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("zoom 0");
59 private static final StructureCommand COLOUR_ALL_WHITE = new StructureCommand(
60 "select *;color white;");
62 private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
63 "select *;color white;select ASP,GLU;color red;"
64 + "select LYS,ARG;color blue;select CYS;color yellow");
66 private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
67 "select *;color chain");
69 private static final String PIPE = "|";
71 private static final String HYPHEN = "-";
73 private static final String COLON = ":";
75 private static final String SLASH = "/";
83 public int getModelStartNo()
89 * Returns a string representation of the given colour suitable for inclusion
95 protected String getColourString(Color c)
97 return c == null ? null
98 : String.format("[%d,%d,%d]", c.getRed(), c.getGreen(),
103 public StructureCommandI colourByChain()
105 return COLOUR_BY_CHAIN;
109 public List<StructureCommandI> colourByCharge()
111 return Arrays.asList(COLOUR_BY_CHARGE);
115 public List<StructureCommandI> colourByResidues(Map<String, Color> colours)
117 List<StructureCommandI> cmds = super.colourByResidues(colours);
118 cmds.add(0, COLOUR_ALL_WHITE);
123 public StructureCommandI setBackgroundColour(Color col)
125 return new StructureCommand("background " + getColourString(col));
129 public StructureCommandI focusView()
135 public List<StructureCommandI> showChains(List<String> toShow)
137 StringBuilder atomSpec = new StringBuilder(128);
138 boolean first = true;
139 for (String chain : toShow)
141 String[] tokens = chain.split(":");
142 if (tokens.length == 2)
146 atomSpec.append(" or ");
149 atomSpec.append(":").append(tokens[1]).append(" /").append(tokens[0]);
153 String spec = atomSpec.toString();
154 String command = "select *;restrict " + spec + ";cartoon;center "
156 return Arrays.asList(new StructureCommand(command));
160 * Returns a command to superpose atoms in {@code atomSpec} to those in
161 * {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
165 * compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
166 * ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
169 * where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
170 * time in seconds to animate the action. For this example, atoms in model 2
171 * are moved towards atoms in model 1.
173 * The two atomspecs should each be for one model only, but may have more than
174 * one chain. The number of atoms specified should be the same for both
175 * models, though if not, Jmol may make a 'best effort' at superposition.
177 * @see https://chemapps.stolaf.edu/jmol/docs/#compare
180 public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
181 AtomSpecModel atomSpec)
183 StringBuilder sb = new StringBuilder(64);
184 String refModel = refAtoms.getModels().iterator().next();
185 String model2 = atomSpec.getModels().iterator().next();
186 sb.append(String.format("compare {%s.1} {%s.1}", model2, refModel));
187 sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
190 * command examples don't include modelspec with atoms, getAtomSpec does;
191 * it works, so leave it as it is for simplicity
193 sb.append(getAtomSpec(atomSpec, true)).append("}{");
194 sb.append(getAtomSpec(refAtoms, true)).append("}");
195 sb.append(" ROTATE TRANSLATE ");
196 sb.append(getCommandSeparator());
199 * show residues used for superposition as ribbon
201 sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|");
202 sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
205 return Arrays.asList(new StructureCommand(sb.toString()));
209 public StructureCommandI openCommandFile(String path)
212 * https://chemapps.stolaf.edu/jmol/docs/#script
213 * not currently used in Jalview
215 return new StructureCommand("script " + path);
219 public StructureCommandI saveSession(String filepath)
222 * https://chemapps.stolaf.edu/jmol/docs/#writemodel
224 return new StructureCommand("write STATE \"" + filepath + "\"");
228 protected StructureCommandI colourResidues(String atomSpec, Color colour)
230 StringBuilder sb = new StringBuilder(atomSpec.length()+20);
231 sb.append("select ").append(atomSpec).append(getCommandSeparator())
232 .append("color").append(getColourString(colour));
233 return new StructureCommand(sb.toString());
237 protected String getResidueSpec(String residue)
243 * Generates a Jmol atomspec string like
246 * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
249 * Parameter {@code alphaOnly} is not used here - this restriction is made by
250 * a separate clause in the {@code compare} (superposition) command.
253 public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
255 StringBuilder sb = new StringBuilder(128);
257 boolean first = true;
258 for (String modelNo : model.getModels())
260 for (String chain : model.getChains(modelNo))
262 for (int[] range : model.getRanges(modelNo, chain))
269 if (range[0] == range[1])
275 sb.append(range[0]).append(HYPHEN).append(range[1]);
277 sb.append(COLON).append(chain.trim()).append(SLASH);
278 sb.append(String.valueOf(modelNo)).append(".1");
283 return sb.toString();
287 public List<StructureCommandI> showBackbone()
289 return Arrays.asList(SHOW_BACKBONE);
293 public StructureCommandI loadFile(String file)
295 // https://chemapps.stolaf.edu/jmol/docs/#loadfiles
296 return new StructureCommand("load FILES \"" +
297 Platform.escapeBackslashes(file) + "\"");
301 * Obsolete method, only referenced from
302 * jalview.javascript.MouseOverStructureListener
312 public String[] colourBySequence(StructureSelectionManager ssm,
313 String[] files, SequenceI[][] sequence, SequenceRenderer sr,
314 AlignmentViewPanel viewPanel)
316 // TODO delete method
318 FeatureRenderer fr = viewPanel.getFeatureRenderer();
319 FeatureColourFinder finder = new FeatureColourFinder(fr);
320 AlignViewportI viewport = viewPanel.getAlignViewport();
321 HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
322 AlignmentI al = viewport.getAlignment();
323 List<String> cset = new ArrayList<>();
325 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
327 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
328 StringBuilder command = new StringBuilder(128);
329 List<String> str = new ArrayList<>();
331 if (mapping == null || mapping.length < 1)
336 for (int s = 0; s < sequence[pdbfnum].length; s++)
338 for (int sp, m = 0; m < mapping.length; m++)
340 if (mapping[m].getSequence() == sequence[pdbfnum][s]
341 && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
343 int lastPos = StructureMapping.UNASSIGNED_VALUE;
344 SequenceI asp = al.getSequenceAt(sp);
345 for (int r = 0; r < asp.getLength(); r++)
347 // no mapping to gaps in sequence
348 if (Comparison.isGap(asp.getCharAt(r)))
352 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
358 if (pos == StructureMapping.UNASSIGNED_VALUE)
360 // terminate current colour op
361 if (command.length() > 0
362 && command.charAt(command.length() - 1) != ';')
367 lastPos = StructureMapping.UNASSIGNED_VALUE;
373 Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
377 * shade hidden regions darker
379 if (!cs.isVisible(r))
384 String newSelcom = (mapping[m].getChain() != " "
385 ? ":" + mapping[m].getChain()
386 : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
387 + getColourString(col);
388 if (command.length() > newSelcom.length() && command
389 .substring(command.length() - newSelcom.length())
392 command = JmolCommands.condenseCommand(command, pos);
395 // TODO: deal with case when buffer is too large for Jmol to parse
396 // - execute command and flush
398 if (command.length() > 0
399 && command.charAt(command.length() - 1) != ';')
404 if (command.length() > 51200)
407 str.add(command.toString());
408 command.setLength(0);
410 command.append("select " + pos);
411 command.append(newSelcom);
419 str.add(command.toString());
420 command.setLength(0);
425 return cset.toArray(new String[cset.size()]);
436 private static StringBuilder condenseCommand(
437 StringBuilder command,
441 // work back to last 'select'
442 int p = command.length(), q = p;
451 } while ((q = command.indexOf("select", p)) == -1 && p > 0);
453 StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
455 command = command.delete(0, q + 7);
459 if (command.indexOf("-") > -1)
461 start = command.substring(0, command.indexOf("-"));
465 start = command.substring(0, command.indexOf(":"));
468 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
474 public StructureCommandI openSession(String filepath)
476 return loadFile(filepath);