNUM indicating start/end of sequence + // sf.setScore(offset+count); + + // 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++) + { + 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++) + { + 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); + } + } + + /** + * Colour start/end of bonds by charge + *
    + *
  • ASP and GLU red
  • + *
  • LYS and ARG blue
  • + *
  • CYS yellow
  • + *
  • others light gray
  • + *
+ */ + public void setChargeColours() + { + for (Bond b : bonds) + { + if (b.at1 != null && b.at2 != null) + { + b.startCol = getChargeColour(b.at1.resName); + b.endCol = getChargeColour(b.at2.resName); + } + else + { + b.startCol = Color.gray; + b.endCol = Color.gray; + } + } + } + + 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) + { + int index; + for (Bond b : bonds) + { + try + { + index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue(); + b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); + + index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue(); + b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); + + } catch (Exception e) + { + b.startCol = Color.gray; + b.endCol = Color.gray; + } + } + } + + public void setChainColours(Color col) + { + for (Bond b : bonds) + { + b.startCol = col; + b.endCol = col; + } + } + + /** + * 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, + jalview.datamodel.Mapping sqmpping) + { + SequenceI sq = mapping.getSequence(); + SequenceI dsq = sq; + if (sq != null) + { + while (dsq.getDatasetSequence() != null) + { + dsq = dsq.getDatasetSequence(); + } + // any annotation will be transferred onto the dataset sequence + + if (shadow != null && shadow.getAnnotation() != null) + { + + for (AlignmentAnnotation ana : shadow.getAnnotation()) + { + 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 + { + if (sequence != null && sequence.getAnnotation() != null) + { + for (AlignmentAnnotation ana : sequence.getAnnotation()) + { + 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; + } + } + } + } + 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)); + } + } + } +}