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();
213 curAtom.name = atom.getAtomName();
214 curAtom.number = atom.getAtomNumber();
215 curAtom.resName = atom.getGroup3(true);
216 curAtom.resNumber = atom.getResno();
217 curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
218 .getIndex()] : Float.valueOf(atom.getOccupancy100());
219 curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
220 curAtom.tfactor = atom.getBfactor100() / 100f;
222 // significantAtoms.add(curAtom);
223 // ignore atoms from subsequent models
224 if (!significantAtoms.contains(curAtom))
226 significantAtoms.add(curAtom);
231 return significantAtoms;
234 private boolean atomValidated(org.jmol.modelset.Atom curAtom,
235 org.jmol.modelset.Atom prevAtom,
236 HashMap<String, org.jmol.modelset.Atom> chainTerMap)
238 // System.out.println("Atom: " + curAtom.getAtomNumber()
239 // + " Last atom index " + curAtom.group.lastAtomIndex);
240 if (chainTerMap == null || prevAtom == null)
244 String curAtomChId = curAtom.getChainIDStr();
245 String prevAtomChId = prevAtom.getChainIDStr();
246 // new chain encoutered
247 if (!prevAtomChId.equals(curAtomChId))
249 // On chain switch add previous chain termination to xTerMap if not exists
250 if (!chainTerMap.containsKey(prevAtomChId))
252 chainTerMap.put(prevAtomChId, prevAtom);
254 // if current atom belongs to an already terminated chain and the resNum
255 // diff < 5 then mark as valid and update termination Atom
256 if (chainTerMap.containsKey(curAtomChId))
258 if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
260 chainTerMap.put(curAtomChId, curAtom);
266 // atom with previously terminated chain encountered
267 else if (chainTerMap.containsKey(curAtomChId))
269 if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
271 chainTerMap.put(curAtomChId, curAtom);
276 // HETATM with resNum jump > 2
277 return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
281 private void createAnnotation(SequenceI sequence, PDBChain chain,
282 org.jmol.modelset.Atom[] jmolAtoms)
284 char[] secstr = new char[sequence.getLength()];
285 char[] secstrcode = new char[sequence.getLength()];
287 // Ensure Residue size equals Seq size
288 if (chain.residues.size() != sequence.getLength())
293 for (Residue residue : chain.residues)
295 Atom repAtom = residue.getAtoms().get(0);
296 STR proteinStructureSubType = jmolAtoms[repAtom.atomIndex].group
297 .getProteinStructureSubType();
298 setSecondaryStructure(proteinStructureSubType, annotIndex, secstr,
302 addSecondaryStructureAnnotation(chain.pdbid, sequence, secstr,
303 secstrcode, chain.id, sequence.getStart());
307 * Helper method that adds an AlignmentAnnotation for secondary structure to
308 * the sequence, provided at least one secondary structure prediction has been
319 protected void addSecondaryStructureAnnotation(String modelTitle,
320 SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
323 char[] seq = sq.getSequence();
324 boolean ssFound = false;
325 Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
326 for (int p = 0; p < seq.length; p++)
328 if (secstr[p] >= 'A' && secstr[p] <= 'z')
332 asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
333 secstrcode[p], Float.NaN);
335 } catch (Exception e)
337 // e.printStackTrace();
344 String mt = modelTitle == null ? getDataName() : modelTitle;
346 AlignmentAnnotation ann = new AlignmentAnnotation(
347 "Secondary Structure", "Secondary Structure for " + mt,
349 ann.belowAlignment = true;
351 ann.autoCalculated = false;
352 ann.setCalcId(getClass().getName());
353 ann.adjustForAlignment();
354 ann.validateRangeAndDisplay();
355 annotations.add(ann);
356 sq.addAlignmentAnnotation(ann);
360 private void waitForScript(Viewer jmd)
362 while (jmd.isScriptExecuting())
368 } catch (InterruptedException x)
375 * Convert Jmol's secondary structure code to Jalview's, and stored it in the
376 * secondary structure arrays at the given sequence position
378 * @param proteinStructureSubType
383 protected void setSecondaryStructure(STR proteinStructureSubType,
384 int pos, char[] secstr, char[] secstrcode)
386 switch (proteinStructureSubType)
405 switch (proteinStructureSubType)
411 secstrcode[pos] = 'H';
414 secstrcode[pos] = 'E';
422 * Convert any non-standard peptide codes to their standard code table
423 * equivalent. (Initial version only does Selenomethionine MSE->MET.)
425 * @param threeLetterCode
429 protected void replaceNonCanonicalResidue(String threeLetterCode,
432 String canonical = ResidueProperties
433 .getCanonicalAminoAcid(threeLetterCode);
434 if (canonical != null && !canonical.equalsIgnoreCase(threeLetterCode))
436 seq[pos] = ResidueProperties.getSingleCharacterCode(canonical);
441 * Not implemented - returns null
444 public String print()
453 public void setCallbackFunction(String callbackType,
454 String callbackFunction)
459 public void notifyCallback(CBK cbType, Object[] data)
461 String strInfo = (data == null || data[1] == null ? null : data[1]
466 sendConsoleEcho(strInfo);
469 notifyScriptTermination((String) data[2],
470 ((Integer) data[3]).intValue());
473 String mystatus = (String) data[3];
474 if (mystatus.indexOf("Picked") >= 0
475 || mystatus.indexOf("Sequence") >= 0)
478 sendConsoleMessage(strInfo);
480 else if (mystatus.indexOf("Completed") >= 0)
482 sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
483 strInfo.length() - 1));
487 sendConsoleMessage(data == null ? null : strInfo);
490 sendConsoleMessage(strInfo);
497 String lastConsoleEcho = "";
499 private void sendConsoleEcho(String string)
501 lastConsoleEcho += string;
502 lastConsoleEcho += "\n";
505 String lastConsoleMessage = "";
507 private void sendConsoleMessage(String string)
509 lastConsoleMessage += string;
510 lastConsoleMessage += "\n";
513 int lastScriptTermination = -1;
515 String lastScriptMessage = "";
517 private void notifyScriptTermination(String string, int intValue)
519 lastScriptMessage += string;
520 lastScriptMessage += "\n";
521 lastScriptTermination = intValue;
525 public boolean notifyEnabled(CBK callbackPick)
527 switch (callbackPick)
541 * Not implemented - returns null
544 public String eval(String strEval)
550 * Not implemented - returns null
553 public float[][] functionXY(String functionName, int x, int y)
559 * Not implemented - returns null
562 public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
568 * Not implemented - returns null
571 public String createImage(String fileName, String imageType,
572 Object text_or_bytes, int quality)
578 * Not implemented - returns null
581 public Map<String, Object> getRegistryInfo()
590 public void showUrl(String url)
595 * Not implemented - returns null
598 public Dimension resizeInnerPanel(String data)
604 public Map<String, Object> getJSpecViewProperty(String arg0)
609 public boolean isPredictSecondaryStructure()
611 return predictSecondaryStructure;
614 public void setPredictSecondaryStructure(boolean predictSecondaryStructure)
616 this.predictSecondaryStructure = predictSecondaryStructure;
619 public boolean isVisibleChainAnnotation()
621 return visibleChainAnnotation;
624 public void setVisibleChainAnnotation(boolean visibleChainAnnotation)
626 this.visibleChainAnnotation = visibleChainAnnotation;