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.SequenceI;
26 import jalview.io.FileParse;
27 import jalview.io.StructureFile;
28 import jalview.schemes.ResidueProperties;
29 import jalview.structure.StructureImportSettings;
30 import jalview.util.MessageManager;
32 import java.io.IOException;
33 import java.util.ArrayList;
34 import java.util.HashMap;
35 import java.util.List;
37 import java.util.Vector;
39 import javajs.awt.Dimension;
41 import org.jmol.api.JmolStatusListener;
42 import org.jmol.api.JmolViewer;
43 import org.jmol.c.CBK;
44 import org.jmol.c.STR;
45 import org.jmol.modelset.ModelSet;
46 import org.jmol.viewer.Viewer;
49 import MCview.PDBChain;
50 import MCview.Residue;
53 * Import and process files with Jmol for file like PDB, mmCIF
58 public class JmolParser extends StructureFile implements JmolStatusListener
62 public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
63 boolean externalSecStr, String inFile, String type)
69 public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
70 boolean externalSecStr, FileParse fp) throws IOException
80 * Calls the Jmol library to parse the PDB/mmCIF file, and then inspects the
81 * resulting object model to generate Jalview-style sequences, with secondary
82 * structure annotation added where available (i.e. where it has been computed
83 * by Jmol using DSSP).
85 * @see jalview.io.AlignFile#parse()
88 public void parse() throws IOException
90 setChains(new Vector<PDBChain>());
91 Viewer jmolModel = getJmolData();
92 jmolModel.openReader(getDataName(), getDataName(), getReader());
93 waitForScript(jmolModel);
96 * Convert one or more Jmol Model objects to Jalview sequences
98 if (jmolModel.ms.mc > 0)
100 transformJmolModelToJalview(jmolModel.ms);
105 * create a headless jmol instance for dataprocessing
109 private Viewer getJmolData()
115 viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
116 null, "-x -o -n", this);
117 // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
118 viewer.setBooleanProperty("defaultStructureDSSP", true);
119 } catch (ClassCastException x)
121 throw new Error(MessageManager.formatMessage(
122 "error.jmol_version_not_compatible_with_jalview_version",
123 new String[] { JmolViewer.getJmolVersion() }), x);
129 public void transformJmolModelToJalview(ModelSet ms) throws IOException
134 List<SequenceI> rna = new ArrayList<SequenceI>();
135 List<SequenceI> prot = new ArrayList<SequenceI>();
137 String pdbId = (String) ms.getInfo(0, "title");
139 List<Atom> significantAtoms = convertSignificantAtoms(ms);
140 for (Atom tmpatom : significantAtoms)
144 tmpchain = findChain(tmpatom.chain);
145 if (tmpatom.resNumIns.trim().equals(lastID))
147 // phosphorylated protein - seen both CA and P..
150 tmpchain.atoms.addElement(tmpatom);
151 } catch (Exception e)
153 tmpchain = new PDBChain(pdbId, tmpatom.chain);
154 getChains().add(tmpchain);
155 tmpchain.atoms.addElement(tmpatom);
157 lastID = tmpatom.resNumIns.trim();
166 setId(safeName(getDataName()));
168 for (PDBChain chain : getChains())
170 SequenceI chainseq = postProcessChain(chain);
180 if (StructureImportSettings.isProcessSecondaryStructure())
182 createAnnotation(chainseq, chain, ms.at);
185 } catch (OutOfMemoryError er)
188 .println("OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
189 throw new IOException(
191 .getString("exception.outofmemory_loading_mmcif_file"));
195 private List<Atom> convertSignificantAtoms(ModelSet ms)
197 List<Atom> significantAtoms = new ArrayList<Atom>();
198 HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>();
199 org.jmol.modelset.Atom prevAtom = null;
200 for (org.jmol.modelset.Atom atom : ms.at)
202 if (atom.getAtomName().equalsIgnoreCase("CA")
203 || atom.getAtomName().equalsIgnoreCase("P"))
205 if (!atomValidated(atom, prevAtom, chainTerMap))
209 Atom curAtom = new Atom(atom.x, atom.y, atom.z);
210 curAtom.atomIndex = atom.getIndex();
211 curAtom.chain = atom.getChainIDStr();
212 curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' '
213 : atom.group.getInsertionCode();
214 curAtom.name = atom.getAtomName();
215 curAtom.number = atom.getAtomNumber();
216 curAtom.resName = atom.getGroup3(true);
217 curAtom.resNumber = atom.getResno();
218 curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
219 .getIndex()] : Float.valueOf(atom.getOccupancy100());
220 curAtom.resNumIns = ("" + curAtom.resNumber + curAtom.insCode)
222 curAtom.tfactor = atom.getBfactor100() / 100f;
224 // significantAtoms.add(curAtom);
225 // ignore atoms from subsequent models
226 if (!significantAtoms.contains(curAtom))
228 significantAtoms.add(curAtom);
233 return significantAtoms;
236 private boolean atomValidated(org.jmol.modelset.Atom curAtom,
237 org.jmol.modelset.Atom prevAtom,
238 HashMap<String, org.jmol.modelset.Atom> chainTerMap)
240 // System.out.println("Atom: " + curAtom.getAtomNumber()
241 // + " Last atom index " + curAtom.group.lastAtomIndex);
242 if (chainTerMap == null || prevAtom == null)
246 String curAtomChId = curAtom.getChainIDStr();
247 String prevAtomChId = prevAtom.getChainIDStr();
248 // new chain encoutered
249 if (!prevAtomChId.equals(curAtomChId))
251 // On chain switch add previous chain termination to xTerMap if not exists
252 if (!chainTerMap.containsKey(prevAtomChId))
254 chainTerMap.put(prevAtomChId, prevAtom);
256 // if current atom belongs to an already terminated chain and the resNum
257 // diff < 5 then mark as valid and update termination Atom
258 if (chainTerMap.containsKey(curAtomChId))
260 if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
262 chainTerMap.put(curAtomChId, curAtom);
268 // atom with previously terminated chain encountered
269 else if (chainTerMap.containsKey(curAtomChId))
271 if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
273 chainTerMap.put(curAtomChId, curAtom);
278 // HETATM with resNum jump > 2
279 return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
283 private void createAnnotation(SequenceI sequence, PDBChain chain,
284 org.jmol.modelset.Atom[] jmolAtoms)
286 char[] secstr = new char[sequence.getLength()];
287 char[] secstrcode = new char[sequence.getLength()];
289 // Ensure Residue size equals Seq size
290 if (chain.residues.size() != sequence.getLength())
295 for (Residue residue : chain.residues)
297 Atom repAtom = residue.getAtoms().get(0);
298 STR proteinStructureSubType = jmolAtoms[repAtom.atomIndex].group
299 .getProteinStructureSubType();
300 setSecondaryStructure(proteinStructureSubType, annotIndex, secstr,
304 addSecondaryStructureAnnotation(chain.pdbid, sequence, secstr,
305 secstrcode, chain.id, sequence.getStart());
309 * Helper method that adds an AlignmentAnnotation for secondary structure to
310 * the sequence, provided at least one secondary structure prediction has been
321 protected void addSecondaryStructureAnnotation(String modelTitle,
322 SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
325 char[] seq = sq.getSequence();
326 boolean ssFound = false;
327 Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
328 for (int p = 0; p < seq.length; p++)
330 if (secstr[p] >= 'A' && secstr[p] <= 'z')
334 asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
335 secstrcode[p], Float.NaN);
337 } catch (Exception e)
339 // e.printStackTrace();
346 String mt = modelTitle == null ? getDataName() : modelTitle;
348 AlignmentAnnotation ann = new AlignmentAnnotation(
349 "Secondary Structure", "Secondary Structure for " + mt,
351 ann.belowAlignment = true;
353 ann.autoCalculated = false;
354 ann.setCalcId(getClass().getName());
355 ann.adjustForAlignment();
356 ann.validateRangeAndDisplay();
357 annotations.add(ann);
358 sq.addAlignmentAnnotation(ann);
362 private void waitForScript(Viewer jmd)
364 while (jmd.isScriptExecuting())
370 } catch (InterruptedException x)
377 * Convert Jmol's secondary structure code to Jalview's, and stored it in the
378 * secondary structure arrays at the given sequence position
380 * @param proteinStructureSubType
385 protected void setSecondaryStructure(STR proteinStructureSubType,
386 int pos, char[] secstr, char[] secstrcode)
388 switch (proteinStructureSubType)
407 switch (proteinStructureSubType)
413 secstrcode[pos] = 'H';
416 secstrcode[pos] = 'E';
424 * Convert any non-standard peptide codes to their standard code table
425 * equivalent. (Initial version only does Selenomethionine MSE->MET.)
427 * @param threeLetterCode
431 protected void replaceNonCanonicalResidue(String threeLetterCode,
434 String canonical = ResidueProperties
435 .getCanonicalAminoAcid(threeLetterCode);
436 if (canonical != null && !canonical.equalsIgnoreCase(threeLetterCode))
438 seq[pos] = ResidueProperties.getSingleCharacterCode(canonical);
443 * Not implemented - returns null
446 public String print()
455 public void setCallbackFunction(String callbackType,
456 String callbackFunction)
461 public void notifyCallback(CBK cbType, Object[] data)
463 String strInfo = (data == null || data[1] == null ? null : data[1]
468 sendConsoleEcho(strInfo);
471 notifyScriptTermination((String) data[2],
472 ((Integer) data[3]).intValue());
475 String mystatus = (String) data[3];
476 if (mystatus.indexOf("Picked") >= 0
477 || mystatus.indexOf("Sequence") >= 0)
480 sendConsoleMessage(strInfo);
482 else if (mystatus.indexOf("Completed") >= 0)
484 sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
485 strInfo.length() - 1));
489 sendConsoleMessage(data == null ? null : strInfo);
492 sendConsoleMessage(strInfo);
499 String lastConsoleEcho = "";
501 private void sendConsoleEcho(String string)
503 lastConsoleEcho += string;
504 lastConsoleEcho += "\n";
507 String lastConsoleMessage = "";
509 private void sendConsoleMessage(String string)
511 lastConsoleMessage += string;
512 lastConsoleMessage += "\n";
515 int lastScriptTermination = -1;
517 String lastScriptMessage = "";
519 private void notifyScriptTermination(String string, int intValue)
521 lastScriptMessage += string;
522 lastScriptMessage += "\n";
523 lastScriptTermination = intValue;
527 public boolean notifyEnabled(CBK callbackPick)
529 switch (callbackPick)
543 * Not implemented - returns null
546 public String eval(String strEval)
552 * Not implemented - returns null
555 public float[][] functionXY(String functionName, int x, int y)
561 * Not implemented - returns null
564 public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
570 * Not implemented - returns null
573 public String createImage(String fileName, String imageType,
574 Object text_or_bytes, int quality)
580 * Not implemented - returns null
583 public Map<String, Object> getRegistryInfo()
592 public void showUrl(String url)
597 * Not implemented - returns null
600 public Dimension resizeInnerPanel(String data)
606 public Map<String, Object> getJSpecViewProperty(String arg0)
611 public boolean isPredictSecondaryStructure()
613 return predictSecondaryStructure;
616 public void setPredictSecondaryStructure(boolean predictSecondaryStructure)
618 this.predictSecondaryStructure = predictSecondaryStructure;
621 public boolean isVisibleChainAnnotation()
623 return visibleChainAnnotation;
626 public void setVisibleChainAnnotation(boolean visibleChainAnnotation)
628 this.visibleChainAnnotation = visibleChainAnnotation;