Package org.jmol.adapter.readers.cif
Class TopoCifParser.TLink
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetObject
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- org.jmol.adapter.smarter.Bond
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- org.jmol.adapter.readers.cif.TopoCifParser.TLink
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- Enclosing class:
- TopoCifParser
private class TopoCifParser.TLink extends Bond
A class to hold the TOPOL_LINK data item information and transform it as needed. A key field is the primitives array of TopoPrimitives. These structures allow us to create a set of "primitive" operation results that operate specifically on the links themselves. Rather than showing those links (as with the Jmol script commented at the end of this class), we choose to first create the standard Jmol atom set using, for example, load hcb.cif PACKED or load xxx.cif {1 1 1} or load xxx.cif {444 666 1}, etc. Then we match those atoms with link edges by unitizing the atom back to its unit cell 555 site and then comparing with the primitive associated with a given operator.
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Field Summary
Fields Modifier and Type Field Description (package private) javajs.util.BS
bsAtoms
(package private) javajs.util.BS
bsBonds
(package private) float
cartesianDistance
(package private) boolean
finalized
(package private) java.lang.String
id
(package private) int
idx
private java.lang.String
line
(package private) TopoCifParser.TNode[]
linkNodes
private java.lang.String
mf
(package private) int
multiplicity
(package private) TopoCifParser.TNet
net
(package private) java.lang.String
netID
(package private) java.lang.String
netLabel
(package private) java.lang.String[]
nodeIds
(package private) java.lang.String[]
nodeLabels
(package private) int[]
symops
(package private) javajs.util.Lst<TopoCifParser.TAtom>
tatoms
(package private) int
topoOrder
(package private) javajs.util.P3[]
translations
(package private) java.lang.String
type
(package private) int
typeBondOrder
(package private) float
voronoiAngle
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Fields inherited from class org.jmol.adapter.smarter.Bond
atomIndex1, atomIndex2, colix, distance, order, radius, uniqueID
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Fields inherited from class org.jmol.adapter.smarter.AtomSetObject
atomSetIndex
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Constructor Summary
Constructors Constructor Description TLink()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) TopoCifParser.TAtom
addAtom(TopoCifParser.TAtom atom)
(package private) void
finalizeLink()
Take all actions prior to applying symmetry.private void
finalizeLinkNode(int index)
(package private) java.util.Map<java.lang.String,java.lang.Object>
getLinkInfo()
private TopoCifParser.TNode
getNodeWithSym(java.lang.String nodeID, java.lang.String nodeLabel, int op, javajs.util.P3 trans)
Find a node that already matches this id and symmetry(package private) java.lang.String
info()
(package private) boolean
setLink(int[] t1, int[] t2, java.lang.String line)
java.lang.String
toString()
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Field Detail
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id
java.lang.String id
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nodeIds
java.lang.String[] nodeIds
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nodeLabels
java.lang.String[] nodeLabels
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symops
int[] symops
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translations
javajs.util.P3[] translations
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netID
java.lang.String netID
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netLabel
java.lang.String netLabel
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type
java.lang.String type
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multiplicity
int multiplicity
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topoOrder
int topoOrder
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voronoiAngle
float voronoiAngle
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cartesianDistance
float cartesianDistance
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idx
int idx
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net
TopoCifParser.TNet net
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linkNodes
TopoCifParser.TNode[] linkNodes
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typeBondOrder
int typeBondOrder
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tatoms
javajs.util.Lst<TopoCifParser.TAtom> tatoms
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bsAtoms
javajs.util.BS bsAtoms
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bsBonds
javajs.util.BS bsBonds
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line
private java.lang.String line
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finalized
boolean finalized
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mf
private java.lang.String mf
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Method Detail
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setLink
boolean setLink(int[] t1, int[] t2, java.lang.String line)
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addAtom
TopoCifParser.TAtom addAtom(TopoCifParser.TAtom atom)
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finalizeLink
void finalizeLink() throws java.lang.Exception
Take all actions prior to applying symmetry. Specifically, create any nodes and atoms- Throws:
java.lang.Exception
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finalizeLinkNode
private void finalizeLinkNode(int index) throws java.lang.Exception
- Parameters:
index
- 0 or 1- Throws:
java.lang.Exception
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getNodeWithSym
private TopoCifParser.TNode getNodeWithSym(java.lang.String nodeID, java.lang.String nodeLabel, int op, javajs.util.P3 trans)
Find a node that already matches this id and symmetry- Parameters:
nodeID
-nodeLabel
-op
- a symmetry operation [9...N-1] or -1 to ignore op and transtrans
- the translation, ignored if op < 0- Returns:
- found node or null
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getLinkInfo
java.util.Map<java.lang.String,java.lang.Object> getLinkInfo()
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info
java.lang.String info()
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