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Merge branch 'develop' into efficiency/JAL-2034_JAL-1421
[jalview.git]
/
src
/
jalview
/
ext
/
jmol
/
JmolParser.java
diff --git
a/src/jalview/ext/jmol/JmolParser.java
b/src/jalview/ext/jmol/JmolParser.java
index
7056f0f
..
ea969ff
100644
(file)
--- a/
src/jalview/ext/jmol/JmolParser.java
+++ b/
src/jalview/ext/jmol/JmolParser.java
@@
-209,7
+209,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
Atom curAtom = new Atom(atom.x, atom.y, atom.z);
curAtom.atomIndex = atom.getIndex();
curAtom.chain = atom.getChainIDStr();
Atom curAtom = new Atom(atom.x, atom.y, atom.z);
curAtom.atomIndex = atom.getIndex();
curAtom.chain = atom.getChainIDStr();
- curAtom.insCode = atom.group.getInsertionCode();
+ curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' '
+ : atom.group.getInsertionCode();
curAtom.name = atom.getAtomName();
curAtom.number = atom.getAtomNumber();
curAtom.resName = atom.getGroup3(true);
curAtom.name = atom.getAtomName();
curAtom.number = atom.getAtomNumber();
curAtom.resName = atom.getGroup3(true);
@@
-219,7
+220,12
@@
public class JmolParser extends StructureFile implements JmolStatusListener
curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
- significantAtoms.add(curAtom);
+ // significantAtoms.add(curAtom);
+ // ignore atoms from subsequent models
+ if (!significantAtoms.contains(curAtom))
+ {
+ significantAtoms.add(curAtom);
+ }
prevAtom = atom;
}
}
prevAtom = atom;
}
}
@@
-230,6
+236,8
@@
public class JmolParser extends StructureFile implements JmolStatusListener
org.jmol.modelset.Atom prevAtom,
HashMap<String, org.jmol.modelset.Atom> chainTerMap)
{
org.jmol.modelset.Atom prevAtom,
HashMap<String, org.jmol.modelset.Atom> chainTerMap)
{
+ // System.out.println("Atom: " + curAtom.getAtomNumber()
+ // + " Last atom index " + curAtom.group.lastAtomIndex);
if (chainTerMap == null || prevAtom == null)
{
return true;
if (chainTerMap == null || prevAtom == null)
{
return true;