2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignSeq;
24 import jalview.datamodel.AlignmentAnnotation;
25 import jalview.datamodel.Annotation;
26 import jalview.datamodel.Mapping;
27 import jalview.datamodel.Sequence;
28 import jalview.datamodel.SequenceFeature;
29 import jalview.datamodel.SequenceI;
30 import jalview.schemes.ColourSchemeI;
31 import jalview.schemes.ResidueProperties;
32 import jalview.structure.StructureMapping;
34 import java.awt.Color;
35 import java.util.List;
36 import java.util.Vector;
41 * SequenceFeature group for PDB File features added to sequences
43 private static final String PDBFILEFEATURE = "PDBFile";
45 private static final String IEASTATUS = "IEA:jalview";
49 public Vector<Bond> bonds = new Vector<Bond>();
51 public Vector<Atom> atoms = new Vector<Atom>();
53 public Vector<Residue> residues = new Vector<Residue>();
58 * sequence is the sequence extracted by the chain parsing code
60 public SequenceI sequence;
63 * shadow is the sequence created by any other parsing processes (e.g. Jmol,
66 public SequenceI shadow = null;
68 public boolean isNa = false;
70 public boolean isVisible = true;
72 public int pdbstart = 0;
74 public int pdbend = 0;
76 public int seqstart = 0;
78 public int seqend = 0;
80 public String pdbid = "";
82 public PDBChain(String pdbid, String id)
84 this.pdbid = pdbid.toLowerCase();
89 * character used to write newlines
91 protected String newline = System.getProperty("line.separator");
93 public Mapping shadowMap;
95 public void setNewlineString(String nl)
100 public String getNewlineString()
105 public String print()
107 StringBuilder tmp = new StringBuilder(256);
111 tmp.append(b.at1.resName).append(" ").append(b.at1.resNumber)
112 .append(" ").append(offset).append(newline);
115 return tmp.toString();
119 * Annotate the residues with their corresponding positions in s1 using the
120 * alignment in as NOTE: This clears all atom.alignmentMapping values on the
126 public void makeExactMapping(AlignSeq as, SequenceI s1)
128 int pdbpos = as.getSeq2Start() - 2;
129 int alignpos = s1.getStart() + as.getSeq1Start() - 3;
130 // first clear out any old alignmentMapping values:
131 for (Atom atom : atoms)
133 atom.alignmentMapping = -1;
135 // and now trace the alignment onto the atom set.
136 for (int i = 0; i < as.astr1.length(); i++)
138 if (as.astr1.charAt(i) != '-')
143 if (as.astr2.charAt(i) != '-')
148 if (as.astr1.charAt(i) == as.astr2.charAt(i))
150 if (pdbpos >= residues.size())
154 Residue res = residues.elementAt(pdbpos);
155 for (Atom atom : res.atoms)
157 atom.alignmentMapping = alignpos;
164 * copy over the RESNUM seqfeatures from the internal chain sequence to the
169 * The Status of the transferred annotation
170 * @return the features added to sq (or its dataset)
172 public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
176 while (sq != null && sq.getDatasetSequence() != null)
178 sq = sq.getDatasetSequence();
185 * Remove any existing features for this chain if they exist ?
186 * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
187 * totfeat=seqsfeatures.length; // Remove any features for this exact chain
188 * ? for (int i=0; i<seqsfeatures.length; i++) { }
192 status = PDBChain.IEASTATUS;
194 SequenceFeature[] features = sequence.getSequenceFeatures();
195 for (int i = 0; i < features.length; i++)
197 if (features[i].getFeatureGroup().equals(pdbid))
199 SequenceFeature tx = new SequenceFeature(features[i]);
200 tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
201 .elementAt(0).alignmentMapping);
202 tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
203 .elementAt(0).alignmentMapping);
205 + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
206 : ":" + tx.getStatus()));
207 if (tx.begin != 0 && tx.end != 0)
209 sq.addSequenceFeature(tx);
217 * Traverses the list of residues and constructs bonds where CA-to-CA atoms or
218 * P-to-P atoms are found. Also sets the 'isNa' flag if more than 99% of
219 * residues contain a P not a CA.
221 public void makeCaBondList()
225 for (int i = 0; i < (residues.size() - 1); i++)
227 Residue tmpres = residues.elementAt(i);
228 Residue tmpres2 = residues.elementAt(i + 1);
229 Atom at1 = tmpres.findAtom("CA");
230 Atom at2 = tmpres2.findAtom("CA");
232 if ((at1 == null) && (at2 == null))
235 at1 = tmpres.findAtom("P");
236 at2 = tmpres2.findAtom("P");
238 if ((at1 != null) && (at2 != null))
240 if (at1.chain.equals(at2.chain))
251 System.out.println("not found " + i);
256 * If > 99% 'P', flag as nucleotide; note the count doesn't include the last
259 if (residues.size() > 1 && (numNa / (residues.size() - 1) > 0.99))
266 * Construct a bond from atom1 to atom2 and add it to the list of bonds for
272 public void makeBond(Atom at1, Atom at2)
274 bonds.addElement(new Bond(at1, at2));
278 * Traverses the list of atoms and
280 * <li>constructs a list of Residues, each containing all the atoms that share
281 * the same residue number</li>
282 * <li>adds a RESNUM sequence feature for each position</li>
283 * <li>creates the sequence string</li>
284 * <li>determines if nucleotide</li>
285 * <li>saves the residue number of the first atom as 'offset'</li>
286 * <li>adds temp factor annotation if the flag is set to do so</li>
289 * @param visibleChainAnnotation
291 public void makeResidueList(boolean visibleChainAnnotation)
295 boolean deoxyn = false;
296 boolean nucleotide = false;
297 StringBuilder seq = new StringBuilder(256);
298 Vector<SequenceFeature> resFeatures = new Vector<SequenceFeature>();
299 Vector<Annotation> resAnnotation = new Vector<Annotation>();
300 int i, iSize = atoms.size() - 1;
303 for (i = 0; i <= iSize; i++)
305 Atom tmp = atoms.elementAt(i);
306 resNumber = tmp.resNumber;
307 insCode = tmp.insCode;
317 Vector<Atom> resAtoms = new Vector<Atom>();
318 // Add atoms to a vector while the residue number
319 // remains the same as the first atom's resNumber (res)
320 while ((resNumber == res) && (ins == insCode) && (i < atoms.size()))
322 resAtoms.add(atoms.elementAt(i));
325 if (i < atoms.size())
327 resNumber = atoms.elementAt(i).resNumber;
328 insCode = atoms.elementAt(i).insCode;
336 // We need this to keep in step with the outer for i = loop
339 // Add inserted residues as features to the base residue
340 Atom currAtom = resAtoms.get(0);
341 if (currAtom.insCode != ' '
342 && residues.lastElement().atoms.get(0).resNumber == currAtom.resNumber)
344 SequenceFeature sf = new SequenceFeature("INSERTION",
345 currAtom.resName + ":" + currAtom.resNumIns + " " + pdbid
346 + id, "", offset + count - 1, offset + count - 1,
348 resFeatures.addElement(sf);
349 residues.lastElement().atoms.addAll(resAtoms);
354 // Make a new Residue object with the new atoms vector
355 residues.addElement(new Residue(resAtoms, resNumber - 1, count));
357 Residue tmpres = residues.lastElement();
358 Atom tmpat = tmpres.atoms.get(0);
359 // Make A new SequenceFeature for the current residue numbering
360 SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
361 + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
362 + count, offset + count, pdbid);
363 // MCview.PDBChain.PDBFILEFEATURE);
364 resFeatures.addElement(sf);
365 resAnnotation.addElement(new Annotation(tmpat.tfactor));
366 // Keep totting up the sequence
367 if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
369 String nucname = tmpat.resName.trim();
370 // use the aaIndex rather than call 'toLower' - which would take a bit
372 deoxyn = nucname.length() == 2
373 && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
374 if (tmpat.name.equalsIgnoreCase("CA")
375 || ResidueProperties.nucleotideIndex[nucname
376 .charAt((deoxyn ? 1 : 0))] == -1)
379 // System.err.println("PDBReader:Null aa3Hash for " +
386 seq.append(nucname.charAt((deoxyn ? 1 : 0)));
394 .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
396 seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
407 sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
411 // Add normalised feature scores to RESNUM indicating start/end of sequence
412 // sf.setScore(offset+count);
414 // System.out.println("PDB Sequence is :\nSequence = " + seq);
415 // System.out.println("No of residues = " + residues.size());
416 for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
418 sequence.addSequenceFeature(resFeatures.elementAt(i));
419 resFeatures.setElementAt(null, i);
421 if (visibleChainAnnotation)
423 Annotation[] annots = new Annotation[resAnnotation.size()];
425 for (i = 0, iSize = annots.length; i < iSize; i++)
427 annots[i] = resAnnotation.elementAt(i);
428 if (annots[i].value > max)
430 max = annots[i].value;
432 resAnnotation.setElementAt(null, i);
435 AlignmentAnnotation tfactorann = new AlignmentAnnotation(
436 "Temperature Factor", "Temperature Factor for " + pdbid + id,
437 annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
438 tfactorann.setSequenceRef(sequence);
439 sequence.addAlignmentAnnotation(tfactorann);
444 * Colour start/end of bonds by charge
446 * <li>ASP and GLU red</li>
447 * <li>LYS and ARG blue</li>
448 * <li>CYS yellow</li>
449 * <li>others light gray</li>
452 public void setChargeColours()
456 if (b.at1 != null && b.at2 != null)
458 b.startCol = getChargeColour(b.at1.resName);
459 b.endCol = getChargeColour(b.at2.resName);
463 b.startCol = Color.gray;
464 b.endCol = Color.gray;
469 public static Color getChargeColour(String resName)
471 Color result = Color.lightGray;
472 if ("ASP".equals(resName) || "GLU".equals(resName))
476 else if ("LYS".equals(resName) || "ARG".equals(resName))
480 else if ("CYS".equals(resName))
482 result = Color.yellow;
488 * Sets the start/end colours of bonds to those of the start/end atoms
489 * according to the specified colour scheme. Note: currently only works for
494 public void setChainColours(ColourSchemeI cs)
501 index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
502 b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
504 index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
505 b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
507 } catch (Exception e)
509 b.startCol = Color.gray;
510 b.endCol = Color.gray;
515 public void setChainColours(Color col)
525 * copy any sequence annotation onto the sequence mapped using the provided
529 * - positional mapping between destination sequence and pdb resnum
531 * - mapping between destination sequence and local chain
533 public void transferResidueAnnotation(StructureMapping mapping,
534 jalview.datamodel.Mapping sqmpping)
536 SequenceI sq = mapping.getSequence();
540 while (dsq.getDatasetSequence() != null)
542 dsq = dsq.getDatasetSequence();
544 // any annotation will be transferred onto the dataset sequence
546 if (shadow != null && shadow.getAnnotation() != null)
549 for (AlignmentAnnotation ana : shadow.getAnnotation())
551 List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
552 ana.getCalcId(), ana.label);
553 if (transfer == null || transfer.size() == 0)
555 ana = new AlignmentAnnotation(ana);
556 ana.liftOver(sequence, shadowMap);
557 ana.liftOver(dsq, sqmpping);
558 dsq.addAlignmentAnnotation(ana);
568 if (sequence != null && sequence.getAnnotation() != null)
570 for (AlignmentAnnotation ana : sequence.getAnnotation())
572 List<AlignmentAnnotation> transfer = sq
573 .getAlignmentAnnotations(ana.getCalcId(), ana.label);
574 if (transfer == null || transfer.size() == 0)
576 ana = new AlignmentAnnotation(ana);
577 ana.liftOver(dsq, sqmpping);
578 // mapping.transfer(ana);
589 // Useful for debugging mappings - adds annotation for mapped position
590 float min = -1, max = 0;
591 Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
592 for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
594 int prn = mapping.getPDBResNum(k + 1);
596 an[k] = new Annotation(prn);
614 sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
615 "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
616 an, min, max, AlignmentAnnotation.LINE_GRAPH));