/* * 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.pymol; import java.awt.Color; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Map; import jalview.structure.AtomSpecModel; import jalview.structure.StructureCommand; import jalview.structure.StructureCommandI; import jalview.structure.StructureCommandsBase; /** * A class that generates commands to send to PyMol over its XML-RPC interface. *

* Note that because the xml-rpc interface can only accept one command at a * time, we can't concatenate commands, and must instead form and send them * individually. * * @see https://pymolwiki.org/index.php/Category:Commands * @see https://pymolwiki.org/index.php/RPC */ public class PymolCommands extends StructureCommandsBase { // https://pymol.org/dokuwiki/doku.php?id=command:zoom // not currently documented on // https://pymolwiki.org/index.php/Category:Commands private static final StructureCommand FOCUS_VIEW = new StructureCommand( "zoom"); // https://pymolwiki.org/index.php/Quit private static final StructureCommand CLOSE_PYMOL = new StructureCommand( "quit"); // not currently documented on // https://pymolwiki.org/index.php/Category:Commands private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand( "spectrum", "chain"); private static final List COLOR_BY_CHARGE = Arrays .asList(new StructureCommand("color", "white", "*"), new StructureCommand("color", "red", "resn ASP resn GLU"), new StructureCommand("color", "blue", "resn LYS resn ARG"), new StructureCommand("color", "yellow", "resn CYS")); private static final List SHOW_BACKBONE = Arrays .asList(new StructureCommand("hide", "everything"), new StructureCommand("show", "ribbon")); @Override public StructureCommandI colourByChain() { return COLOUR_BY_CHAIN; } @Override public List colourByCharge() { return COLOR_BY_CHARGE; } @Override public StructureCommandI setBackgroundColour(Color col) { // https://pymolwiki.org/index.php/Bg_Color return new StructureCommand("bg_color", getColourString(col)); } /** * Returns a colour formatted suitable for use in viewer command syntax. For * example, red is {@code "0xff0000"}. * * @param c * @return */ protected String getColourString(Color c) { return String.format("0x%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue()); } @Override public StructureCommandI focusView() { return FOCUS_VIEW; } @Override public List showChains(List toShow) { // https://pymolwiki.org/index.php/Show List commands = new ArrayList<>(); commands.add(new StructureCommand("hide", "everything")); commands.add(new StructureCommand("show", "lines")); StringBuilder chains = new StringBuilder(); for (String chain : toShow) { chains.append(" chain ").append(chain); } commands.add( new StructureCommand("show", "cartoon", chains.toString())); return commands; } @Override public List superposeStructures(AtomSpecModel refAtoms, AtomSpecModel atomSpec, AtomSpecType specType) { // https://pymolwiki.org/index.php/Super List commands = new ArrayList<>(); String refAtomsAlphaOnly = "(" + getAtomSpec(refAtoms, specType) + " and (altloc '' or altloc 'a'))"; String atomSpec2AlphaOnly = "(" + getAtomSpec(atomSpec, specType) + " and (altloc '' or altloc 'a'))"; // pair_fit mobile -> reference // crashes when undo is enabled on 2.5.2 (incentive) commands.add(new StructureCommand("undo_disable")); commands.add(new StructureCommand("pair_fit", atomSpec2AlphaOnly, refAtomsAlphaOnly)); commands.add(new StructureCommand("undo_enable")); /* * and show superposed residues as cartoon */ String refAtomsAll = getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY); String atomSpec2All = getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY); commands.add(new StructureCommand("show", "cartoon", refAtomsAll + " " + atomSpec2All)); return commands; } @Override public StructureCommandI openCommandFile(String path) { // https://pymolwiki.org/index.php/Run return new StructureCommand("run", path); // should be .pml } @Override public StructureCommandI saveSession(String filepath) { // https://pymolwiki.org/index.php/Save#EXAMPLES return new StructureCommand("save", filepath); // should be .pse } /** * Returns a selection string in PyMOL 'selection macro' format: * *

   * modelId// chain/residues/
   * 
* * If more than one chain, makes a selection expression for each, and they are * separated by spaces. * * @see https://pymolwiki.org/index.php/Selection_Macros */ @Override public String getAtomSpec(AtomSpecModel model, AtomSpecType specType) { StringBuilder sb = new StringBuilder(64); boolean first = true; for (String modelId : model.getModels()) { for (String chain : model.getChains(modelId)) { if (!first) { sb.append(" "); } first = false; List rangeList = model.getRanges(modelId, chain); chain = chain.trim(); sb.append(modelId).append("//").append(chain).append("/"); boolean firstRange = true; for (int[] range : rangeList) { if (!firstRange) { sb.append("+"); } firstRange = false; sb.append(String.valueOf(range[0])); if (range[0] != range[1]) { sb.append("-").append(String.valueOf(range[1])); } } sb.append("/"); if (specType == AtomSpecType.ALPHA) { sb.append("CA"); } if (specType == AtomSpecType.PHOSPHATE) { sb.append("P"); } } } return sb.toString(); } @Override public List showBackbone() { return SHOW_BACKBONE; } @Override protected StructureCommandI colourResidues(String atomSpec, Color colour) { // https://pymolwiki.org/index.php/Color return new StructureCommand("color", getColourString(colour), atomSpec); } @Override protected String getResidueSpec(String residue) { // https://pymolwiki.org/index.php/Selection_Algebra return "resn " + residue; } @Override public StructureCommandI loadFile(String file) { return new StructureCommand("load", file); } /** * Overrides the default implementation (which generates concatenated * commands) to generate one per colour (because the XML-RPC interface to * PyMOL only accepts one command at a time) * * @param colourMap * @return */ @Override public List colourBySequence( Map colourMap) { List commands = new ArrayList<>(); for (Object key : colourMap.keySet()) { Color colour = (Color) key; final AtomSpecModel colourData = colourMap.get(colour); commands.add(getColourCommand(colourData, colour)); } return commands; } /** * Returns a viewer command to set the given atom property value on atoms * specified by the AtomSpecModel, for example * *
   * iterate 4zho//B/12-34,48-55/CA,jv_chain='primary'
   * 
* * @param attributeName * @param attributeValue * @param atomSpecModel * @return */ protected StructureCommandI setAttribute(String attributeName, String attributeValue, AtomSpecModel atomSpecModel) { StringBuilder sb = new StringBuilder(128); sb.append("p.").append(attributeName).append("='") .append(attributeValue).append("'"); String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY); return new StructureCommand("iterate", atomSpec, sb.toString()); } /** * Traverse the map of features/values/models/chains/positions to construct a * list of 'set property' commands (one per distinct feature type and value). * The values are stored in the 'p' dictionary of user-defined properties of * each atom. *

* The format of each command is * *

   * 
iterate atomspec, p.featureName='value' * e.g. iterate 4zho//A/23,28-29/CA, p.jv_Metal='Fe' *
*
* * @param featureMap * @return */ @Override public List setAttributes( Map> featureMap) { List commands = new ArrayList<>(); for (String featureType : featureMap.keySet()) { String attributeName = makeAttributeName(featureType); /* * todo: clear down existing attributes for this feature? */ // commands.add(new StructureCommand("iterate", "all", // "p."+attributeName+"='None'"); //? Map values = featureMap.get(featureType); for (Object value : values.keySet()) { /* * for each distinct value recorded for this feature type, * add a command to set the attribute on the mapped residues * Put values in single quotes, encoding any embedded single quotes */ AtomSpecModel atomSpecModel = values.get(value); String featureValue = value.toString(); featureValue = featureValue.replaceAll("\\'", "'"); StructureCommandI cmd = setAttribute(attributeName, featureValue, atomSpecModel); commands.add(cmd); } } return commands; } @Override public StructureCommandI openSession(String filepath) { // https://pymolwiki.org/index.php/Load // this version of the command has no dependency on file extension return new StructureCommand("load", filepath, "", "0", "pse"); } @Override public StructureCommandI closeViewer() { // https://pymolwiki.org/index.php/Quit return CLOSE_PYMOL; } @Override public List centerViewOn(List residues) { // TODO Auto-generated method stub return null; } }