toShow)
+ {
+ StringBuilder atomSpec = new StringBuilder(128);
+ boolean first = true;
+ for (String chain : toShow)
+ {
+ String[] tokens = chain.split(":");
+ if (tokens.length == 2)
+ {
+ if (!first)
+ {
+ atomSpec.append(" or ");
+ }
+ first = false;
+ atomSpec.append(":").append(tokens[1]).append(" /")
+ .append(tokens[0]);
+ }
+ }
+
+ String spec = atomSpec.toString();
+ String command = "select *;restrict " + spec + ";cartoon;center "
+ + spec;
+ return Arrays.asList(new StructureCommand(command));
+ }
+
+ /**
+ * Returns a command to superpose atoms in {@code atomSpec} to those in
+ * {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
+ * For example
+ *
+ *
+ * compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
+ * ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
+ *
+ *
+ * where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
+ * time in seconds to animate the action. For this example, atoms in model 2
+ * are moved towards atoms in model 1.
+ *
+ * The two atomspecs should each be for one model only, but may have more than
+ * one chain. The number of atoms specified should be the same for both
+ * models, though if not, Jmol may make a 'best effort' at superposition.
+ *
+ * @see https://chemapps.stolaf.edu/jmol/docs/#compare
+ */
+ @Override
+ public List superposeStructures(AtomSpecModel refAtoms,
+ AtomSpecModel atomSpec, AtomSpecType backbone)
+ {
+ StringBuilder sb = new StringBuilder(64);
+ String refModel = refAtoms.getModels().iterator().next();
+ String model2 = atomSpec.getModels().iterator().next();
+ sb.append(String.format("compare {%s.1} {%s.1}", model2, refModel));
+ sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
+
+ /*
+ * command examples don't include modelspec with atoms, getAtomSpec does;
+ * it works, so leave it as it is for simplicity
+ */
+ sb.append(getAtomSpec(atomSpec, backbone)).append("}{");
+ sb.append(getAtomSpec(refAtoms, backbone)).append("}");
+ sb.append(" ROTATE TRANSLATE ");
+ sb.append(getCommandSeparator());
+
+ /*
+ * show residues used for superposition as ribbon
+ */
+ sb.append("select ")
+ .append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY))
+ .append("|");
+ sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY))
+ .append(getCommandSeparator()).append("cartoons");
+ return Arrays.asList(new StructureCommand(sb.toString()));
+ }
+
+ @Override
+ public List centerViewOn(List residues)
+ {
+ StringBuilder sb = new StringBuilder(64);
+ sb.append("center ");
+ for (AtomSpecModel ranges : residues)
+ {
+ if (sb.length() > 9)
+ {
+ sb.append(" or ");
+ }
+ sb.append(getAtomSpec(ranges, AtomSpecType.RESIDUE_ONLY));
+ }
+ return Arrays.asList(new StructureCommand(sb.toString()));
+ }
+
+ @Override
+ public StructureCommandI openCommandFile(String path)
+ {
+ /*
+ * https://chemapps.stolaf.edu/jmol/docs/#script
+ * not currently used in Jalview
+ */
+ return new StructureCommand("script " + path);
+ }
+
+ @Override
+ public StructureCommandI saveSession(String filepath)
+ {
+ /*
+ * https://chemapps.stolaf.edu/jmol/docs/#writemodel
+ */
+ StructureCommand sc = new StructureCommand(
+ "write STATE \"" + filepath + "\"");
+ sc.setWaitNeeded(true);
+ return sc;
+ }
+
+ @Override
+ protected StructureCommandI colourResidues(String atomSpec, Color colour)
+ {
+ StringBuilder sb = new StringBuilder(atomSpec.length() + 20);
+ sb.append("select ").append(atomSpec).append(getCommandSeparator())
+ .append("color").append(getColourString(colour));
+ return new StructureCommand(sb.toString());
+ }
+
+ @Override
+ protected String getResidueSpec(String residue)
+ {
+ return residue;
+ }
+
+ /**
+ * Generates a Jmol atomspec string like
+ *
+ *
+ * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
+ *
+ *
+ * Parameter {@code alphaOnly} is not used here - this restriction is made by
+ * a separate clause in the {@code compare} (superposition) command.
+ */
+ @Override
+ public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
+ {
+ StringBuilder sb = new StringBuilder(128);
+
+ boolean first = true;
+ for (String modelNo : model.getModels())
+ {
+ for (String chain : model.getChains(modelNo))
+ {
+ for (int[] range : model.getRanges(modelNo, chain))
+ {
+ if (!first)
+ {
+ sb.append(PIPE);
+ }
+ first = false;
+ if (range[0] == range[1])
+ {
+ sb.append(range[0]);
+ }
+ else
+ {
+ sb.append(range[0]).append(HYPHEN).append(range[1]);
+ }
+ sb.append(COLON).append(chain.trim()).append(SLASH);
+ sb.append(String.valueOf(modelNo)).append(".1");
+ }
+ }
+ }
+
+ return sb.toString();
+ }
+
+ @Override
+ public List showBackbone()
+ {
+ return Arrays.asList(SHOW_BACKBONE);
+ }
+
+ @Override
+ public StructureCommandI loadFile(String file)
+ {
+ // https://chemapps.stolaf.edu/jmol/docs/#loadfiles
+ return new StructureCommand(
+ "load FILES \"" + Platform.escapeBackslashes(file) + "\"");
+ }
+
+ @Override
+ public StructureCommandI restoreSession(String filePath)
+ {
+ return new StructureCommand("restore STATE \""
+ + Platform.escapeBackslashes(filePath) + "\"");
+ }
+
+ @Override
+ public List showHetatms(List toShow)
+ {
+ // always clear the current hetero cpk display
+
+ StringBuilder sb = new StringBuilder();
+ sb.append("select hetero; cpk off;");
+
+ if (toShow != null && !toShow.isEmpty())
+ {
+ // select what was requested
+ sb.append("select ");
+ boolean or = false;
+ for (String k : toShow)
+ {
+ sb.append(or ? " or " : " ");
+ sb.append(k);
+ or = true;
+ }
+ // and show as
+ sb.append("; cpk;");
+ }
+
+ return Arrays.asList(new StructureCommand(sb.toString()));
+ }
+
+ /**
+ * Obsolete method, only referenced from
+ * jalview.javascript.MouseOverStructureListener
+ *
+ * @param ssm
+ * @param files
+ * @param sequence
+ * @param sr
+ * @param viewPanel
+ * @return
+ */
+ @Deprecated
+ public String[] colourBySequence(StructureSelectionManager ssm,
+ String[] files, SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
+ {
+ // TODO delete method
+
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+ AlignViewportI viewport = viewPanel.getAlignViewport();
+ HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
+ AlignmentI al = viewport.getAlignment();
+ List cset = new ArrayList<>();
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+ StringBuilder command = new StringBuilder(128);
+ List str = new ArrayList<>();
+
+ if (mapping == null || mapping.length < 1)
+ {
+ continue;
+ }
+
+ for (int s = 0; s < sequence[pdbfnum].length; s++)
+ {
+ for (int sp, m = 0; m < mapping.length; m++)
+ {
+ if (mapping[m].getSequence() == sequence[pdbfnum][s]
+ && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
+ {
+ int lastPos = StructureMapping.UNASSIGNED_VALUE;
+ SequenceI asp = al.getSequenceAt(sp);
+ for (int r = 0; r < asp.getLength(); r++)
+ {
+ // no mapping to gaps in sequence
+ if (Comparison.isGap(asp.getCharAt(r)))
+ {
+ continue;
+ }
+ int pos = mapping[m].getPDBResNum(asp.findPosition(r));
+
+ if (pos == lastPos)
+ {
+ continue;
+ }
+ if (pos == StructureMapping.UNASSIGNED_VALUE)
+ {
+ // terminate current colour op
+ if (command.length() > 0
+ && command.charAt(command.length() - 1) != ';')
+ {
+ command.append(";");
+ }
+ // reset lastPos
+ lastPos = StructureMapping.UNASSIGNED_VALUE;
+ continue;
+ }
+
+ lastPos = pos;
+
+ Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
+ finder);
+
+ /*
+ * shade hidden regions darker
+ */
+ if (!cs.isVisible(r))
+ {
+ col = Color.GRAY;
+ }
+
+ String newSelcom = (mapping[m].getChain() != " "
+ ? ":" + mapping[m].getChain()
+ : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
+ + getColourString(col);
+ if (command.length() > newSelcom.length() && command
+ .substring(command.length() - newSelcom.length())
+ .equals(newSelcom))
+ {
+ command = JmolCommands.condenseCommand(command, pos);
+ continue;
+ }
+ // TODO: deal with case when buffer is too large for Jmol to parse
+ // - execute command and flush
+
+ if (command.length() > 0
+ && command.charAt(command.length() - 1) != ';')
+ {
+ command.append(";");
+ }
+
+ if (command.length() > 51200)
+ {
+ // add another chunk
+ str.add(command.toString());
+ command.setLength(0);
+ }
+ command.append("select " + pos);
+ command.append(newSelcom);
+ }
+ // break;
+ }
+ }
+ }
+ {
+ // add final chunk
+ str.add(command.toString());
+ command.setLength(0);
+ }
+ cset.addAll(str);
+
+ }
+ return cset.toArray(new String[cset.size()]);
+ }
+
+ /**
+ * Helper method
+ *
+ * @param command
+ * @param pos
+ * @return
+ */
+ @Deprecated
+ private static StringBuilder condenseCommand(StringBuilder command,
+ int pos)
+ {
+
+ // work back to last 'select'
+ int p = command.length(), q = p;
+ do
+ {
+ p -= 6;
+ if (p < 1)
+ {
+ p = 0;
+ }
+ ;
+ } while ((q = command.indexOf("select", p)) == -1 && p > 0);
+
+ StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
+
+ command = command.delete(0, q + 7);
+
+ String start;
+
+ if (command.indexOf("-") > -1)
+ {
+ start = command.substring(0, command.indexOf("-"));
+ }
+ else
+ {
+ start = command.substring(0, command.indexOf(":"));
+ }
+
+ sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
+
+ return sb;
+ }
+
+ @Override
+ public StructureCommandI openSession(String filepath)
+ {
+ return loadFile(filepath);
+ }
+
+ @Override
+ public StructureCommandI closeViewer()
+ {
+ return null; // not an external viewer
+ }
+}