--- /dev/null
+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.
+ * <p>
+ * 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<StructureCommandI> 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<StructureCommandI> SHOW_BACKBONE = Arrays
+ .asList(new StructureCommand("hide", "everything"),
+ new StructureCommand("show", "ribbon"));
+
+ @Override
+ public StructureCommandI colourByChain()
+ {
+ return COLOUR_BY_CHAIN;
+ }
+
+ @Override
+ public List<StructureCommandI> 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<StructureCommandI> showChains(List<String> toShow)
+ {
+ // https://pymolwiki.org/index.php/Show
+ List<StructureCommandI> 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<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
+ AtomSpecModel atomSpec)
+ {
+ // https://pymolwiki.org/index.php/Super
+ List<StructureCommandI> 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:
+ *
+ * <pre>
+ * modelId// chain/residues/
+ * </pre>
+ *
+ * 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<int[]> 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<StructureCommandI> 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<StructureCommandI> colourBySequence(
+ Map<Object, AtomSpecModel> colourMap)
+ {
+ List<StructureCommandI> 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
+ *
+ * <pre>
+ * iterate 4zho//B/12-34,48-55/CA,jv_chain='primary'
+ * </pre>
+ *
+ * @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.
+ * <p>
+ * The format of each command is
+ *
+ * <pre>
+ * <blockquote> iterate atomspec, p.featureName='value'
+ * e.g. iterate 4zho//A/23,28-29/CA, p.jv_Metal='Fe'
+ * </blockquote>
+ * </pre>
+ *
+ * @param featureMap
+ * @return
+ */
+ @Override
+ public List<StructureCommandI> setAttributes(
+ Map<String, Map<Object, AtomSpecModel>> featureMap)
+ {
+ List<StructureCommandI> 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<Object, AtomSpecModel> 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;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff