X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fpymol%2FPymolCommands.java;h=ae91aa581954bec873a4314a28ad3fbfaf0b619e;hb=0b6e9403e96ee9f0d41211b2f90130ff850c4e98;hp=910aae1d69eef0428c7299519946eb95f432ff8b;hpb=8c29d4d93761896bb75c6c3b24c3fdd0612c7bb3;p=jalview.git
diff --git a/src/jalview/ext/pymol/PymolCommands.java b/src/jalview/ext/pymol/PymolCommands.java
index 910aae1..ae91aa5 100644
--- a/src/jalview/ext/pymol/PymolCommands.java
+++ b/src/jalview/ext/pymol/PymolCommands.java
@@ -1,14 +1,16 @@
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;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.List;
-
/**
* A class that generates commands to send to PyMol over its XML-RPC interface.
*
@@ -21,23 +23,31 @@ import java.util.List;
*/
public class PymolCommands extends StructureCommandsBase
{
- private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand("spectrum", "chain");
+ // 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");
- private static final List COLOR_BY_CHARGE = new ArrayList<>();
+ // https://pymolwiki.org/index.php/Quit
+ private static final StructureCommand CLOSE_PYMOL = new StructureCommand(
+ "quit");
- private static final List SHOW_BACKBONE = new ArrayList<>();
+ // not currently documented on
+ // https://pymolwiki.org/index.php/Category:Commands
+ private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand(
+ "spectrum", "chain");
- 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", "yellow", "resn CYS"));
- SHOW_BACKBONE.add(new StructureCommand("hide", "everything"));
- SHOW_BACKBONE.add(new StructureCommand("show", "ribbon"));
- }
+ 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()
@@ -74,8 +84,7 @@ public class PymolCommands extends StructureCommandsBase
@Override
public StructureCommandI focusView()
{
- // TODO what?
- return null;
+ return FOCUS_VIEW;
}
@Override
@@ -90,20 +99,22 @@ public class PymolCommands extends StructureCommandsBase
{
chains.append(" chain ").append(chain);
}
- commands.add(new StructureCommand("show", "cartoon", chains.toString()));
+ commands.add(
+ new StructureCommand("show", "cartoon", chains.toString()));
return commands;
}
@Override
public List superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec)
+ AtomSpecModel atomSpec, boolean isNucleotide)
{
// 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));
+ String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, true)+" and (altloc '' or altloc 'a'))";
+ String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, true)+" and (altloc '' or altloc 'a'))";
+ // pair_fit mobile -> reference
+ commands.add(new StructureCommand("pair_fit",
+ atomSpec2AlphaOnly, refAtomsAlphaOnly));
/*
* and show superposed residues as cartoon
@@ -119,9 +130,8 @@ public class PymolCommands extends StructureCommandsBase
@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
+ // https://pymolwiki.org/index.php/Run
+ return new StructureCommand("run", path); // should be .pml
}
@Override
@@ -191,7 +201,7 @@ public class PymolCommands extends StructureCommandsBase
}
@Override
- protected StructureCommandI getColourCommand(String atomSpec, Color colour)
+ protected StructureCommandI colourResidues(String atomSpec, Color colour)
{
// https://pymolwiki.org/index.php/Color
return new StructureCommand("color", getColourString(colour), atomSpec);
@@ -210,4 +220,117 @@ public class PymolCommands extends StructureCommandsBase
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