X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=904a8601f18865002dc0a43cc4870b80475fe1bb;hb=e94c33abc7983e947f64803ab294282a236bf671;hp=12e79787703d54d07a91d1646d5dfdbae8f3552c;hpb=f8ccad28f3a8fc90f4f0a13ec0c8d230dec6b230;p=jalview.git
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 12e7978..904a860 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,309 +1,689 @@
/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.datamodel.*;
-
+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.StructureImportSettings;
+import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
-import java.awt.*;
+import java.awt.Color;
+import java.util.List;
+import java.util.Vector;
-import java.util.*;
-import jalview.analysis.AlignSeq;
+public class PDBChain
+{
+ public static final String RESNUM_FEATURE = "RESNUM";
+ private static final String IEASTATUS = "IEA:jalview";
-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;
- public Sequence sequence;
- 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;
- }
+ public String id;
- public String print() {
- String tmp = "";
+ public Vector bonds = new Vector<>();
- for (int i = 0; i < bonds.size(); i++) {
- tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " " +
- ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset +
- "\n";
- }
+ public Vector atoms = new Vector<>();
- return tmp;
- }
+ public Vector residues = new Vector<>();
- void makeExactMapping(AlignSeq as, Sequence s1)
- {
- int pdbpos = as.getSeq2Start()-2;
- int alignpos = s1.getStart() + as.getSeq1Start()-3;
+ public int offset;
- for(int i=0; i= residues.size())
+ {
+ continue;
}
- }
-
- public void setChargeColours() {
- for (int i = 0; i < bonds.size(); i++) {
- try {
- 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 {
- //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();
- 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 {
- //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
- b.endCol = Color.lightGray;
- }
- } catch (Exception e) {
- Bond b = (Bond) bonds.elementAt(i);
- b.startCol = Color.gray;
- b.endCol = Color.gray;
- }
+ Residue res = residues.elementAt(pdbpos);
+ for (Atom atom : res.atoms)
+ {
+ atom.alignmentMapping = alignpos;
+ }
+ }
+ }
+ }
+
+ /**
+ * 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(StructureMapping mapping, SequenceI s1)
+ {
+ // first clear out any old alignmentMapping values:
+ for (Atom atom : atoms)
+ {
+ atom.alignmentMapping = -1;
+ }
+ SequenceI ds = s1;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ int pdboffset = 0;
+ for (Residue res : residues)
+ {
+ // res.number isn't set correctly for discontinuous/mismapped residues
+ int seqpos = mapping.getSeqPos(res.atoms.get(0).resNumber);
+ char strchar = sequence.getCharAt(pdboffset++);
+ if (seqpos == StructureMapping.UNASSIGNED_VALUE)
+ {
+ continue;
+ }
+ char seqchar = ds.getCharAt(seqpos - ds.getStart());
+
+ boolean sameResidue = Comparison.isSameResidue(
+ seqchar, strchar, false);
+ if (sameResidue)
+ {
+ for (Atom atom : res.atoms)
+ {
+ atom.alignmentMapping = seqpos - 1;
}
+ }
+ }
+ }
+
+ /**
+ * Copies over the RESNUM seqfeatures from the internal chain sequence to the
+ * mapped sequence
+ *
+ * @param seq
+ * @param status
+ * The Status of the transferred annotation
+ */
+ public void transferRESNUMFeatures(SequenceI seq,
+ String status)
+ {
+ SequenceI sq = seq;
+ while (sq != null && sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+ if (sq == sequence)
+ {
+ return;
+ }
+ }
+
+ /*
+ * 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 features = sequence.getSequenceFeatures();
+ for (SequenceFeature feature : features)
+ {
+ if (feature.getFeatureGroup() != null
+ && feature.getFeatureGroup().equals(pdbid))
+ {
+ int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms
+ .elementAt(0).alignmentMapping;
+ int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
+ .elementAt(0).alignmentMapping;
+ SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
+ feature.getFeatureGroup(), feature.getScore());
+ tx.setStatus(status
+ + ((tx.getStatus() == null || tx.getStatus().length() == 0)
+ ? ""
+ : ":" + tx.getStatus()));
+ if (tx.begin != 0 && tx.end != 0)
+ {
+ sq.addSequenceFeature(tx);
+ }
+ }
+ }
+ }
+
+ /**
+ * 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 = residues.elementAt(i);
+ Residue tmpres2 = residues.elementAt(i + 1);
+ Atom at1 = tmpres.findAtom("CA");
+ Atom at2 = tmpres2.findAtom("CA");
+ na = false;
+ if ((at1 == null) && (at2 == null))
+ {
+ na = true;
+ at1 = tmpres.findAtom("P");
+ at2 = tmpres2.findAtom("P");
+ }
+ if ((at1 != null) && (at2 != null))
+ {
+ if (at1.chain.equals(at2.chain))
+ {
+ if (na)
+ {
+ numNa++;
+ }
+ makeBond(at1, at2);
+ }
+ }
+ else
+ {
+ System.out.println("not found " + i);
+ }
+ }
- public void setChainColours(jalview.schemes.ColourSchemeI cs)
+ /*
+ * 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))
{
- Bond b;
- for (int i = 0; i < bonds.size(); i++) {
- try {
- b = (Bond) bonds.elementAt(i);
-
- /* ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(
- ResidueProperties.codonTranslate(
- ResidueProperties.aa3Hash.get(b.at1.resName).toString().charAt(0)
- );
-
- b.endCol = cs.findColour(
- ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
- get(b.at2.resName)).intValue()]
- );*/
-
- } catch (Exception e)
- {
- b = (Bond) bonds.elementAt(i);
- b.startCol = Color.gray;
- b.endCol = Color.gray;
- }
+ 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 iSize = atoms.size() - 1;
+ int resNumber = -1;
+ char insCode = ' ';
+
+ for (int 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)
+ {
+ 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) && (ins == insCode) && (i < atoms.size()))
+ {
+ resAtoms.add(atoms.elementAt(i));
+ i++;
+
+ if (i < atoms.size())
+ {
+ resNumber = atoms.elementAt(i).resNumber;
+ insCode = atoms.elementAt(i).insCode;
+ }
+ else
+ {
+ resNumber++;
+ }
+ }
+
+ // 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.isEmpty()
+ && residues.lastElement().atoms
+ .get(0).resNumber == currAtom.resNumber)
+ {
+ String desc = currAtom.resName + ":" + currAtom.resNumIns + " "
+ + pdbid + id;
+ SequenceFeature sf = new SequenceFeature("INSERTION", desc, 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 = residues.lastElement();
+ Atom tmpat = tmpres.atoms.get(0);
+ // Make A new SequenceFeature for the current residue numbering
+ String desc = tmpat.resName
+ + ":" + tmpat.resNumIns + " " + pdbid + id;
+ SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
+ 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)
+ {
+ 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()]);
}
+ 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());
+
+ if (StructureImportSettings.isShowSeqFeatures())
+ {
+ iSize = resFeatures.size();
+ for (int i = 0; i < iSize; i++)
+ {
+ sequence.addSequenceFeature(resFeatures.elementAt(i));
+ resFeatures.setElementAt(null, i);
+ }
+ }
+ if (visibleChainAnnotation)
+ {
+ Annotation[] annots = new Annotation[resAnnotation.size()];
+ float max = 0f;
+ float min = 0f;
+ iSize = annots.length;
+ for (int i = 0; i < iSize; i++)
+ {
+ annots[i] = resAnnotation.elementAt(i);
+ max = Math.max(max, annots[i].value);
+ min = Math.min(min, annots[i].value);
+ resAnnotation.setElementAt(null, i);
+ }
+
+ AlignmentAnnotation tfactorann = new AlignmentAnnotation(
+ "Temperature Factor", "Temperature Factor for " + pdbid + id,
+ annots, min, 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), 0,
+ null, null, 0f);
+
+ 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.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 (sqmpping == null)
+ {
+ // SIFTS mappings are recorded in the StructureMapping object...
- public void setChainColours(Color col)
+ sqmpping = mapping.getSeqToPdbMapping();
+ }
+ if (sq != null)
{
- for (int i = 0; i < bonds.size(); i++)
+ 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 = 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
+ {
+ 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++)
{
- Bond tmp = (Bond) bonds.elementAt(i);
- tmp.startCol = col;
- tmp.endCol = col;
+ 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));
+ }
}
+ }
}