X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fpymol%2FPymolCommands.java;fp=src%2Fjalview%2Fext%2Fpymol%2FPymolCommands.java;h=36957f5548785aec9dc0043eff733c88fad798a8;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=0000000000000000000000000000000000000000;hpb=cfb79b69d9fa44595560659bd95d1d1cd27677ad;p=jalview.git diff --git a/src/jalview/ext/pymol/PymolCommands.java b/src/jalview/ext/pymol/PymolCommands.java new file mode 100644 index 0000000..36957f5 --- /dev/null +++ b/src/jalview/ext/pymol/PymolCommands.java @@ -0,0 +1,335 @@ +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) + { + // https://pymolwiki.org/index.php/Super + List commands = new ArrayList<>(); + String refAtomsAlphaOnly = getAtomSpec(refAtoms, true); + String atomSpec2AlphaOnly = getAtomSpec(atomSpec, true); + commands.add(new StructureCommand("super", refAtomsAlphaOnly, + atomSpec2AlphaOnly)); + + /* + * and show superposed residues as cartoon + */ + String refAtomsAll = getAtomSpec(refAtoms, false); + String atomSpec2All = getAtomSpec(atomSpec, false); + 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, boolean alphaOnly) + { + 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 (alphaOnly) + { + sb.append("CA"); + } + } + } + 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, false); + 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; + } + +}