2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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
101 * alignment in as NOTE: This clears all atom.alignmentMapping values on the
107 public void makeExactMapping(AlignSeq as, SequenceI s1)
109 int pdbpos = as.getSeq2Start() - 2;
110 int alignpos = s1.getStart() + as.getSeq1Start() - 3;
111 // first clear out any old alignmentMapping values:
112 for (Atom atom : (Vector<Atom>) atoms)
114 atom.alignmentMapping = -1;
116 // and now trace the alignment onto the atom set.
117 for (int i = 0; i < as.astr1.length(); i++)
119 if (as.astr1.charAt(i) != '-')
124 if (as.astr2.charAt(i) != '-')
129 if (as.astr1.charAt(i) == as.astr2.charAt(i))
131 Residue res = (Residue) residues.elementAt(pdbpos);
132 Enumeration en = res.atoms.elements();
133 while (en.hasMoreElements())
135 Atom atom = (Atom) en.nextElement();
136 atom.alignmentMapping = alignpos;
143 * copy over the RESNUM seqfeatures from the internal chain sequence to the
148 * The Status of the transferred annotation
149 * @return the features added to sq (or its dataset)
151 public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
155 while (sq != null && sq.getDatasetSequence() != null)
157 sq = sq.getDatasetSequence();
164 * Remove any existing features for this chain if they exist ?
165 * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
166 * totfeat=seqsfeatures.length; // Remove any features for this exact chain
167 * ? for (int i=0; i<seqsfeatures.length; i++) { }
171 status = PDBChain.IEASTATUS;
173 SequenceFeature[] features = sequence.getSequenceFeatures();
174 for (int i = 0; i < features.length; i++)
176 if (features[i].getFeatureGroup().equals(pdbid))
178 SequenceFeature tx = new SequenceFeature(features[i]);
179 tx.setBegin(1 + ((Atom) ((Residue) residues.elementAt(tx.getBegin()
180 - offset)).atoms.elementAt(0)).alignmentMapping);
181 tx.setEnd(1 + ((Atom) ((Residue) residues.elementAt(tx.getEnd()
182 - offset)).atoms.elementAt(0)).alignmentMapping);
184 + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
185 : ":" + tx.getStatus()));
186 if (tx.begin != 0 && tx.end != 0)
187 sq.addSequenceFeature(tx);
193 public void makeCaBondList()
197 for (int i = 0; i < (residues.size() - 1); i++)
199 Residue tmpres = (Residue) residues.elementAt(i);
200 Residue tmpres2 = (Residue) residues.elementAt(i + 1);
201 Atom at1 = tmpres.findAtom("CA");
202 Atom at2 = tmpres2.findAtom("CA");
204 if ((at1 == null) && (at2 == null))
207 at1 = tmpres.findAtom("P");
208 at2 = tmpres2.findAtom("P");
210 if ((at1 != null) && (at2 != null))
212 if (at1.chain.equals(at2.chain))
223 System.out.println("not found " + i);
226 if (numNa > 0 && ((numNa / residues.size()) > 0.99))
232 public void makeBond(Atom at1, Atom at2)
234 float[] start = new float[3];
235 float[] end = new float[3];
245 bonds.addElement(new Bond(start, end, at1, at2));
248 public void makeResidueList()
252 boolean deoxyn = false;
253 boolean nucleotide = false;
254 StringBuffer seq = new StringBuffer();
255 Vector resFeatures = new Vector();
256 Vector resAnnotation = new Vector();
257 int i, iSize = atoms.size() - 1;
259 for (i = 0; i <= iSize; i++)
261 Atom tmp = (Atom) atoms.elementAt(i);
262 resNumber = tmp.resNumber;
270 Vector resAtoms = new Vector();
271 // Add atoms to a vector while the residue number
272 // remains the same as the first atom's resNumber (res)
273 while ((resNumber == res) && (i < atoms.size()))
275 resAtoms.addElement((Atom) atoms.elementAt(i));
278 if (i < atoms.size())
280 resNumber = ((Atom) atoms.elementAt(i)).resNumber;
288 // We need this to keep in step with the outer for i = loop
291 // Make a new Residue object with the new atoms vector
292 residues.addElement(new Residue(resAtoms, resNumber - 1, count));
294 Residue tmpres = (Residue) residues.lastElement();
295 Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
296 // Make A new SequenceFeature for the current residue numbering
297 SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
298 + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
299 + count, offset + count, pdbid);
300 // MCview.PDBChain.PDBFILEFEATURE);
301 resFeatures.addElement(sf);
302 resAnnotation.addElement(new Annotation(tmpat.tfactor));
303 // Keep totting up the sequence
304 if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
306 String nucname = tmpat.resName.trim();
307 // use the aaIndex rather than call 'toLower' - which would take a bit
309 deoxyn = nucname.length() == 2
310 && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
311 if (tmpat.name.equalsIgnoreCase("CA")
312 || ResidueProperties.nucleotideIndex[nucname
313 .charAt((deoxyn ? 1 : 0))] == -1)
316 // System.err.println("PDBReader:Null aa3Hash for " +
323 seq.append(nucname.charAt((deoxyn ? 1 : 0)));
331 .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
333 seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
343 sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
347 // Add normalised feature scores to RESNUM indicating start/end of sequence
348 // sf.setScore(offset+count);
350 // System.out.println("PDB Sequence is :\nSequence = " + seq);
351 // System.out.println("No of residues = " + residues.size());
352 for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
354 sequence.addSequenceFeature((SequenceFeature) resFeatures
356 resFeatures.setElementAt(null, i);
358 Annotation[] annots = new Annotation[resAnnotation.size()];
360 for (i = 0, iSize = annots.length; i < iSize; i++)
362 annots[i] = (Annotation) resAnnotation.elementAt(i);
363 if (annots[i].value > max)
364 max = annots[i].value;
365 resAnnotation.setElementAt(null, i);
367 AlignmentAnnotation tfactorann = new AlignmentAnnotation(
368 "PDB.TempFactor", "Temperature Factor for "
369 + sequence.getName(), annots, 0, max,
370 AlignmentAnnotation.LINE_GRAPH);
371 tfactorann.setSequenceRef(sequence);
372 sequence.addAlignmentAnnotation(tfactorann);
375 public void setChargeColours()
377 for (int i = 0; i < bonds.size(); i++)
381 Bond b = (Bond) bonds.elementAt(i);
383 if (b.at1.resName.equalsIgnoreCase("ASP")
384 || b.at1.resName.equalsIgnoreCase("GLU"))
386 b.startCol = Color.red;
388 else if (b.at1.resName.equalsIgnoreCase("LYS")
389 || b.at1.resName.equalsIgnoreCase("ARG"))
391 b.startCol = Color.blue;
393 else if (b.at1.resName.equalsIgnoreCase("CYS"))
395 b.startCol = Color.yellow;
399 b.startCol = Color.lightGray;
402 if (b.at2.resName.equalsIgnoreCase("ASP")
403 || b.at2.resName.equalsIgnoreCase("GLU"))
405 b.endCol = Color.red;
407 else if (b.at2.resName.equalsIgnoreCase("LYS")
408 || b.at2.resName.equalsIgnoreCase("ARG"))
410 b.endCol = Color.blue;
412 else if (b.at2.resName.equalsIgnoreCase("CYS"))
414 b.endCol = Color.yellow;
418 b.endCol = Color.lightGray;
420 } catch (Exception e)
422 Bond b = (Bond) bonds.elementAt(i);
423 b.startCol = Color.gray;
424 b.endCol = Color.gray;
429 public void setChainColours(jalview.schemes.ColourSchemeI cs)
433 for (int i = 0; i < bonds.size(); i++)
437 b = (Bond) bonds.elementAt(i);
439 index = ((Integer) ResidueProperties.aa3Hash.get(b.at1.resName))
441 b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
443 index = ((Integer) ResidueProperties.aa3Hash.get(b.at2.resName))
445 b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
447 } catch (Exception e)
449 b = (Bond) bonds.elementAt(i);
450 b.startCol = Color.gray;
451 b.endCol = Color.gray;
456 public void setChainColours(Color col)
458 for (int i = 0; i < bonds.size(); i++)
460 Bond tmp = (Bond) bonds.elementAt(i);
466 public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq,
469 AlignmentAnnotation[] transferred = null;
476 * copy any sequence annotation onto the sequence mapped using the provided
481 public void transferResidueAnnotation(StructureMapping mapping)
483 SequenceI sq = mapping.getSequence();
486 if (sequence != null && sequence.getAnnotation() != null)
490 float min = -1, max = 0;
491 Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
492 for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
494 int prn = mapping.getPDBResNum(k + 1);
496 an[k] = new Annotation((float) prn);
514 sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
515 "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
516 an, (float) min, (float) max, AlignmentAnnotation.LINE_GRAPH));