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.structure.StructureCommandsI.AtomSpecType;
44 import jalview.util.Comparison;
45 import jalview.util.Platform;
48 * Routines for generating Jmol commands for Jalview/Jmol binding
53 public class JmolCommands extends StructureCommandsBase
55 private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
56 "select *; cartoons off; backbone");
58 private static final StructureCommand FOCUS_VIEW = new StructureCommand(
61 private static final StructureCommand COLOUR_ALL_WHITE = new StructureCommand(
62 "select *;color white;");
64 private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
65 "select *;color white;select ASP,GLU;color red;"
66 + "select LYS,ARG;color blue;select CYS;color yellow");
68 private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
69 "select *;color chain");
71 private static final String PIPE = "|";
73 private static final String HYPHEN = "-";
75 private static final String COLON = ":";
77 private static final String SLASH = "/";
85 public int getModelStartNo()
91 * Returns a string representation of the given colour suitable for inclusion
97 protected String getColourString(Color c)
99 return c == null ? null
100 : String.format("[%d,%d,%d]", c.getRed(), c.getGreen(),
105 public StructureCommandI colourByChain()
107 return COLOUR_BY_CHAIN;
111 public List<StructureCommandI> colourByCharge()
113 return Arrays.asList(COLOUR_BY_CHARGE);
117 public List<StructureCommandI> colourByResidues(
118 Map<String, Color> colours)
120 List<StructureCommandI> cmds = super.colourByResidues(colours);
121 cmds.add(0, COLOUR_ALL_WHITE);
126 public StructureCommandI setBackgroundColour(Color col)
128 return new StructureCommand("background " + getColourString(col));
132 public StructureCommandI focusView()
138 public List<StructureCommandI> showChains(List<String> toShow)
140 StringBuilder atomSpec = new StringBuilder(128);
141 boolean first = true;
142 for (String chain : toShow)
144 String[] tokens = chain.split(":");
145 if (tokens.length == 2)
149 atomSpec.append(" or ");
152 atomSpec.append(":").append(tokens[1]).append(" /")
157 String spec = atomSpec.toString();
158 String command = "select *;restrict " + spec + ";cartoon;center "
160 return Arrays.asList(new StructureCommand(command));
164 * Returns a command to superpose atoms in {@code atomSpec} to those in
165 * {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
169 * compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
170 * ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
173 * where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
174 * time in seconds to animate the action. For this example, atoms in model 2
175 * are moved towards atoms in model 1.
177 * The two atomspecs should each be for one model only, but may have more than
178 * one chain. The number of atoms specified should be the same for both
179 * models, though if not, Jmol may make a 'best effort' at superposition.
181 * @see https://chemapps.stolaf.edu/jmol/docs/#compare
184 public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
185 AtomSpecModel atomSpec, AtomSpecType backbone)
187 StringBuilder sb = new StringBuilder(64);
188 String refModel = refAtoms.getModels().iterator().next();
189 String model2 = atomSpec.getModels().iterator().next();
190 sb.append(String.format("compare {%s.1} {%s.1}", model2, refModel));
191 sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
194 * command examples don't include modelspec with atoms, getAtomSpec does;
195 * it works, so leave it as it is for simplicity
197 sb.append(getAtomSpec(atomSpec, backbone)).append("}{");
198 sb.append(getAtomSpec(refAtoms, backbone)).append("}");
199 sb.append(" ROTATE TRANSLATE ");
200 sb.append(getCommandSeparator());
203 * show residues used for superposition as ribbon
206 .append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY))
208 sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY))
209 .append(getCommandSeparator()).append("cartoons");
211 return Arrays.asList(new StructureCommand(sb.toString()));
215 public StructureCommandI openCommandFile(String path)
218 * https://chemapps.stolaf.edu/jmol/docs/#script
219 * not currently used in Jalview
221 return new StructureCommand("script " + path);
225 public StructureCommandI saveSession(String filepath)
228 * https://chemapps.stolaf.edu/jmol/docs/#writemodel
230 return new StructureCommand("write STATE \"" + filepath + "\"");
234 protected StructureCommandI colourResidues(String atomSpec, Color colour)
236 StringBuilder sb = new StringBuilder(atomSpec.length() + 20);
237 sb.append("select ").append(atomSpec).append(getCommandSeparator())
238 .append("color").append(getColourString(colour));
239 return new StructureCommand(sb.toString());
243 protected String getResidueSpec(String residue)
249 * Generates a Jmol atomspec string like
252 * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
255 * Parameter {@code alphaOnly} is not used here - this restriction is made by
256 * a separate clause in the {@code compare} (superposition) command.
259 public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
261 StringBuilder sb = new StringBuilder(128);
263 boolean first = true;
264 for (String modelNo : model.getModels())
266 for (String chain : model.getChains(modelNo))
268 for (int[] range : model.getRanges(modelNo, chain))
275 if (range[0] == range[1])
281 sb.append(range[0]).append(HYPHEN).append(range[1]);
283 sb.append(COLON).append(chain.trim()).append(SLASH);
284 sb.append(String.valueOf(modelNo)).append(".1");
289 return sb.toString();
293 public List<StructureCommandI> showBackbone()
295 return Arrays.asList(SHOW_BACKBONE);
299 public StructureCommandI loadFile(String file)
301 // https://chemapps.stolaf.edu/jmol/docs/#loadfiles
302 return new StructureCommand(
303 "load FILES \"" + Platform.escapeBackslashes(file) + "\"");
307 * Obsolete method, only referenced from
308 * jalview.javascript.MouseOverStructureListener
318 public String[] colourBySequence(StructureSelectionManager ssm,
319 String[] files, SequenceI[][] sequence, SequenceRenderer sr,
320 AlignmentViewPanel viewPanel)
322 // TODO delete method
324 FeatureRenderer fr = viewPanel.getFeatureRenderer();
325 FeatureColourFinder finder = new FeatureColourFinder(fr);
326 AlignViewportI viewport = viewPanel.getAlignViewport();
327 HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
328 AlignmentI al = viewport.getAlignment();
329 List<String> cset = new ArrayList<>();
331 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
333 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
334 StringBuilder command = new StringBuilder(128);
335 List<String> str = new ArrayList<>();
337 if (mapping == null || mapping.length < 1)
342 for (int s = 0; s < sequence[pdbfnum].length; s++)
344 for (int sp, m = 0; m < mapping.length; m++)
346 if (mapping[m].getSequence() == sequence[pdbfnum][s]
347 && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
349 int lastPos = StructureMapping.UNASSIGNED_VALUE;
350 SequenceI asp = al.getSequenceAt(sp);
351 for (int r = 0; r < asp.getLength(); r++)
353 // no mapping to gaps in sequence
354 if (Comparison.isGap(asp.getCharAt(r)))
358 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
364 if (pos == StructureMapping.UNASSIGNED_VALUE)
366 // terminate current colour op
367 if (command.length() > 0
368 && command.charAt(command.length() - 1) != ';')
373 lastPos = StructureMapping.UNASSIGNED_VALUE;
379 Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
383 * shade hidden regions darker
385 if (!cs.isVisible(r))
390 String newSelcom = (mapping[m].getChain() != " "
391 ? ":" + mapping[m].getChain()
392 : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
393 + getColourString(col);
394 if (command.length() > newSelcom.length() && command
395 .substring(command.length() - newSelcom.length())
398 command = JmolCommands.condenseCommand(command, pos);
401 // TODO: deal with case when buffer is too large for Jmol to parse
402 // - execute command and flush
404 if (command.length() > 0
405 && command.charAt(command.length() - 1) != ';')
410 if (command.length() > 51200)
413 str.add(command.toString());
414 command.setLength(0);
416 command.append("select " + pos);
417 command.append(newSelcom);
425 str.add(command.toString());
426 command.setLength(0);
431 return cset.toArray(new String[cset.size()]);
442 private static StringBuilder condenseCommand(StringBuilder command,
446 // work back to last 'select'
447 int p = command.length(), q = p;
456 } while ((q = command.indexOf("select", p)) == -1 && p > 0);
458 StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
460 command = command.delete(0, q + 7);
464 if (command.indexOf("-") > -1)
466 start = command.substring(0, command.indexOf("-"));
470 start = command.substring(0, command.indexOf(":"));
473 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
479 public StructureCommandI openSession(String filepath)
481 return loadFile(filepath);
485 public StructureCommandI closeViewer()
487 return null; // not an external viewer