Author: scooter
Date: 2010-07-08 22:24:24 -0700 (Thu, 08 Jul 2010)
New Revision: 20865
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/AnalysisCommands.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/StructureVizCommandHandler.java
Log:
Started work on Align
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/AnalysisCommands.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/AnalysisCommands.java
2010-07-09 05:01:18 UTC (rev 20864)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/AnalysisCommands.java
2010-07-09 05:24:24 UTC (rev 20865)
@@ -103,4 +103,19 @@
return result;
}
+ static public CyCommandResult alignStructures(Chimera chimera,
CyCommandResult result,
+
List<Structure>referenceStruct,
+
List<Structure>structureList) {
+ // Do the alignment
+
+ return result;
+ }
+
+ static public CyCommandResult alignChains(Chimera chimera,
CyCommandResult result,
+
List<ChimeraStructuralObject>reference,
+
List<ChimeraStructuralObject>chainList) {
+ // Make sure everything is a chain
+ // Do the alignment
+ return result;
+ }
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/StructureVizCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/StructureVizCommandHandler.java
2010-07-09 05:01:18 UTC (rev 20864)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/commands/StructureVizCommandHandler.java
2010-07-09 05:24:24 UTC (rev 20865)
@@ -58,7 +58,10 @@
enum Command {
ALIGNSTRUCTURES("alignstructures",
"Perform sequence-driven structural superposition on a
group of structures",
- "reference|structureList|referencechain|chainlist"),
+ "reference|structurelist"),
+ ALIGNCHAINS("alignchains",
+ "Perform sequence-driven structural superposition on a
group of structures by chain",
+ "referencechain|chainlist"),
CLEARCLASHES("clear clashes", "Clear clashes", ""),
CLEARHBONDS("clear hbonds", "Clear hydrogen bonds", ""),
CLEARSELECT("clear selection", "Clear all selection", ""),
@@ -76,7 +79,7 @@
LISTRES("list residues", "List the residues in a structure",
"structurelist=all|chain"),
LISTSTRUCTURES("list structures", "List all of the open structures",""),
MOVE("move", "Move (translate) a model","x|y|z|structurelist=selected"),
- OPENSTRUCTURE("open structure", "Open a new structure in
Chimera","pdbid|modbaseid|nodeList"),
+ OPENSTRUCTURE("open structure", "Open a new structure in
Chimera","pdbid|modbaseid|nodelist"),
RAINBOW("rainbow", "Color part of all of a structure in a rainbow
scheme",
"structurelist|atomspec"),
ROTATE("rotate", "Rotate a
model","x|y|z|center|structurelist=selected"),
@@ -110,11 +113,14 @@
public static final String ATOMSPEC = "atomspec";
public static final String CHAIN = "chain";
+ public static final String CHAINLIST = "chainlist";
public static final String CONTINUOUS = "continuous";
public static final String LABELS = "labels";
- public static final String MODELLIST = "modelList";
- public static final String NODELIST = "nodeList";
+ public static final String MODELLIST = "modellist";
+ public static final String NODELIST = "nodelist";
public static final String PRESET = "preset";
+ public static final String REFERENCE = "reference";
+ public static final String REFERENCECHAIN = "referencechain";
public static final String RESIDUES = "residues";
public static final String RIBBONS = "ribbons";
public static final String RIBBONSTYLE = "ribbonstyle";
@@ -161,7 +167,36 @@
List<Structure> structureList =
CommandUtils.getStructureList(structureSpec, chimera);
// Main command cascade
+
+ //
+ // ALIGNSTRUCTURES("alignstructures",
+ // "Perform sequence-driven structural superposition
on a group of structures",
+ // "reference|structurelist"),
+ //
if (Command.ALIGNSTRUCTURES.equals(command)) {
+ String reference = getArg(command,REFERENCE, args);
+ if (reference != null && structureList == null)
+ throw new CyCommandException("Need a list of
structures to compare against "+reference);
+ if (reference == null)
+ throw new CyCommandException("Must specify a
reference structure");
+ List<Structure> referenceStruct =
CommandUtils.getStructureList(reference, chimera);
+ result = AnalysisCommands.alignStructures(chimera,
result, referenceStruct, structureList);
+
+ //
+ // ALIGNCHAINS("alignchains",
+ // "Perform sequence-driven structural superposition on a
group of structures by chain",
+ // "referencechain|chainlist"),
+ //
+ } else if (Command.ALIGNCHAINS.equals(command)) {
+ String reference = getArg(command,REFERENCECHAIN, args);
+ String chainlist = getArg(command,CHAINLIST, args);
+ if (reference != null && chainlist == null)
+ throw new CyCommandException("Need a list of
chains to compare against "+reference);
+ if (reference == null)
+ throw new CyCommandException("Must specify a
reference chain");
+ List<ChimeraStructuralObject> referenceCSO =
CommandUtils.getSpecList(reference,chimera);
+ List<ChimeraStructuralObject> chainList =
CommandUtils.getSpecList(chainlist,chimera);
+ result = AnalysisCommands.alignChains(chimera, result,
referenceCSO, chainList);
//
// CLEARCLASHES("clear clashes", "Clear clashes"),
@@ -320,15 +355,15 @@
}
//
- // OPENSTRUCTURE("open structure", "Open a new structure in
Chimera","pdbid|modbaseid|nodeList"),
+ // OPENSTRUCTURE("open structure", "Open a new structure in
Chimera","pdbid|modbaseid|nodelist"),
//
} else if (Command.OPENSTRUCTURE.equals(command)) {
String pdb = getArg(command, "pdbid", args);
String modbaseid = getArg(command, "modbaseid", args);
String smiles = getArg(command, "smiles", args);
- String nodelist = getArg(command, "nodeList", args);
+ String nodelist = getArg(command, NODELIST, args);
if (pdb == null && modbaseid == null && smiles == null
&& nodelist == null)
- throw new CyCommandException("One of nodeList,
pdbid, modbaseid, or smiles must be specified");
+ throw new CyCommandException("One of nodelist,
pdbid, modbaseid, or smiles must be specified");
if (nodelist != null) {
return StructureCommands.openCommand(chimera,
result, nodelist);
--
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