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.api.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.api.FeatureRenderer;
26 import jalview.api.SequenceRenderer;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.HiddenColumns;
29 import jalview.datamodel.SequenceI;
30 import jalview.renderer.seqfeatures.FeatureColourFinder;
31 import jalview.structure.AtomSpecModel;
32 import jalview.structure.StructureCommandsBase;
33 import jalview.structure.StructureMapping;
34 import jalview.structure.StructureSelectionManager;
35 import jalview.util.Comparison;
37 import java.awt.Color;
38 import java.util.ArrayList;
39 import java.util.List;
43 * Routines for generating Jmol commands for Jalview/Jmol binding
48 public class JmolCommands extends StructureCommandsBase
50 private static final String CMD_COLOUR_BY_CHARGE = "select *;color white;select ASP,GLU;color red;"
51 + "select LYS,ARG;color blue;select CYS;color yellow";
53 private static final String CMD_COLOUR_BY_CHAIN = "select *;color chain";
55 private static final String PIPE = "|";
57 private static final String HYPHEN = "-";
59 private static final String COLON = ":";
61 private static final String SLASH = "/";
69 public int getModelStartNo()
75 * Returns a string representation of the given colour suitable for inclusion
81 protected String getColourString(Color c)
83 return c == null ? null
84 : String.format("[%d,%d,%d]", c.getRed(), c.getGreen(),
89 public String[] colourBySequence(StructureSelectionManager ssm,
91 SequenceI[][] sequence, SequenceRenderer sr,
92 AlignmentViewPanel viewPanel)
96 FeatureRenderer fr = viewPanel.getFeatureRenderer();
97 FeatureColourFinder finder = new FeatureColourFinder(fr);
98 AlignViewportI viewport = viewPanel.getAlignViewport();
99 HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
100 AlignmentI al = viewport.getAlignment();
101 List<String> cset = new ArrayList<>();
103 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
105 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
106 StringBuilder command = new StringBuilder(128);
107 List<String> str = new ArrayList<>();
109 if (mapping == null || mapping.length < 1)
114 for (int s = 0; s < sequence[pdbfnum].length; s++)
116 for (int sp, m = 0; m < mapping.length; m++)
118 if (mapping[m].getSequence() == sequence[pdbfnum][s]
119 && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
121 int lastPos = StructureMapping.UNASSIGNED_VALUE;
122 SequenceI asp = al.getSequenceAt(sp);
123 for (int r = 0; r < asp.getLength(); r++)
125 // no mapping to gaps in sequence
126 if (Comparison.isGap(asp.getCharAt(r)))
130 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
136 if (pos == StructureMapping.UNASSIGNED_VALUE)
138 // terminate current colour op
139 if (command.length() > 0
140 && command.charAt(command.length() - 1) != ';')
145 lastPos = StructureMapping.UNASSIGNED_VALUE;
151 Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
155 * shade hidden regions darker
157 if (!cs.isVisible(r))
162 String newSelcom = (mapping[m].getChain() != " "
163 ? ":" + mapping[m].getChain()
164 : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
165 + getColourString(col);
166 if (command.length() > newSelcom.length() && command
167 .substring(command.length() - newSelcom.length())
170 command = JmolCommands.condenseCommand(command, pos);
173 // TODO: deal with case when buffer is too large for Jmol to parse
174 // - execute command and flush
176 if (command.length() > 0
177 && command.charAt(command.length() - 1) != ';')
182 if (command.length() > 51200)
185 str.add(command.toString());
186 command.setLength(0);
188 command.append("select " + pos);
189 command.append(newSelcom);
197 str.add(command.toString());
198 command.setLength(0);
203 return cset.toArray(new String[cset.size()]);
206 public static StringBuilder condenseCommand(StringBuilder command,
210 // work back to last 'select'
211 int p = command.length(), q = p;
220 } while ((q = command.indexOf("select", p)) == -1 && p > 0);
222 StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
224 command = command.delete(0, q + 7);
228 if (command.indexOf("-") > -1)
230 start = command.substring(0, command.indexOf("-"));
234 start = command.substring(0, command.indexOf(":"));
237 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
243 public String colourByChain()
245 return CMD_COLOUR_BY_CHAIN;
249 public String colourByCharge()
251 return CMD_COLOUR_BY_CHARGE;
255 public String colourByResidues(Map<String, Color> colours)
257 StringBuilder cmd = new StringBuilder(128);
258 cmd.append("select *;color white;");
259 cmd.append(super.colourByResidues(colours));
261 return cmd.toString();
265 public String setBackgroundColour(Color col)
267 return "background " + getColourString(col);
271 public String focusView()
277 public String showChains(List<String> toShow)
279 StringBuilder atomSpec = new StringBuilder(128);
280 boolean first = true;
281 for (String chain : toShow)
283 String[] tokens = chain.split(":");
284 if (tokens.length == 2)
288 atomSpec.append(" or ");
291 atomSpec.append(":").append(tokens[1]).append(" /").append(tokens[0]);
295 String spec = atomSpec.toString();
296 String command = "select *;restrict " + spec + ";cartoon;center "
302 * Returns a command to superpose atoms in {@code atomSpec} to those in
303 * {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
307 * compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
308 * ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
311 * where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
312 * time in seconds to animate the action. For this example, atoms in model 2
313 * are moved towards atoms in model 1.
315 * The two atomspecs should each be for one model only, but may have more than
316 * one chain. The number of atoms specified should be the same for both
317 * models, though if not, Jmol may make a 'best effort' at superposition.
319 * @see https://chemapps.stolaf.edu/jmol/docs/#compare
322 public String superposeStructures(AtomSpecModel refAtoms,
323 AtomSpecModel atomSpec)
325 StringBuilder sb = new StringBuilder(64);
326 int refModel = refAtoms.getModels().iterator().next();
327 int model2 = atomSpec.getModels().iterator().next();
328 sb.append(String.format("compare {%d.1} {%d.1}", model2, refModel));
329 sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
332 * command examples don't include modelspec with atoms, getAtomSpec does;
333 * it works, so leave it as it is for simplicity
335 sb.append(getAtomSpec(atomSpec, true)).append("}{");
336 sb.append(getAtomSpec(refAtoms, true)).append("}");
337 sb.append(" ROTATE TRANSLATE ");
338 sb.append(getCommandSeparator());
341 * show residues used for superposition as ribbon
343 sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|");
344 sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
347 return sb.toString();
351 public String openCommandFile(String path)
354 * https://chemapps.stolaf.edu/jmol/docs/#script
355 * not currently used in Jalview
357 return "script " + path;
361 public String saveSession(String filepath)
364 * https://chemapps.stolaf.edu/jmol/docs/#write
365 * not currently used in Jalview
367 return "write \"" + filepath + "\"";
371 protected String getColourCommand(String atomSpec, Color colour)
373 StringBuilder sb = new StringBuilder(atomSpec.length()+20);
374 sb.append("select ").append(atomSpec).append(getCommandSeparator())
375 .append("color").append(getColourString(colour));
376 return sb.toString();
380 protected String getResidueSpec(String residue)
386 * Generates a Jmol atomspec string like
389 * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
392 * Parameter {@code alphaOnly} is not used here - this restriction is made by
393 * a separate clause in the {@code compare} (superposition) command.
396 public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
398 StringBuilder sb = new StringBuilder(128);
400 boolean first = true;
401 for (int modelNo : model.getModels())
403 for (String chain : model.getChains(modelNo))
405 for (int[] range : model.getRanges(modelNo, chain))
412 if (range[0] == range[1])
418 sb.append(range[0]).append(HYPHEN).append(range[1]);
420 sb.append(COLON).append(chain.trim()).append(SLASH);
421 sb.append(String.valueOf(modelNo)).append(".1");
426 return sb.toString();
430 public String showBackbone()
432 return "select *; cartoons off; backbone";