Package org.jmol.adapter.writers
Class PDBWriter
java.lang.Object
org.jmol.adapter.writers.PDBWriter
- All Implemented Interfaces:
JmolWriter
An XCrysDen XSF writer
see http://www.xcrysden.org/doc/XSF.html
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate boolean
private boolean
private boolean
private javajs.util.OC
private Viewer
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate int
fixPDBFormat
(javajs.util.Lst<String> lines, Map<String, 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 String
pdbKey
(int np) void
toString()
write
(javajs.util.BS bs)
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Field Details
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vwr
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oc
private javajs.util.OC oc -
isPQR
private boolean isPQR -
doTransform
private boolean doTransform -
allTrajectories
private boolean allTrajectories
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Constructor Details
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PDBWriter
public PDBWriter()
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Method Details
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set
- Specified by:
set
in interfaceJmolWriter
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write
- Specified by:
write
in interfaceJmolWriter
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pdbKey
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fixPDBFormat
private int fixPDBFormat(javajs.util.Lst<String> lines, Map<String, 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
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