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 java.awt.Color;
24 import java.util.ArrayList;
25 import java.util.Arrays;
26 import java.util.List;
29 import jalview.api.AlignViewportI;
30 import jalview.api.AlignmentViewPanel;
31 import jalview.api.FeatureRenderer;
32 import jalview.api.SequenceRenderer;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.HiddenColumns;
35 import jalview.datamodel.SequenceI;
36 import jalview.renderer.seqfeatures.FeatureColourFinder;
37 import jalview.structure.AtomSpecModel;
38 import jalview.structure.StructureCommand;
39 import jalview.structure.StructureCommandI;
40 import jalview.structure.StructureCommandsBase;
41 import jalview.structure.StructureMapping;
42 import jalview.structure.StructureSelectionManager;
43 import jalview.util.Comparison;
44 import jalview.util.Platform;
47 * Routines for generating Jmol commands for Jalview/Jmol binding
52 public class JmolCommands extends StructureCommandsBase
54 private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
55 "select *; cartoons off; backbone");
57 private static final StructureCommand FOCUS_VIEW = new StructureCommand(
60 private static final StructureCommand COLOUR_ALL_WHITE = new StructureCommand(
61 "select *;color white;");
63 private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
64 "select *;color white;select ASP,GLU;color red;"
65 + "select LYS,ARG;color blue;select CYS;color yellow");
67 private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
68 "select *;color chain");
70 private static final String PIPE = "|";
72 private static final String HYPHEN = "-";
74 private static final String COLON = ":";
76 private static final String SLASH = "/";
84 public int getModelStartNo()
90 * Returns a string representation of the given colour suitable for inclusion
96 protected String getColourString(Color c)
98 return c == null ? null
99 : String.format("[%d,%d,%d]", c.getRed(), c.getGreen(),
104 public StructureCommandI colourByChain()
106 return COLOUR_BY_CHAIN;
110 public List<StructureCommandI> colourByCharge()
112 return Arrays.asList(COLOUR_BY_CHARGE);
116 public List<StructureCommandI> colourByResidues(
117 Map<String, Color> colours)
119 List<StructureCommandI> cmds = super.colourByResidues(colours);
120 cmds.add(0, COLOUR_ALL_WHITE);
125 public StructureCommandI setBackgroundColour(Color col)
127 return new StructureCommand("background " + getColourString(col));
131 public StructureCommandI focusView()
137 public List<StructureCommandI> showChains(List<String> toShow)
139 StringBuilder atomSpec = new StringBuilder(128);
140 boolean first = true;
141 for (String chain : toShow)
143 String[] tokens = chain.split(":");
144 if (tokens.length == 2)
148 atomSpec.append(" or ");
151 atomSpec.append(":").append(tokens[1]).append(" /")
156 String spec = atomSpec.toString();
157 String command = "select *;restrict " + spec + ";cartoon;center "
159 return Arrays.asList(new StructureCommand(command));
163 * Returns a command to superpose atoms in {@code atomSpec} to those in
164 * {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
168 * compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
169 * ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
172 * where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
173 * time in seconds to animate the action. For this example, atoms in model 2
174 * are moved towards atoms in model 1.
176 * The two atomspecs should each be for one model only, but may have more than
177 * one chain. The number of atoms specified should be the same for both
178 * models, though if not, Jmol may make a 'best effort' at superposition.
180 * @see https://chemapps.stolaf.edu/jmol/docs/#compare
183 public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
184 AtomSpecModel atomSpec, AtomSpecType backbone)
186 StringBuilder sb = new StringBuilder(64);
187 String refModel = refAtoms.getModels().iterator().next();
188 String model2 = atomSpec.getModels().iterator().next();
189 sb.append(String.format("compare {%s.1} {%s.1}", model2, refModel));
190 sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
193 * command examples don't include modelspec with atoms, getAtomSpec does;
194 * it works, so leave it as it is for simplicity
196 sb.append(getAtomSpec(atomSpec, backbone)).append("}{");
197 sb.append(getAtomSpec(refAtoms, backbone)).append("}");
198 sb.append(" ROTATE TRANSLATE ");
199 sb.append(getCommandSeparator());
202 * show residues used for superposition as ribbon
205 .append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY))
207 sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY))
208 .append(getCommandSeparator()).append("cartoons");
209 return Arrays.asList(new StructureCommand(sb.toString()));
213 public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues)
215 StringBuilder sb = new StringBuilder(64);
216 sb.append("center ");
217 for (AtomSpecModel ranges : residues)
223 sb.append(getAtomSpec(ranges, AtomSpecType.RESIDUE_ONLY));
225 return Arrays.asList(new StructureCommand(sb.toString()));
229 public StructureCommandI openCommandFile(String path)
232 * https://chemapps.stolaf.edu/jmol/docs/#script
233 * not currently used in Jalview
235 return new StructureCommand("script " + path);
239 public StructureCommandI saveSession(String filepath)
242 * https://chemapps.stolaf.edu/jmol/docs/#writemodel
244 return new StructureCommand("write STATE \"" + filepath + "\"");
248 protected StructureCommandI colourResidues(String atomSpec, Color colour)
250 StringBuilder sb = new StringBuilder(atomSpec.length() + 20);
251 sb.append("select ").append(atomSpec).append(getCommandSeparator())
252 .append("color").append(getColourString(colour));
253 return new StructureCommand(sb.toString());
257 protected String getResidueSpec(String residue)
263 * Generates a Jmol atomspec string like
266 * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
269 * Parameter {@code alphaOnly} is not used here - this restriction is made by
270 * a separate clause in the {@code compare} (superposition) command.
273 public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
275 StringBuilder sb = new StringBuilder(128);
277 boolean first = true;
278 for (String modelNo : model.getModels())
280 for (String chain : model.getChains(modelNo))
282 for (int[] range : model.getRanges(modelNo, chain))
289 if (range[0] == range[1])
295 sb.append(range[0]).append(HYPHEN).append(range[1]);
297 sb.append(COLON).append(chain.trim()).append(SLASH);
298 sb.append(String.valueOf(modelNo)).append(".1");
303 return sb.toString();
307 public List<StructureCommandI> showBackbone()
309 return Arrays.asList(SHOW_BACKBONE);
313 public StructureCommandI loadFile(String file)
315 // https://chemapps.stolaf.edu/jmol/docs/#loadfiles
316 return new StructureCommand(
317 "load FILES \"" + Platform.escapeBackslashes(file) + "\"");
321 * Obsolete method, only referenced from
322 * jalview.javascript.MouseOverStructureListener
332 public String[] colourBySequence(StructureSelectionManager ssm,
333 String[] files, SequenceI[][] sequence, SequenceRenderer sr,
334 AlignmentViewPanel viewPanel)
336 // TODO delete method
338 FeatureRenderer fr = viewPanel.getFeatureRenderer();
339 FeatureColourFinder finder = new FeatureColourFinder(fr);
340 AlignViewportI viewport = viewPanel.getAlignViewport();
341 HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
342 AlignmentI al = viewport.getAlignment();
343 List<String> cset = new ArrayList<>();
345 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
347 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
348 StringBuilder command = new StringBuilder(128);
349 List<String> str = new ArrayList<>();
351 if (mapping == null || mapping.length < 1)
356 for (int s = 0; s < sequence[pdbfnum].length; s++)
358 for (int sp, m = 0; m < mapping.length; m++)
360 if (mapping[m].getSequence() == sequence[pdbfnum][s]
361 && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
363 int lastPos = StructureMapping.UNASSIGNED_VALUE;
364 SequenceI asp = al.getSequenceAt(sp);
365 for (int r = 0; r < asp.getLength(); r++)
367 // no mapping to gaps in sequence
368 if (Comparison.isGap(asp.getCharAt(r)))
372 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
378 if (pos == StructureMapping.UNASSIGNED_VALUE)
380 // terminate current colour op
381 if (command.length() > 0
382 && command.charAt(command.length() - 1) != ';')
387 lastPos = StructureMapping.UNASSIGNED_VALUE;
393 Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
397 * shade hidden regions darker
399 if (!cs.isVisible(r))
404 String newSelcom = (mapping[m].getChain() != " "
405 ? ":" + mapping[m].getChain()
406 : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
407 + getColourString(col);
408 if (command.length() > newSelcom.length() && command
409 .substring(command.length() - newSelcom.length())
412 command = JmolCommands.condenseCommand(command, pos);
415 // TODO: deal with case when buffer is too large for Jmol to parse
416 // - execute command and flush
418 if (command.length() > 0
419 && command.charAt(command.length() - 1) != ';')
424 if (command.length() > 51200)
427 str.add(command.toString());
428 command.setLength(0);
430 command.append("select " + pos);
431 command.append(newSelcom);
439 str.add(command.toString());
440 command.setLength(0);
445 return cset.toArray(new String[cset.size()]);
456 private static StringBuilder condenseCommand(StringBuilder command,
460 // work back to last 'select'
461 int p = command.length(), q = p;
470 } while ((q = command.indexOf("select", p)) == -1 && p > 0);
472 StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
474 command = command.delete(0, q + 7);
478 if (command.indexOf("-") > -1)
480 start = command.substring(0, command.indexOf("-"));
484 start = command.substring(0, command.indexOf(":"));
487 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
493 public StructureCommandI openSession(String filepath)
495 return loadFile(filepath);
499 public StructureCommandI closeViewer()
501 return null; // not an external viewer
504 public StructureCommandI saveState(String label)
506 return new StructureCommand("save STATE " + label);
509 public StructureCommandI restoreState(String label)
511 return new StructureCommand("restore STATE " + label);