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.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 javajs.awt.Dimension;
39 import org.jmol.api.JmolStatusListener;
40 import org.jmol.api.JmolViewer;
41 import org.jmol.c.CBK;
42 import org.jmol.modelset.Group;
43 import org.jmol.modelset.Model;
44 import org.jmol.modelset.ModelSet;
45 import org.jmol.modelsetbio.BioModel;
46 import org.jmol.modelsetbio.BioPolymer;
47 import org.jmol.viewer.Viewer;
48 import org.openscience.jmol.app.JmolApp;
51 * Import and process PDB files with Jmol
56 public class PDBFileWithJmol extends AlignFile implements
60 JmolApp jmolApp = null;
64 public PDBFileWithJmol(String inFile, String type) throws IOException
69 public PDBFileWithJmol(FileParse fp) throws IOException
74 public PDBFileWithJmol()
76 // TODO Auto-generated constructor stub
80 * create a headless jmol instance for dataprocessing
84 private Viewer getJmolData()
87 { // note that -o -n -x are all implied // TODO check for Jmol 14.2
88 jmolApp = new JmolApp();
89 jmolApp.isDataOnly = true;
90 jmolApp.haveConsole = false;
91 jmolApp.haveDisplay = false;
94 viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
95 null, "-x -o -n", this);
96 viewer.setScreenDimension(jmolApp.startupWidth,
97 jmolApp.startupHeight);
98 jmolApp.startViewer(viewer, null, false);
99 } catch (ClassCastException x)
101 throw new Error(MessageManager.formatMessage("error.jmol_version_not_compatible_with_jalview_version", new String[]{JmolViewer.getJmolVersion()}),
108 private void waitForScript(Viewer jmd)
110 while (jmd.isScriptExecuting())
116 } catch (InterruptedException x)
125 * @see jalview.io.AlignFile#parse()
128 public void parse() throws IOException
130 Viewer jmd = getJmolData();
131 jmd.openReader(getDataName(), getDataName(), getReader());
136 ModelSet ms = jmd.ms;
137 // Jmol 14.2 added third argument doReport = false
138 ms.calculateStructures(null, true, false, false, true);
139 // System.out.println("Structs\n"+structs);
142 for (Model model : ms.am)
145 for (BioPolymer bp : ((BioModel) model).bioPolymers)
147 int lastChainId = 0; // int value of character e.g. 65 for A
148 String lastChainIdAlpha = "";
150 int[] groups = bp.getLeadAtomIndices();
151 char seq[] = new char[groups.length], secstr[] = new char[groups.length], secstrcode[] = new char[groups.length];
152 int groupc = 0, len = 0, firstrnum = 1, lastrnum = 0;
156 if (groupc >= groups.length
157 || ms.at[groups[groupc]].group.chain.chainID != lastChainId)
160 * on change of chain (or at end), construct the sequence and
161 * secondary structure annotation for the last chain
165 boolean isNa = bp.isNucleic();
166 // normalise sequence from Jmol to jalview
167 int[] cinds = isNa ? ResidueProperties.nucleotideIndex
168 : ResidueProperties.aaIndex;
169 int nonGap = isNa ? ResidueProperties.maxNucleotideIndex
170 : ResidueProperties.maxProteinIndex;
172 char newseq[] = new char[len];
173 Annotation asecstr[] = new Annotation[len + firstrnum - 1];
174 for (int p = 0; p < len; p++)
176 newseq[p] = cinds[seq[p]] == nonGap ? ngc : seq[p];
177 if (secstr[p] >= 'A' && secstr[p] <= 'z')
181 asecstr[p] = new Annotation("" + secstr[p], null,
182 secstrcode[p], Float.NaN);
183 } catch (ArrayIndexOutOfBoundsException e)
185 // skip - patch for JAL-1836
189 String modelTitle = (String) ms
190 .getInfo(modelIndex, "title");
191 SequenceI sq = new Sequence("" + getDataName() + "|"
192 + modelTitle + "|" + lastChainIdAlpha, newseq,
193 firstrnum, lastrnum);
194 PDBEntry pdbe = new PDBEntry();
195 pdbe.setFile(getDataName());
196 pdbe.setId(getDataName());
197 pdbe.setProperty(new Hashtable());
198 // pdbe.getProperty().put("CHAIN", "" + _lastChainId);
199 pdbe.setChainCode(lastChainIdAlpha);
202 // Need to put the number of models for this polymer somewhere
203 // for Chimera/others to grab
204 // pdbe.getProperty().put("PDBMODELS", biopoly.)
208 String mt = modelTitle == null ? getDataName()
210 if (lastChainId >= ' ')
212 mt += lastChainIdAlpha;
214 AlignmentAnnotation ann = new AlignmentAnnotation(
215 "Secondary Structure", "Secondary Structure for "
217 ann.belowAlignment = true;
219 ann.autoCalculated = false;
220 ann.setCalcId(getClass().getName());
221 sq.addAlignmentAnnotation(ann);
222 ann.adjustForAlignment();
223 ann.validateRangeAndDisplay();
224 annotations.add(ann);
231 if (groupc < groups.length)
233 group = ms.at[groups[groupc]].group;
236 firstrnum = group.getResno();
237 lastChainId = group.chain.chainID;
238 lastChainIdAlpha = group.chain.getIDStr();
242 lastrnum = group.getResno();
244 seq[len] = group.getGroup1();
245 switch (group.getProteinStructureSubType())
248 if (secstr[len] == 0)
253 if (secstr[len] == 0)
258 if (secstr[len] == 0)
263 if (secstr[len] == 0)
267 secstrcode[len] = 'H';
271 secstrcode[len] = 'E';
279 } while (groupc++ < groups.length);
284 * lastScriptTermination = -9465; String dsspOut =
285 * jmd.evalString("calculate STRUCTURE"); if (dsspOut.equals("pending")) {
286 * while (lastScriptTermination == -9465) { try { Thread.sleep(50); }
287 * catch (Exception x) { } ; } } System.out.println(lastConsoleEcho);
295 * @see jalview.io.AlignFile#print()
298 public String print()
300 // TODO Auto-generated method stub
305 public void setCallbackFunction(String callbackType,
306 String callbackFunction)
308 // TODO Auto-generated method stub
313 * @Override public void notifyCallback(EnumCallback type, Object[] data) {
314 * try { switch (type) { case ERROR: case SCRIPT:
315 * notifyScriptTermination((String) data[2], ((Integer) data[3]).intValue());
316 * break; case MESSAGE: sendConsoleMessage((data == null) ? ((String) null) :
317 * (String) data[1]); break; case LOADSTRUCT: notifyFileLoaded((String)
318 * data[1], (String) data[2], (String) data[3], (String) data[4], ((Integer)
319 * data[5]).intValue());
321 * break; default: // System.err.println("Unhandled callback " + type + " " //
322 * + data[1].toString()); break; } } catch (Exception e) {
323 * System.err.println("Squashed Jmol callback handler error:");
324 * e.printStackTrace(); } }
326 public void notifyCallback(CBK type, Object[] data)
328 String strInfo = (data == null || data[1] == null ? null : data[1]
333 sendConsoleEcho(strInfo);
336 notifyScriptTermination((String) data[2],
337 ((Integer) data[3]).intValue());
340 String mystatus = (String) data[3];
341 if (mystatus.indexOf("Picked") >= 0
342 || mystatus.indexOf("Sequence") >= 0)
345 sendConsoleMessage(strInfo);
347 else if (mystatus.indexOf("Completed") >= 0)
349 sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
350 strInfo.length() - 1));
354 sendConsoleMessage(data == null ? null : strInfo);
357 sendConsoleMessage(strInfo);
364 String lastConsoleEcho = "";
366 private void sendConsoleEcho(String string)
368 lastConsoleEcho += string;
369 lastConsoleEcho += "\n";
372 String lastConsoleMessage = "";
374 private void sendConsoleMessage(String string)
376 lastConsoleMessage += string;
377 lastConsoleMessage += "\n";
380 int lastScriptTermination = -1;
382 String lastScriptMessage = "";
384 private void notifyScriptTermination(String string, int intValue)
386 lastScriptMessage += string;
387 lastScriptMessage += "\n";
388 lastScriptTermination = intValue;
392 public boolean notifyEnabled(CBK callbackPick)
394 switch (callbackPick)
408 public String eval(String strEval)
410 // TODO Auto-generated method stub
415 public float[][] functionXY(String functionName, int x, int y)
417 // TODO Auto-generated method stub
422 public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
424 // TODO Auto-generated method stub
429 public String createImage(String fileName, String type,
430 Object text_or_bytes, int quality)
432 // TODO Auto-generated method stub
437 public Map<String, Object> getRegistryInfo()
439 // TODO Auto-generated method stub
444 public void showUrl(String url)
446 // TODO Auto-generated method stub
451 public Dimension resizeInnerPanel(String data)
457 public Map<String, Object> getJSpecViewProperty(String arg0)