It seems to me that there is a small problem with parsing pdb files
that contain hydrogen atoms. I don't see this problem with most pdb
files.
--Chuck
Using 1GXX this code snippet produces the output below:
private String[] getMoleculeElements(String script)
{
if(null != script)
{
System.out.println("\nViewer.getMoleculeElements
script: " + script);
MySelectionListener mySelectionListener = new
MySelectionListener();
getJmolViewer().addSelectionListener(mySelectionListener);
getJmolViewer().scriptWait(script);
int atomCount = getJmolViewer().getSelectionCount();
BitSet bitSet =
mySelectionListener.getSelectionBitSet();
getJmolViewer().removeSelectionListener(mySelectionListener);
return extractArray(atomCount, bitSet);
}
return null;
}
public String[] extractArray(int count, BitSet bitset)
{
ArrayList<String> arrayList = new ArrayList<String>();
String current = null;
int bitIndex = 0;
for(int i=0; count != i; i++)
{
bitIndex = bitset.nextSetBit(bitIndex);
String atomInfo =
getJmolViewer().getAtomInfo(bitIndex++);
System.err.println("Viewer.extractArray atomInfo: " +
atomInfo);
}
return arrayList.toArray(new String[0]);
}
class MySelectionListener implements JmolSelectionListener
{
BitSet selectionBitSet = null;
public BitSet getSelectionBitSet()
{
return this.selectionBitSet;
}
public synchronized void selectionChanged(BitSet
selectionBitSet)
{
this.selectionBitSet = (BitSet) selectionBitSet.clone();
}
}
Viewer.getMoleculeElements script: select none; select water; ---
SHOULD PRODUCE ON WATER
Viewer.extractArray atomInfo: [LYS]1:A.H1 #10
Viewer.extractArray atomInfo: [ARG]21:A.HH21 #341
Viewer.extractArray atomInfo: [THR]40:A.OG1 #613
Viewer.extractArray atomInfo: [THR]40:A.HG1 #618
Viewer.extractArray atomInfo: [SER]50:A.OG #753
Viewer.extractArray atomInfo: [SER]50:A.HG #758
Viewer.extractArray atomInfo: [ASN]59:A.HD22 #900
Viewer.extractArray atomInfo: [SER]60:A.HG #911
Viewer.extractArray atomInfo: [THR]69:A.OG1 #1056
Viewer.extractArray atomInfo: [THR]69:A.HG1 #1061
Viewer.extractArray atomInfo: [SER]100:A.OG #1502
Viewer.extractArray atomInfo: [SER]100:A.HG #1507
Viewer.extractArray atomInfo: [HOH]130:A.O #1962
Viewer.extractArray atomInfo: [HOH]130:A.H1 #1963
Viewer.extractArray atomInfo: [HOH]130:A.H2 #1964
Viewer.extractArray atomInfo: [HOH]131:A.O #1965
Viewer.extractArray atomInfo: [HOH]131:A.H1 #1966
Viewer.extractArray atomInfo: [HOH]131:A.H2 #1967
Viewer.extractArray atomInfo: [HOH]132:A.O #1968
Viewer.extractArray atomInfo: [HOH]132:A.H1 #1969
Viewer.extractArray atomInfo: [HOH]132:A.H2 #1970
Viewer.extractArray atomInfo: [HOH]133:A.O #1971
Viewer.extractArray atomInfo: [HOH]133:A.H1 #1972
Viewer.extractArray atomInfo: [HOH]133:A.H2 #1973
Viewer.extractArray atomInfo: [HOH]134:A.O #1974
Viewer.extractArray atomInfo: [HOH]134:A.H1 #1975
Viewer.extractArray atomInfo: [HOH]134:A.H2 #1976
Viewer.getMoleculeElements script: select none; select hetero xor
water; --- SHOULDN'T PRODUCE ANYTHING
Viewer.extractArray atomInfo: [LYS]1:A.H1 #10
Viewer.extractArray atomInfo: [ARG]21:A.HH21 #341
Viewer.extractArray atomInfo: [THR]40:A.OG1 #613
Viewer.extractArray atomInfo: [THR]40:A.HG1 #618
Viewer.extractArray atomInfo: [SER]50:A.OG #753
Viewer.extractArray atomInfo: [SER]50:A.HG #758
Viewer.extractArray atomInfo: [ASN]59:A.HD22 #900
Viewer.extractArray atomInfo: [SER]60:A.HG #911
Viewer.extractArray atomInfo: [THR]69:A.OG1 #1056
Viewer.extractArray atomInfo: [THR]69:A.HG1 #1061
Viewer.extractArray atomInfo: [SER]100:A.OG #1502
Viewer.extractArray atomInfo: [SER]100:A.HG #1507
------------------------------------------------------------------------------
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