Author: scooter
Date: 2011-10-08 14:09:00 -0700 (Sat, 08 Oct 2011)
New Revision: 27114
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
Log:
Added fixes for changes to SFLD network downloads
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
2011-10-08 19:43:55 UTC (rev 27113)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
2011-10-08 21:09:00 UTC (rev 27114)
@@ -73,7 +73,7 @@
* @author scooter
*/
public class CyChimera {
- public static final String[] structureKeys =
{"Structure","pdb","pdbFileName","PDB ID","structure","biopax.xref.PDB",null};
+ public static final String[] structureKeys =
{"Structure","pdb","pdbFileName","PDB
ID","structure","biopax.xref.PDB","pdb_ids",null};
public static final String[] chemStructKeys =
{"Smiles","smiles","SMILES",null};
public static final String[] residueKeys =
{"FunctionalResidues","ResidueList",null};
public static final String[] sequenceKeys = {"sequence",null};
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2011-10-08 19:43:55 UTC (rev 27113)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2011-10-08 21:09:00 UTC (rev 27114)
@@ -358,6 +358,15 @@
chain = resChain[1];
range[res] = resChain[0];
}
+ // Fix weird SFLD syntax...
+ if (range[res].indexOf('|') > 0 &&
+ Character.isDigit(range[res].charAt(0))) {
+ int offset = range[res].indexOf('|');
+ String str =
range[res].substring(offset+1) +
+ range[res].substring(0,
offset);
+ range[res] = str;
+ }
+
// Convert to legal atom-spec
if (Character.isDigit(range[res].charAt(0))) {
resRange = resRange.concat(range[res]);
--
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