X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=e25dfd01f01b6bb36a1e170d2b0ee28407fbc7b3;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=4bfe2559558fc7d7c75ca3c99a10c58a6b524b23;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 4bfe255..e25dfd0 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,283 +1,485 @@
-/*
-* 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.*;
-
-
-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 = false;
- public int pdbstart = 0;
- public int pdbend = 0;
- public int seqstart = 0;
- public int seqend = 0;
-
- //public DrawableSequence ds;
- 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;
- }
-
- public void makeCaBondList() {
- for (int i = 0; i < (residues.size() - 1); i++) {
- Residue tmpres = (Residue) residues.elementAt(i);
- Residue tmpres2 = (Residue) residues.elementAt(i + 1);
- myAtom at1 = tmpres.findAtom("CA");
- myAtom at2 = tmpres2.findAtom("CA");
-
- if ((at1 != null) && (at2 != null)) {
- if (at1.chain.equals(at2.chain)) {
- makeBond(at1, at2);
- }
- }
- }
- }
-
- public void makeBond(myAtom at1, myAtom 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));
- }
-
- public void makeResidueList() {
- int count = 0;
- String seq = "";
-
- for (int i = 0; i < atoms.size(); i++) {
- myAtom tmp = (myAtom) atoms.elementAt(i);
- String resName = tmp.resName;
- int resNumber = tmp.resNumber;
- int res = resNumber;
-
- if (i == 0) {
- offset = resNumber;
- }
-
- Vector resAtoms = new Vector();
-
- resAtoms.addElement((myAtom) atoms.elementAt(i));
- i++;
- resNumber = ((myAtom) atoms.elementAt(i)).resNumber;
-
- //Add atoms to a vector while the residue number
- //remains the same
- while ((resNumber == res) && (i < atoms.size())) {
- resAtoms.addElement((myAtom) atoms.elementAt(i));
- i++;
-
- if (i < atoms.size()) {
- resNumber = ((myAtom) 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));
- count++;
-
- Residue tmpres = (Residue) residues.lastElement();
- myAtom tmpat = (myAtom) tmpres.atoms.elementAt(0);
-
- // Keep totting up the sequence
- if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {
- System.err.println("PDBReader:Null aa3Hash for " +
- tmpat.resName);
- } else {
- String tmpres2 = ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()
- .get(tmpat.resName)).intValue()];
- seq = seq + tmpres2;
- }
-
- // System.out.println(tmpat.resName + " " + tmpres2);
- }
-
- sequence = new Sequence("PDB_seq", seq, 1, seq.length());
- System.out.println("PDB Sequence is :\nSequence = " + seq);
- System.out.println("No of residues = " + residues.size());
- }
-
- public void setChargeColours() {
- for (int i = 0; i < bonds.size(); i++) {
- try {
- Bond b = (Bond) bonds.elementAt(i);
-
- if (b.at1.resName.toUpperCase().equals("ASP") ||
- b.at1.resName.toUpperCase().equals("GLU")) {
- b.startCol = Color.red;
- } else if (b.at1.resName.toUpperCase().equals("LYS") ||
- b.at1.resName.toUpperCase().equals("ARG")) {
- b.startCol = Color.blue;
- } else if (b.at1.resName.toUpperCase().equals("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.toUpperCase().equals("ASP") ||
- b.at2.resName.toUpperCase().equals("GLU")) {
- b.endCol = Color.red;
- } else if (b.at2.resName.toUpperCase().equals("LYS") ||
- b.at2.resName.toUpperCase().equals("ARG")) {
- b.endCol = Color.blue;
- } else if (b.at2.resName.toUpperCase().equals("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;
- }
- }
- }
-
- public void setHydrophobicityColours() {
- float hydmin = (float) ResidueProperties.getHydmin();
- float hydmax = (float) ResidueProperties.getHydmax();
- double[] hyd = ResidueProperties.getHyd();
-
- Hashtable AA3Hash = ResidueProperties.getAA3Hash();
-
- for (int i = 0; i < bonds.size(); i++) {
- try {
- Bond b = (Bond) bonds.elementAt(i);
-
- int atno = ((Integer) AA3Hash.get(b.at1.resName.toUpperCase())).intValue();
- float 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.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 colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {
- jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);
-
- for (int i = 0; i < bonds.size(); i++) {
- Bond tmp = (Bond) bonds.elementAt(i);
-
- try {
- if ((tmp.at1.resNumber >= ((offset + pdbstart) - 1)) &&
- (tmp.at1.resNumber <= ((offset + pdbend) - 1))) {
- int pos = seqstart +
- (tmp.at1.resNumber - pdbstart - offset);
- int index = seq.findIndex(pos);
-
- tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(),
- seq, index);
- } else {
- tmp.startCol = Color.gray;
- }
-
- if ((tmp.at2.resNumber >= ((offset + pdbstart) - 1)) &&
- (tmp.at2.resNumber <= ((pdbend + offset) - 1))) {
- int pos = seqstart +
- (tmp.at2.resNumber - pdbstart - offset);
- int index = seq.findIndex(pos);
-
- tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(),
- seq, index);
- } else {
- tmp.endCol = Color.gray;
- }
- } catch (Exception e) {
- tmp.startCol = Color.lightGray;
- tmp.endCol = Color.lightGray;
- }
- }
- }
-
- public void setChainColours() {
- for (int i = 0; i < bonds.size(); i++) {
- Bond tmp = (Bond) bonds.elementAt(i);
-
- try {
- tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);
- tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);
- } catch (Exception e) {
- tmp.startCol = Color.lightGray;
- tmp.endCol = Color.lightGray;
- }
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ */
+package MCview;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.structure.StructureMapping;
+
+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 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;
+ }
+
+ 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;
+ }
+
+ public void makeExactMapping(AlignSeq as, SequenceI s1)
+ {
+ int pdbpos = as.getSeq2Start() - 2;
+ int alignpos = s1.getStart() + as.getSeq1Start() - 3;
+
+ 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 = (Residue) residues.elementAt(pdbpos);
+ Enumeration en = res.atoms.elements();
+ while (en.hasMoreElements())
+ {
+ Atom atom = (Atom) en.nextElement();
+ 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; i0 && ((numNa/residues.size())>0.99))
+ {
+ isNa=true;
+ }
+ }
+
+ 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));
+ }
+
+ public void makeResidueList()
+ {
+ int count = 0;
+ Object symbol;
+ boolean nucleotide = false;
+ StringBuffer seq = new StringBuffer();
+ 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);
+ 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.addElement((Atom) atoms.elementAt(i));
+ i++;
+
+ if (i < atoms.size())
+ {
+ resNumber = ((Atom) 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 = (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)
+ {
+ String nucname=tmpat.resName.trim();
+ if (ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
+ {
+ seq.append("X");
+ // System.err.println("PDBReader:Null aa3Hash for " +
+ // tmpat.resName);
+ }
+ else
+ {
+ // nucleotide flag
+ nucleotide = true;
+ seq.append(nucname.charAt(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((SequenceFeature) 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++)
+ {
+ annots[i] = (Annotation) resAnnotation.elementAt(i);
+ if (annots[i].value > max)
+ max = annots[i].value;
+ resAnnotation.setElementAt(null, i);
+ }
+ AlignmentAnnotation tfactorann = new AlignmentAnnotation(
+ "PDB.TempFactor", "Temperature Factor for "
+ + sequence.getName(), annots, 0, max,
+ AlignmentAnnotation.LINE_GRAPH);
+ tfactorann.setSequenceRef(sequence);
+ sequence.addAlignmentAnnotation(tfactorann);
+ }
+
+ 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
+ {
+ 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)
+ {
+ Bond b = (Bond) bonds.elementAt(i);
+ b.startCol = Color.gray;
+ b.endCol = Color.gray;
+ }
+ }
+ }
+
+ public void setChainColours(jalview.schemes.ColourSchemeI cs)
+ {
+ Bond b;
+ int index;
+ for (int i = 0; i < bonds.size(); i++)
+ {
+ 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 = ((Integer) 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;
+ }
+ }
+ }
+
+ 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;
+ }
+ }
+
+ 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
+ */
+ public void transferResidueAnnotation(StructureMapping mapping)
+ {
+ SequenceI sq = mapping.getSequence();
+ if (sq != null)
+ {
+ if (sequence != null && sequence.getAnnotation() != null)
+ {
+
+ }
+ 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((float) 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, (float) min, (float) max,
+ AlignmentAnnotation.LINE_GRAPH));
+ }
+ }
+}