2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
24 import jalview.analysis.*;
25 import jalview.datamodel.*;
26 import jalview.schemes.*;
27 import jalview.structure.StructureMapping;
32 * SequenceFeature group for PDB File features added to sequences
34 private static final String PDBFILEFEATURE = "PDBFile";
36 private static final String IEASTATUS = "IEA:jalview";
40 public Vector bonds = new Vector();
42 public Vector atoms = new Vector();
44 public Vector residues = new Vector();
48 public Sequence sequence;
50 public boolean isNa = false;
52 public boolean isVisible = true;
54 public int pdbstart = 0;
56 public int pdbend = 0;
58 public int seqstart = 0;
60 public int seqend = 0;
62 public String pdbid = "";
64 public PDBChain(String pdbid, String id)
66 this.pdbid = pdbid.toLowerCase();
71 * character used to write newlines
73 protected String newline = System.getProperty("line.separator");
75 public void setNewlineString(String nl)
80 public String getNewlineString()
89 for (int i = 0; i < bonds.size(); i++)
91 tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
92 + ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
100 * Annotate the residues with their corresponding positions in s1 using the
106 public void makeExactMapping(AlignSeq as, SequenceI s1)
108 int pdbpos = as.getSeq2Start() - 2;
109 int alignpos = s1.getStart() + as.getSeq1Start() - 3;
111 for (int i = 0; i < as.astr1.length(); i++)
113 if (as.astr1.charAt(i) != '-')
118 if (as.astr2.charAt(i) != '-')
123 if (as.astr1.charAt(i) == as.astr2.charAt(i))
125 Residue res = (Residue) residues.elementAt(pdbpos);
126 Enumeration en = res.atoms.elements();
127 while (en.hasMoreElements())
129 Atom atom = (Atom) en.nextElement();
130 atom.alignmentMapping = alignpos;
137 * copy over the RESNUM seqfeatures from the internal chain sequence to the
142 * The Status of the transferred annotation
143 * @return the features added to sq (or its dataset)
145 public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
149 while (sq != null && sq.getDatasetSequence() != null)
151 sq = sq.getDatasetSequence();
158 * Remove any existing features for this chain if they exist ?
159 * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
160 * totfeat=seqsfeatures.length; // Remove any features for this exact chain
161 * ? for (int i=0; i<seqsfeatures.length; i++) { }
165 status = PDBChain.IEASTATUS;
167 SequenceFeature[] features = sequence.getSequenceFeatures();
168 for (int i = 0; i < features.length; i++)
170 if (features[i].getFeatureGroup().equals(pdbid))
172 SequenceFeature tx = new SequenceFeature(features[i]);
173 tx.setBegin(1 + ((Atom) ((Residue) residues.elementAt(tx.getBegin()
174 - offset)).atoms.elementAt(0)).alignmentMapping);
175 tx.setEnd(1 + ((Atom) ((Residue) residues.elementAt(tx.getEnd()
176 - offset)).atoms.elementAt(0)).alignmentMapping);
178 + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
179 : ":" + tx.getStatus()));
180 if (tx.begin != 0 && tx.end != 0)
181 sq.addSequenceFeature(tx);
187 public void makeCaBondList()
191 for (int i = 0; i < (residues.size() - 1); i++)
193 Residue tmpres = (Residue) residues.elementAt(i);
194 Residue tmpres2 = (Residue) residues.elementAt(i + 1);
195 Atom at1 = tmpres.findAtom("CA");
196 Atom at2 = tmpres2.findAtom("CA");
198 if ((at1 == null) && (at2 == null))
201 at1 = tmpres.findAtom("P");
202 at2 = tmpres2.findAtom("P");
204 if ((at1 != null) && (at2 != null))
206 if (at1.chain.equals(at2.chain))
217 System.out.println("not found " + i);
220 if (numNa > 0 && ((numNa / residues.size()) > 0.99))
226 public void makeBond(Atom at1, Atom at2)
228 float[] start = new float[3];
229 float[] end = new float[3];
239 bonds.addElement(new Bond(start, end, at1, at2));
242 public void makeResidueList()
246 boolean nucleotide = false;
247 StringBuffer seq = new StringBuffer();
248 Vector resFeatures = new Vector();
249 Vector resAnnotation = new Vector();
250 int i, iSize = atoms.size() - 1;
252 for (i = 0; i <= iSize; i++)
254 Atom tmp = (Atom) atoms.elementAt(i);
255 resNumber = tmp.resNumber;
263 Vector resAtoms = new Vector();
264 // Add atoms to a vector while the residue number
265 // remains the same as the first atom's resNumber (res)
266 while ((resNumber == res) && (i < atoms.size()))
268 resAtoms.addElement((Atom) atoms.elementAt(i));
271 if (i < atoms.size())
273 resNumber = ((Atom) atoms.elementAt(i)).resNumber;
281 // We need this to keep in step with the outer for i = loop
284 // Make a new Residue object with the new atoms vector
285 residues.addElement(new Residue(resAtoms, resNumber - 1, count));
287 Residue tmpres = (Residue) residues.lastElement();
288 Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
289 // Make A new SequenceFeature for the current residue numbering
290 SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
291 + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
292 + count, offset + count, pdbid);
293 // MCview.PDBChain.PDBFILEFEATURE);
294 resFeatures.addElement(sf);
295 resAnnotation.addElement(new Annotation(tmpat.tfactor));
296 // Keep totting up the sequence
297 if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
299 String nucname = tmpat.resName.trim();
300 if (tmpat.name.equalsIgnoreCase("CA")
301 || ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
304 // System.err.println("PDBReader:Null aa3Hash for " +
311 seq.append(nucname.charAt(0));
319 .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
321 seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
331 sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
335 // Add normalised feature scores to RESNUM indicating start/end of sequence
336 // sf.setScore(offset+count);
338 // System.out.println("PDB Sequence is :\nSequence = " + seq);
339 // System.out.println("No of residues = " + residues.size());
340 for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
342 sequence.addSequenceFeature((SequenceFeature) resFeatures
344 resFeatures.setElementAt(null, i);
346 Annotation[] annots = new Annotation[resAnnotation.size()];
348 for (i = 0, iSize = annots.length; i < iSize; i++)
350 annots[i] = (Annotation) resAnnotation.elementAt(i);
351 if (annots[i].value > max)
352 max = annots[i].value;
353 resAnnotation.setElementAt(null, i);
355 AlignmentAnnotation tfactorann = new AlignmentAnnotation(
356 "PDB.TempFactor", "Temperature Factor for "
357 + sequence.getName(), annots, 0, max,
358 AlignmentAnnotation.LINE_GRAPH);
359 tfactorann.setSequenceRef(sequence);
360 sequence.addAlignmentAnnotation(tfactorann);
363 public void setChargeColours()
365 for (int i = 0; i < bonds.size(); i++)
369 Bond b = (Bond) bonds.elementAt(i);
371 if (b.at1.resName.equalsIgnoreCase("ASP")
372 || b.at1.resName.equalsIgnoreCase("GLU"))
374 b.startCol = Color.red;
376 else if (b.at1.resName.equalsIgnoreCase("LYS")
377 || b.at1.resName.equalsIgnoreCase("ARG"))
379 b.startCol = Color.blue;
381 else if (b.at1.resName.equalsIgnoreCase("CYS"))
383 b.startCol = Color.yellow;
387 b.startCol = Color.lightGray;
390 if (b.at2.resName.equalsIgnoreCase("ASP")
391 || b.at2.resName.equalsIgnoreCase("GLU"))
393 b.endCol = Color.red;
395 else if (b.at2.resName.equalsIgnoreCase("LYS")
396 || b.at2.resName.equalsIgnoreCase("ARG"))
398 b.endCol = Color.blue;
400 else if (b.at2.resName.equalsIgnoreCase("CYS"))
402 b.endCol = Color.yellow;
406 b.endCol = Color.lightGray;
408 } catch (Exception e)
410 Bond b = (Bond) bonds.elementAt(i);
411 b.startCol = Color.gray;
412 b.endCol = Color.gray;
417 public void setChainColours(jalview.schemes.ColourSchemeI cs)
421 for (int i = 0; i < bonds.size(); i++)
425 b = (Bond) bonds.elementAt(i);
427 index = ((Integer) ResidueProperties.aa3Hash.get(b.at1.resName))
429 b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
431 index = ((Integer) ResidueProperties.aa3Hash.get(b.at2.resName))
433 b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
435 } catch (Exception e)
437 b = (Bond) bonds.elementAt(i);
438 b.startCol = Color.gray;
439 b.endCol = Color.gray;
444 public void setChainColours(Color col)
446 for (int i = 0; i < bonds.size(); i++)
448 Bond tmp = (Bond) bonds.elementAt(i);
454 public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq,
457 AlignmentAnnotation[] transferred = null;
464 * copy any sequence annotation onto the sequence mapped using the provided
469 public void transferResidueAnnotation(StructureMapping mapping)
471 SequenceI sq = mapping.getSequence();
474 if (sequence != null && sequence.getAnnotation() != null)
478 float min = -1, max = 0;
479 Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
480 for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
482 int prn = mapping.getPDBResNum(k + 1);
484 an[k] = new Annotation((float) prn);
502 sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
503 "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
504 an, (float) min, (float) max, AlignmentAnnotation.LINE_GRAPH));