X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=8338c63e6a160554cf02ee3c7940e436d2b20d73;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=fa4bbf9e210b77a066fea1039bf04ec26874f772;hpb=c44b1974aea543db46790f6cb88f5ac0aae10a94;p=jalview.git
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index fa4bbf9..8338c63 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,269 +1,520 @@
-/*
-* 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.
+ * 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.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;
+ }
+
+ /**
+ * character used to write newlines
+ */
+ protected String newline = System.getProperty("line.separator");
+
+ public void setNewlineString(String nl)
+ {
+ newline = nl;
+ }
+
+ public String getNewlineString()
+ {
+ return newline;
+ }
+
+ 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
+ + newline;
+ }
+
+ return tmp;
+ }
+
+ /**
+ * 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 : (Vector) 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 = (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; i 0 && ((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 deoxyn = false;
+ 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();
+ // 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((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));
+ }
+ }
+}