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("zoom 0");
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(Map<String, Color> colours)
118 List<StructureCommandI> cmds = super.colourByResidues(colours);
119 cmds.add(0, COLOUR_ALL_WHITE);
124 public StructureCommandI setBackgroundColour(Color col)
126 return new StructureCommand("background " + getColourString(col));
130 public StructureCommandI focusView()
136 public List<StructureCommandI> showChains(List<String> toShow)
138 StringBuilder atomSpec = new StringBuilder(128);
139 boolean first = true;
140 for (String chain : toShow)
142 String[] tokens = chain.split(":");
143 if (tokens.length == 2)
147 atomSpec.append(" or ");
150 atomSpec.append(":").append(tokens[1]).append(" /").append(tokens[0]);
154 String spec = atomSpec.toString();
155 String command = "select *;restrict " + spec + ";cartoon;center "
157 return Arrays.asList(new StructureCommand(command));
161 * Returns a command to superpose atoms in {@code atomSpec} to those in
162 * {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
166 * compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
167 * ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
170 * where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
171 * time in seconds to animate the action. For this example, atoms in model 2
172 * are moved towards atoms in model 1.
174 * The two atomspecs should each be for one model only, but may have more than
175 * one chain. The number of atoms specified should be the same for both
176 * models, though if not, Jmol may make a 'best effort' at superposition.
178 * @see https://chemapps.stolaf.edu/jmol/docs/#compare
181 public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
182 AtomSpecModel atomSpec, AtomSpecType backbone)
184 StringBuilder sb = new StringBuilder(64);
185 String refModel = refAtoms.getModels().iterator().next();
186 String model2 = atomSpec.getModels().iterator().next();
187 sb.append(String.format("compare {%s.1} {%s.1}", model2, refModel));
188 sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
191 * command examples don't include modelspec with atoms, getAtomSpec does;
192 * it works, so leave it as it is for simplicity
194 sb.append(getAtomSpec(atomSpec, backbone)).append("}{");
195 sb.append(getAtomSpec(refAtoms, backbone)).append("}");
196 sb.append(" ROTATE TRANSLATE ");
197 sb.append(getCommandSeparator());
200 * show residues used for superposition as ribbon
202 sb.append("select ").append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY)).append("|");
203 sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY)).append(getCommandSeparator())
206 return Arrays.asList(new StructureCommand(sb.toString()));
210 public StructureCommandI openCommandFile(String path)
213 * https://chemapps.stolaf.edu/jmol/docs/#script
214 * not currently used in Jalview
216 return new StructureCommand("script " + path);
220 public StructureCommandI saveSession(String filepath)
223 * https://chemapps.stolaf.edu/jmol/docs/#writemodel
225 return new StructureCommand("write STATE \"" + filepath + "\"");
229 protected StructureCommandI colourResidues(String atomSpec, Color colour)
231 StringBuilder sb = new StringBuilder(atomSpec.length()+20);
232 sb.append("select ").append(atomSpec).append(getCommandSeparator())
233 .append("color").append(getColourString(colour));
234 return new StructureCommand(sb.toString());
238 protected String getResidueSpec(String residue)
244 * Generates a Jmol atomspec string like
247 * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
250 * Parameter {@code alphaOnly} is not used here - this restriction is made by
251 * a separate clause in the {@code compare} (superposition) command.
254 public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
256 StringBuilder sb = new StringBuilder(128);
258 boolean first = true;
259 for (String modelNo : model.getModels())
261 for (String chain : model.getChains(modelNo))
263 for (int[] range : model.getRanges(modelNo, chain))
270 if (range[0] == range[1])
276 sb.append(range[0]).append(HYPHEN).append(range[1]);
278 sb.append(COLON).append(chain.trim()).append(SLASH);
279 sb.append(String.valueOf(modelNo)).append(".1");
284 return sb.toString();
288 public List<StructureCommandI> showBackbone()
290 return Arrays.asList(SHOW_BACKBONE);
294 public StructureCommandI loadFile(String file)
296 // https://chemapps.stolaf.edu/jmol/docs/#loadfiles
297 return new StructureCommand("load FILES \"" +
298 Platform.escapeBackslashes(file) + "\"");
302 * Obsolete method, only referenced from
303 * jalview.javascript.MouseOverStructureListener
313 public String[] colourBySequence(StructureSelectionManager ssm,
314 String[] files, SequenceI[][] sequence, SequenceRenderer sr,
315 AlignmentViewPanel viewPanel)
317 // TODO delete method
319 FeatureRenderer fr = viewPanel.getFeatureRenderer();
320 FeatureColourFinder finder = new FeatureColourFinder(fr);
321 AlignViewportI viewport = viewPanel.getAlignViewport();
322 HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
323 AlignmentI al = viewport.getAlignment();
324 List<String> cset = new ArrayList<>();
326 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
328 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
329 StringBuilder command = new StringBuilder(128);
330 List<String> str = new ArrayList<>();
332 if (mapping == null || mapping.length < 1)
337 for (int s = 0; s < sequence[pdbfnum].length; s++)
339 for (int sp, m = 0; m < mapping.length; m++)
341 if (mapping[m].getSequence() == sequence[pdbfnum][s]
342 && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
344 int lastPos = StructureMapping.UNASSIGNED_VALUE;
345 SequenceI asp = al.getSequenceAt(sp);
346 for (int r = 0; r < asp.getLength(); r++)
348 // no mapping to gaps in sequence
349 if (Comparison.isGap(asp.getCharAt(r)))
353 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
359 if (pos == StructureMapping.UNASSIGNED_VALUE)
361 // terminate current colour op
362 if (command.length() > 0
363 && command.charAt(command.length() - 1) != ';')
368 lastPos = StructureMapping.UNASSIGNED_VALUE;
374 Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
378 * shade hidden regions darker
380 if (!cs.isVisible(r))
385 String newSelcom = (mapping[m].getChain() != " "
386 ? ":" + mapping[m].getChain()
387 : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
388 + getColourString(col);
389 if (command.length() > newSelcom.length() && command
390 .substring(command.length() - newSelcom.length())
393 command = JmolCommands.condenseCommand(command, pos);
396 // TODO: deal with case when buffer is too large for Jmol to parse
397 // - execute command and flush
399 if (command.length() > 0
400 && command.charAt(command.length() - 1) != ';')
405 if (command.length() > 51200)
408 str.add(command.toString());
409 command.setLength(0);
411 command.append("select " + pos);
412 command.append(newSelcom);
420 str.add(command.toString());
421 command.setLength(0);
426 return cset.toArray(new String[cset.size()]);
437 private static StringBuilder condenseCommand(
438 StringBuilder command,
442 // work back to last 'select'
443 int p = command.length(), q = p;
452 } while ((q = command.indexOf("select", p)) == -1 && p > 0);
454 StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
456 command = command.delete(0, q + 7);
460 if (command.indexOf("-") > -1)
462 start = command.substring(0, command.indexOf("-"));
466 start = command.substring(0, command.indexOf(":"));
469 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
475 public StructureCommandI openSession(String filepath)
477 return loadFile(filepath);
481 public StructureCommandI closeViewer()
483 return null; // not an external viewer