* 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 String superposeStructures(AtomSpecModel refAtoms, AtomSpecModel atomSpec) { StringBuilder sb = new StringBuilder(64); int refModel = refAtoms.getModels().iterator().next(); int model2 = atomSpec.getModels().iterator().next(); sb.append(String.format("compare {%d.1} {%d.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, true)).append("}{"); sb.append(getAtomSpec(refAtoms, true)).append("}"); sb.append(" ROTATE TRANSLATE "); sb.append(getCommandSeparator()); /* * show residues used for superposition as ribbon */ sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|"); sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator()) .append("cartoons"); return sb.toString(); } @Override public String openCommandFile(String path) { /* * https://chemapps.stolaf.edu/jmol/docs/#script * not currently used in Jalview */ return "script " + path; } @Override public String saveSession(String filepath) { /* * https://chemapps.stolaf.edu/jmol/docs/#write * not currently used in Jalview */ return "write \"" + filepath + "\""; } @Override protected String getColourCommand(String atomSpec, Color colour) { StringBuilder sb = new StringBuilder(atomSpec.length()+20); sb.append("select ").append(atomSpec).append(getCommandSeparator()) .append("color").append(getColourString(colour)); return 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, boolean alphaOnly) { StringBuilder sb = new StringBuilder(128); boolean first = true; for (int 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 String showBackbone() { return "select *; cartoons off; backbone"; } }