/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.ext.jmol; import java.awt.Color; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Map; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; import jalview.renderer.seqfeatures.FeatureColourFinder; import jalview.structure.AtomSpecModel; import jalview.structure.StructureCommand; import jalview.structure.StructureCommandI; import jalview.structure.StructureCommandsBase; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; import jalview.util.Comparison; import jalview.util.Platform; /** * Routines for generating Jmol commands for Jalview/Jmol binding * * @author JimP * */ public class JmolCommands extends StructureCommandsBase { private static final StructureCommand SHOW_BACKBONE = new StructureCommand( "select *; cartoons off; backbone"); private static final StructureCommand FOCUS_VIEW = new StructureCommand("zoom 0"); private static final StructureCommand COLOUR_ALL_WHITE = new StructureCommand( "select *;color white;"); private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand( "select *;color white;select ASP,GLU;color red;" + "select LYS,ARG;color blue;select CYS;color yellow"); private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand( "select *;color chain"); private static final String PIPE = "|"; private static final String HYPHEN = "-"; private static final String COLON = ":"; private static final String SLASH = "/"; /** * {@inheritDoc} * * @return */ @Override public int getModelStartNo() { return 1; } /** * Returns a string representation of the given colour suitable for inclusion * in Jmol commands * * @param c * @return */ protected String getColourString(Color c) { return c == null ? null : String.format("[%d,%d,%d]", c.getRed(), c.getGreen(), c.getBlue()); } @Override public StructureCommandI colourByChain() { return COLOUR_BY_CHAIN; } @Override public List colourByCharge() { return Arrays.asList(COLOUR_BY_CHARGE); } @Override public List colourByResidues(Map colours) { List cmds = super.colourByResidues(colours); cmds.add(0, COLOUR_ALL_WHITE); return cmds; } @Override public StructureCommandI setBackgroundColour(Color col) { return new StructureCommand("background " + getColourString(col)); } @Override public StructureCommandI focusView() { return FOCUS_VIEW; } @Override public List showChains(List 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) { 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, 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 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 */ return new StructureCommand("write STATE \"" + filepath + "\""); } @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, boolean alphaOnly) { 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) + "\""); } /** * 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 } }