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.
21 package jalview.ext.jmol;
23 import jalview.datamodel.AlignmentAnnotation;
24 import jalview.datamodel.Annotation;
25 import jalview.datamodel.PDBEntry;
26 import jalview.datamodel.SequenceI;
27 import jalview.io.DataSourceType;
28 import jalview.io.FileParse;
29 import jalview.io.StructureFile;
30 import jalview.schemes.ResidueProperties;
31 import jalview.structure.StructureImportSettings;
32 import jalview.util.Format;
33 import jalview.util.MessageManager;
35 import java.io.IOException;
36 import java.util.ArrayList;
37 import java.util.HashMap;
38 import java.util.List;
40 import java.util.Vector;
42 import org.jmol.api.JmolStatusListener;
43 import org.jmol.api.JmolViewer;
44 import org.jmol.c.CBK;
45 import org.jmol.c.STR;
46 import org.jmol.modelset.ModelSet;
47 import org.jmol.viewer.Viewer;
50 import MCview.PDBChain;
51 import MCview.Residue;
54 * Import and process files with Jmol for file like PDB, mmCIF
59 public class JmolParser extends StructureFile implements JmolStatusListener
63 public JmolParser(String inFile, DataSourceType sourceType)
66 super(inFile, sourceType);
69 public JmolParser(FileParse fp) throws IOException
79 * Calls the Jmol library to parse the PDB/mmCIF file, and then inspects the
80 * resulting object model to generate Jalview-style sequences, with secondary
81 * structure annotation added where available (i.e. where it has been computed
82 * by Jmol using DSSP).
84 * @see jalview.io.AlignFile#parse()
87 public void parse() throws IOException
89 setChains(new Vector<PDBChain>());
90 Viewer jmolModel = getJmolData();
91 jmolModel.openReader(getDataName(), getDataName(), getReader());
92 waitForScript(jmolModel);
95 * Convert one or more Jmol Model objects to Jalview sequences
97 if (jmolModel.ms.mc > 0)
102 // setStructureFileType(jmolModel.evalString("show _fileType"));
103 // } catch (Exception q)
107 // instead, we distinguish .cif from non-.cif by filename
108 setStructureFileType(getDataName().toLowerCase().endsWith(".cif") ? PDBEntry.Type.MMCIF
109 .toString() : "PDB");
111 transformJmolModelToJalview(jmolModel.ms);
116 * create a headless jmol instance for dataprocessing
120 private Viewer getJmolData()
127 * params -o (output to sysout) -n (nodisplay) -x (exit when finished)
128 * see http://wiki.jmol.org/index.php/Jmol_Application
130 viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
131 null, "-x -o -n", this);
132 // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
133 viewer.setBooleanProperty("defaultStructureDSSP", true);
134 } catch (ClassCastException x)
136 throw new Error(MessageManager.formatMessage(
137 "error.jmol_version_not_compatible_with_jalview_version",
138 new String[] { JmolViewer.getJmolVersion() }), x);
144 public void transformJmolModelToJalview(ModelSet ms) throws IOException
149 List<SequenceI> rna = new ArrayList<SequenceI>();
150 List<SequenceI> prot = new ArrayList<SequenceI>();
152 String pdbId = (String) ms.getInfo(0, "title");
156 setId(safeName(getDataName()));
157 setPDBIdAvailable(false);
162 setPDBIdAvailable(true);
164 List<Atom> significantAtoms = convertSignificantAtoms(ms);
165 for (Atom tmpatom : significantAtoms)
169 tmpchain = findChain(tmpatom.chain);
170 if (tmpatom.resNumIns.trim().equals(lastID))
172 // phosphorylated protein - seen both CA and P..
175 tmpchain.atoms.addElement(tmpatom);
176 } catch (Exception e)
178 tmpchain = new PDBChain(getId(), tmpatom.chain);
179 getChains().add(tmpchain);
180 tmpchain.atoms.addElement(tmpatom);
182 lastID = tmpatom.resNumIns.trim();
189 for (PDBChain chain : getChains())
191 SequenceI chainseq = postProcessChain(chain);
201 if (StructureImportSettings.isProcessSecondaryStructure())
203 createAnnotation(chainseq, chain, ms.at);
206 } catch (OutOfMemoryError er)
209 .println("OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
210 throw new IOException(
212 .getString("exception.outofmemory_loading_mmcif_file"));
216 private List<Atom> convertSignificantAtoms(ModelSet ms)
218 List<Atom> significantAtoms = new ArrayList<Atom>();
219 HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>();
220 org.jmol.modelset.Atom prevAtom = null;
221 for (org.jmol.modelset.Atom atom : ms.at)
223 if (atom.getAtomName().equalsIgnoreCase("CA")
224 || atom.getAtomName().equalsIgnoreCase("P"))
226 if (!atomValidated(atom, prevAtom, chainTerMap))
230 Atom curAtom = new Atom(atom.x, atom.y, atom.z);
231 curAtom.atomIndex = atom.getIndex();
232 curAtom.chain = atom.getChainIDStr();
233 curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' '
234 : atom.group.getInsertionCode();
235 curAtom.name = atom.getAtomName();
236 curAtom.number = atom.getAtomNumber();
237 curAtom.resName = atom.getGroup3(true);
238 curAtom.resNumber = atom.getResno();
239 curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
240 .getIndex()] : Float.valueOf(atom.getOccupancy100());
241 String fmt = new Format("%4i").form(curAtom.resNumber);
242 curAtom.resNumIns = (fmt + curAtom.insCode);
243 curAtom.tfactor = atom.getBfactor100() / 100f;
245 // significantAtoms.add(curAtom);
246 // ignore atoms from subsequent models
247 if (!significantAtoms.contains(curAtom))
249 significantAtoms.add(curAtom);
254 return significantAtoms;
257 private boolean atomValidated(org.jmol.modelset.Atom curAtom,
258 org.jmol.modelset.Atom prevAtom,
259 HashMap<String, org.jmol.modelset.Atom> chainTerMap)
261 // System.out.println("Atom: " + curAtom.getAtomNumber()
262 // + " Last atom index " + curAtom.group.lastAtomIndex);
263 if (chainTerMap == null || prevAtom == null)
267 String curAtomChId = curAtom.getChainIDStr();
268 String prevAtomChId = prevAtom.getChainIDStr();
269 // new chain encoutered
270 if (!prevAtomChId.equals(curAtomChId))
272 // On chain switch add previous chain termination to xTerMap if not exists
273 if (!chainTerMap.containsKey(prevAtomChId))
275 chainTerMap.put(prevAtomChId, prevAtom);
277 // if current atom belongs to an already terminated chain and the resNum
278 // diff < 5 then mark as valid and update termination Atom
279 if (chainTerMap.containsKey(curAtomChId))
281 if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
285 if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
287 chainTerMap.put(curAtomChId, curAtom);
293 // atom with previously terminated chain encountered
294 else if (chainTerMap.containsKey(curAtomChId))
296 if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
300 if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
302 chainTerMap.put(curAtomChId, curAtom);
307 // HETATM with resNum jump > 2
308 return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
312 private void createAnnotation(SequenceI sequence, PDBChain chain,
313 org.jmol.modelset.Atom[] jmolAtoms)
315 char[] secstr = new char[sequence.getLength()];
316 char[] secstrcode = new char[sequence.getLength()];
318 // Ensure Residue size equals Seq size
319 if (chain.residues.size() != sequence.getLength())
324 for (Residue residue : chain.residues)
326 Atom repAtom = residue.getAtoms().get(0);
327 STR proteinStructureSubType = jmolAtoms[repAtom.atomIndex].group
328 .getProteinStructureSubType();
329 setSecondaryStructure(proteinStructureSubType, annotIndex, secstr,
333 addSecondaryStructureAnnotation(chain.pdbid, sequence, secstr,
334 secstrcode, chain.id, sequence.getStart());
338 * Helper method that adds an AlignmentAnnotation for secondary structure to
339 * the sequence, provided at least one secondary structure prediction has been
350 protected void addSecondaryStructureAnnotation(String modelTitle,
351 SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
354 char[] seq = sq.getSequence();
355 boolean ssFound = false;
356 Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
357 for (int p = 0; p < seq.length; p++)
359 if (secstr[p] >= 'A' && secstr[p] <= 'z')
363 asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
364 secstrcode[p], Float.NaN);
366 } catch (Exception e)
368 // e.printStackTrace();
375 String mt = modelTitle == null ? getDataName() : modelTitle;
377 AlignmentAnnotation ann = new AlignmentAnnotation(
378 "Secondary Structure", "Secondary Structure for " + mt,
380 ann.belowAlignment = true;
382 ann.autoCalculated = false;
383 ann.setCalcId(getClass().getName());
384 ann.adjustForAlignment();
385 ann.validateRangeAndDisplay();
386 annotations.add(ann);
387 sq.addAlignmentAnnotation(ann);
391 private void waitForScript(Viewer jmd)
393 while (jmd.isScriptExecuting())
399 } catch (InterruptedException x)
406 * Convert Jmol's secondary structure code to Jalview's, and stored it in the
407 * secondary structure arrays at the given sequence position
409 * @param proteinStructureSubType
414 protected void setSecondaryStructure(STR proteinStructureSubType,
415 int pos, char[] secstr, char[] secstrcode)
417 switch (proteinStructureSubType)
436 switch (proteinStructureSubType)
442 secstrcode[pos] = 'H';
445 secstrcode[pos] = 'E';
453 * Convert any non-standard peptide codes to their standard code table
454 * equivalent. (Initial version only does Selenomethionine MSE->MET.)
456 * @param threeLetterCode
460 protected void replaceNonCanonicalResidue(String threeLetterCode,
463 String canonical = ResidueProperties
464 .getCanonicalAminoAcid(threeLetterCode);
465 if (canonical != null && !canonical.equalsIgnoreCase(threeLetterCode))
467 seq[pos] = ResidueProperties.getSingleCharacterCode(canonical);
472 * Not implemented - returns null
475 public String print(SequenceI[] seqs, boolean jvSuffix)
484 public void setCallbackFunction(String callbackType,
485 String callbackFunction)
490 public void notifyCallback(CBK cbType, Object[] data)
492 String strInfo = (data == null || data[1] == null ? null : data[1]
497 sendConsoleEcho(strInfo);
500 notifyScriptTermination((String) data[2],
501 ((Integer) data[3]).intValue());
504 String mystatus = (String) data[3];
505 if (mystatus.indexOf("Picked") >= 0
506 || mystatus.indexOf("Sequence") >= 0)
509 sendConsoleMessage(strInfo);
511 else if (mystatus.indexOf("Completed") >= 0)
513 sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
514 strInfo.length() - 1));
518 sendConsoleMessage(data == null ? null : strInfo);
521 sendConsoleMessage(strInfo);
528 String lastConsoleEcho = "";
530 private void sendConsoleEcho(String string)
532 lastConsoleEcho += string;
533 lastConsoleEcho += "\n";
536 String lastConsoleMessage = "";
538 private void sendConsoleMessage(String string)
540 lastConsoleMessage += string;
541 lastConsoleMessage += "\n";
544 int lastScriptTermination = -1;
546 String lastScriptMessage = "";
548 private void notifyScriptTermination(String string, int intValue)
550 lastScriptMessage += string;
551 lastScriptMessage += "\n";
552 lastScriptTermination = intValue;
556 public boolean notifyEnabled(CBK callbackPick)
558 switch (callbackPick)
572 * Not implemented - returns null
575 public String eval(String strEval)
581 * Not implemented - returns null
584 public float[][] functionXY(String functionName, int x, int y)
590 * Not implemented - returns null
593 public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
599 * Not implemented - returns null
602 public String createImage(String fileName, String imageType,
603 Object text_or_bytes, int quality)
609 * Not implemented - returns null
612 public Map<String, Object> getRegistryInfo()
621 public void showUrl(String url)
626 * Not implemented - returns null
629 public int[] resizeInnerPanel(String data)
635 public Map<String, Object> getJSpecViewProperty(String arg0)
640 public boolean isPredictSecondaryStructure()
642 return predictSecondaryStructure;
645 public void setPredictSecondaryStructure(boolean predictSecondaryStructure)
647 this.predictSecondaryStructure = predictSecondaryStructure;
650 public boolean isVisibleChainAnnotation()
652 return visibleChainAnnotation;
655 public void setVisibleChainAnnotation(boolean visibleChainAnnotation)
657 this.visibleChainAnnotation = visibleChainAnnotation;