Package org.jmol.adapter.writers
Class PDBWriter
- java.lang.Object
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- org.jmol.adapter.writers.PDBWriter
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- All Implemented Interfaces:
JmolWriter
public class PDBWriter extends java.lang.Object implements JmolWriter
An XCrysDen XSF writer see http://www.xcrysden.org/doc/XSF.html
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Field Summary
Fields Modifier and Type Field Description private boolean
allTrajectories
private boolean
doTransform
private boolean
isPQR
private javajs.util.OC
oc
private Viewer
vwr
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Constructor Summary
Constructors Constructor Description PDBWriter()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private int
fixPDBFormat(javajs.util.Lst<java.lang.String> lines, java.util.Map<java.lang.String,java.lang.Integer> map, javajs.util.OC out, int[] firstAtomIndexNew, int modelPt)
must re-order by resno and then renumber atoms and add TER records based on BioPolymers note: 3hbt has a break between residues 39 and 51 with no TER record, but Jmol will put that in.private java.lang.String
pdbKey(int np)
void
set(Viewer viewer, javajs.util.OC oc, java.lang.Object[] data)
java.lang.String
toString()
java.lang.String
write(javajs.util.BS bs)
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Field Detail
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vwr
private Viewer vwr
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oc
private javajs.util.OC oc
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isPQR
private boolean isPQR
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doTransform
private boolean doTransform
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allTrajectories
private boolean allTrajectories
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Method Detail
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set
public void set(Viewer viewer, javajs.util.OC oc, java.lang.Object[] data)
- Specified by:
set
in interfaceJmolWriter
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write
public java.lang.String write(javajs.util.BS bs)
- Specified by:
write
in interfaceJmolWriter
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pdbKey
private java.lang.String pdbKey(int np)
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fixPDBFormat
private int fixPDBFormat(javajs.util.Lst<java.lang.String> lines, java.util.Map<java.lang.String,java.lang.Integer> map, javajs.util.OC out, int[] firstAtomIndexNew, int modelPt)
must re-order by resno and then renumber atoms and add TER records based on BioPolymers note: 3hbt has a break between residues 39 and 51 with no TER record, but Jmol will put that in.- Parameters:
lines
-map
-out
-modelPt
-firstAtomIndexNew
-- Returns:
- new modelPt
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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