--- /dev/null
+package jalview.ext.pymol;
+
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsBase;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * A class that generates commands to send to PyMol
+ *
+ * @see https://pymolwiki.org/index.php/Category:Commands
+ */
+public class PymolCommands extends StructureCommandsBase
+{
+ private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
+ "util.cbc");
+
+ /*
+ * 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
+ */
+ private static final List<StructureCommandI> COLOR_BY_CHARGE = new ArrayList<>();
+
+ private static final List<StructureCommandI> SHOW_BACKBONE = new ArrayList<>();
+
+ static {
+ COLOR_BY_CHARGE.add(new StructureCommand("color", "white", "*"));
+ COLOR_BY_CHARGE
+ .add(new StructureCommand("color", "red", "resn ASP resn GLU"));
+ COLOR_BY_CHARGE.add(
+ new StructureCommand("color", "blue", "resn LYS resn ARG"));
+ COLOR_BY_CHARGE.add(new StructureCommand("color"));
+ SHOW_BACKBONE.add(new StructureCommand("hide", "everything"));
+ SHOW_BACKBONE.add(new StructureCommand("show", "ribbon"));
+ }
+
+ @Override
+ public StructureCommandI colourByChain()
+ {
+ // https://pymolwiki.org/index.php/CBC
+ // TODO this doesn't execute as an xml-rpc command
+ 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()
+ {
+ // TODO what?
+ return null;
+ }
+
+ @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)
+ {
+ // where is this documented by PyMol?
+ // todo : xml-rpc answers 'method "@" is not supported'
+ return new StructureCommand("@" + 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 getColourCommand(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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff