2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.Sequence;
27 import jalview.datamodel.SequenceI;
28 import jalview.io.AlignFile;
29 import jalview.io.FileParse;
30 import jalview.schemes.ResidueProperties;
31 import jalview.util.MessageManager;
33 import java.io.IOException;
34 import java.util.Hashtable;
37 import org.jmol.api.JmolStatusListener;
38 import org.jmol.api.JmolViewer;
39 import org.jmol.constant.EnumCallback;
40 import org.jmol.modelset.Group;
41 import org.jmol.modelset.Model;
42 import org.jmol.modelset.ModelSet;
43 import org.jmol.modelset.Polymer;
44 import org.jmol.modelsetbio.BioPolymer;
45 import org.jmol.viewer.Viewer;
46 import org.openscience.jmol.app.JmolApp;
49 * Import and process PDB files with Jmol
54 public class PDBFileWithJmol extends AlignFile implements
58 JmolApp jmolApp = null;
62 public PDBFileWithJmol(String inFile, String type) throws IOException
67 public PDBFileWithJmol(FileParse fp) throws IOException
72 public PDBFileWithJmol()
74 // TODO Auto-generated constructor stub
78 * create a headless jmol instance for dataprocessing
82 private Viewer getJmolData()
85 { // note that -o -n -x are all implied
86 jmolApp = new JmolApp();
87 jmolApp.isDataOnly = true;
88 jmolApp.haveConsole = false;
89 jmolApp.haveDisplay = false;
90 jmolApp.exitUponCompletion = true;
93 viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
94 null, jmolApp.commandOptions, this);
95 viewer.setScreenDimension(jmolApp.startupWidth,
96 jmolApp.startupHeight);
97 jmolApp.startViewer(viewer, null);
98 } catch (ClassCastException x)
100 throw new Error(MessageManager.formatMessage("error.jmol_version_not_compatible_with_jalview_version", new String[]{JmolViewer.getJmolVersion()}),
107 private void waitForScript(Viewer jmd)
109 while (jmd.isScriptExecuting())
115 } catch (InterruptedException x)
124 * @see jalview.io.AlignFile#parse()
127 public void parse() throws IOException
129 Viewer jmd = getJmolData();
130 jmd.openReader(getDataName(), getDataName(), getReader());
132 if (jmd.getModelCount() > 0)
134 ModelSet ms = jmd.getModelSet();
135 String structs = ms.calculateStructures(null, true, false, true);
136 // System.out.println("Structs\n"+structs);
137 for (Model model : ms.getModels())
139 for (int _bp = 0, _bpc = model.getBioPolymerCount(); _bp < _bpc; _bp++)
141 Polymer bp = model.getBioPolymer(_bp);
142 if (bp instanceof BioPolymer)
144 BioPolymer biopoly = (BioPolymer) bp;
145 char _lastChainId = 0;
146 int[] groups = biopoly.getLeadAtomIndices();
147 Group[] bpgrp = biopoly.getGroups();
148 char seq[] = new char[groups.length], secstr[] = new char[groups.length], secstrcode[] = new char[groups.length];
149 int groupc = 0, len = 0, firstrnum = 1, lastrnum = 0;
152 if (groupc >= groups.length
153 || ms.atoms[groups[groupc]].getChainID() != _lastChainId)
157 boolean isNa = (biopoly.isDna() || biopoly.isRna());
158 // normalise sequence from Jmol to jalview
159 int[] cinds = isNa ? ResidueProperties.nucleotideIndex : ResidueProperties.aaIndex;
160 int nonGap = isNa ? ResidueProperties.maxNucleotideIndex
161 : ResidueProperties.maxProteinIndex;
163 char newseq[] = new char[len];
164 Annotation asecstr[] = new Annotation[len+firstrnum-1];
165 for (int p = 0; p < len; p++)
167 newseq[p] = cinds[seq[p]] == nonGap ? ngc : seq[p];
168 if (secstr[p] >= 'A' && secstr[p] <= 'z')
170 asecstr[p] = new Annotation("" + secstr[p], null,
171 secstrcode[p], Float.NaN);
174 SequenceI sq = new Sequence("" + getDataName() + "|"
175 + model.getModelTitle() + "|" + _lastChainId,
176 newseq, firstrnum, lastrnum);
177 PDBEntry pdbe = new PDBEntry();
178 pdbe.setFile(getDataName());
179 pdbe.setId(getDataName());
181 pdbe.setProperty(new Hashtable());
182 pdbe.getProperty().put("CHAIN", "" + _lastChainId);
184 // Need to put the number of models for this polymer somewhere for Chimera/others to grab
185 // pdbe.getProperty().put("PDBMODELS", biopoly.)
189 String mt = model.getModelTitle() == null ? getDataName()
190 : model.getModelTitle();
191 if (_lastChainId >= ' ')
195 AlignmentAnnotation ann = new AlignmentAnnotation(
196 "Secondary Structure",
197 "Secondary Structure for " + mt, asecstr);
198 ann.belowAlignment=true;
200 ann.autoCalculated=false;
201 ann.setCalcId(getClass().getName());
202 sq.addAlignmentAnnotation(ann);
203 ann.adjustForAlignment();
204 ann.validateRangeAndDisplay();
205 annotations.add(ann);
212 if (groupc < groups.length)
216 firstrnum = bpgrp[groupc].getResno();
217 _lastChainId = bpgrp[groupc].getChainID();
221 lastrnum = bpgrp[groupc].getResno();
223 seq[len] = bpgrp[groupc].getGroup1();
224 switch (bpgrp[groupc].getProteinStructureSubType())
227 if (secstr[len] == 0)
232 if (secstr[len] == 0)
237 if (secstr[len] == 0)
242 if (secstr[len] == 0)
246 secstrcode[len] = 'H';
250 secstrcode[len] = 'E';
258 } while (groupc++ < groups.length);
265 * lastScriptTermination = -9465; String dsspOut =
266 * jmd.evalString("calculate STRUCTURE"); if (dsspOut.equals("pending")) {
267 * while (lastScriptTermination == -9465) { try { Thread.sleep(50); }
268 * catch (Exception x) { } ; } } System.out.println(lastConsoleEcho);
276 * @see jalview.io.AlignFile#print()
279 public String print()
281 // TODO Auto-generated method stub
286 public void setCallbackFunction(String callbackType,
287 String callbackFunction)
289 // TODO Auto-generated method stub
294 * @Override public void notifyCallback(EnumCallback type, Object[] data) {
295 * try { switch (type) { case ERROR: case SCRIPT:
296 * notifyScriptTermination((String) data[2], ((Integer) data[3]).intValue());
297 * break; case MESSAGE: sendConsoleMessage((data == null) ? ((String) null) :
298 * (String) data[1]); break; case LOADSTRUCT: notifyFileLoaded((String)
299 * data[1], (String) data[2], (String) data[3], (String) data[4], ((Integer)
300 * data[5]).intValue());
302 * break; default: // System.err.println("Unhandled callback " + type + " " //
303 * + data[1].toString()); break; } } catch (Exception e) {
304 * System.err.println("Squashed Jmol callback handler error:");
305 * e.printStackTrace(); } }
307 public void notifyCallback(EnumCallback type, Object[] data)
309 String strInfo = (data == null || data[1] == null ? null : data[1]
314 sendConsoleEcho(strInfo);
317 notifyScriptTermination((String) data[2],
318 ((Integer) data[3]).intValue());
321 String mystatus = (String) data[3];
322 if (mystatus.indexOf("Picked") >= 0
323 || mystatus.indexOf("Sequence") >= 0)
326 sendConsoleMessage(strInfo);
328 else if (mystatus.indexOf("Completed") >= 0)
330 sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
331 strInfo.length() - 1));
335 sendConsoleMessage(data == null ? null : strInfo);
338 sendConsoleMessage(strInfo);
345 private void notifyFileLoaded(String string, String string2,
346 String string3, String string4, int intValue)
348 // TODO Auto-generated method stub
352 String lastConsoleEcho = "";
354 private void sendConsoleEcho(String string)
356 lastConsoleEcho += string;
357 lastConsoleEcho += "\n";
360 String lastConsoleMessage = "";
362 private void sendConsoleMessage(String string)
364 lastConsoleMessage += string;
365 lastConsoleMessage += "\n";
368 int lastScriptTermination = -1;
370 String lastScriptMessage = "";
372 private void notifyScriptTermination(String string, int intValue)
374 lastScriptMessage += string;
375 lastScriptMessage += "\n";
376 lastScriptTermination = intValue;
380 public boolean notifyEnabled(EnumCallback callbackPick)
382 switch (callbackPick)
403 public String eval(String strEval)
405 // TODO Auto-generated method stub
410 public float[][] functionXY(String functionName, int x, int y)
412 // TODO Auto-generated method stub
417 public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
419 // TODO Auto-generated method stub
424 public String createImage(String fileName, String type,
425 Object text_or_bytes, int quality)
427 // TODO Auto-generated method stub
432 public Map<String, Object> getRegistryInfo()
434 // TODO Auto-generated method stub
439 public void showUrl(String url)
441 // TODO Auto-generated method stub
446 public void resizeInnerPanel(String data)
448 // TODO Auto-generated method stub