Package org.jmol.adapter.readers.cif
Class TopoCifParser.TLink
java.lang.Object
org.jmol.adapter.smarter.AtomSetObject
org.jmol.adapter.smarter.Bond
org.jmol.adapter.readers.cif.TopoCifParser.TLink
- Enclosing class:
- TopoCifParser
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
FieldsModifier and TypeFieldDescription(package private) javajs.util.BS
(package private) javajs.util.BS
(package private) float
(package private) boolean
(package private) String
(package private) int
private String
(package private) TopoCifParser.TNode[]
private String
(package private) int
(package private) TopoCifParser.TNet
(package private) String
(package private) String
(package private) String[]
(package private) String[]
(package private) int[]
(package private) javajs.util.Lst<TopoCifParser.TAtom>
(package private) int
(package private) javajs.util.P3[]
(package private) String
(package private) int
(package private) float
Fields inherited from class org.jmol.adapter.smarter.Bond
atomIndex1, atomIndex2, colix, distance, order, radius, uniqueID
Fields inherited from class org.jmol.adapter.smarter.AtomSetObject
atomSetIndex
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescription(package private) TopoCifParser.TAtom
addAtom
(TopoCifParser.TAtom atom) (package private) void
Take all actions prior to applying symmetry.private void
finalizeLinkNode
(int index) private TopoCifParser.TNode
getNodeWithSym
(String nodeID, String nodeLabel, int op, javajs.util.P3 trans) Find a node that already matches this id and symmetry(package private) String
info()
(package private) boolean
toString()
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Field Details
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id
String id -
nodeIds
String[] nodeIds -
nodeLabels
String[] nodeLabels -
symops
int[] symops -
translations
javajs.util.P3[] translations -
netID
String netID -
netLabel
String netLabel -
type
String type -
multiplicity
int multiplicity -
topoOrder
int topoOrder -
voronoiAngle
float voronoiAngle -
cartesianDistance
float cartesianDistance -
idx
int idx -
net
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linkNodes
TopoCifParser.TNode[] linkNodes -
typeBondOrder
int typeBondOrder -
tatoms
javajs.util.Lst<TopoCifParser.TAtom> tatoms -
bsAtoms
javajs.util.BS bsAtoms -
bsBonds
javajs.util.BS bsBonds -
line
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finalized
boolean finalized -
mf
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Constructor Details
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TLink
public TLink()
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Method Details
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setLink
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addAtom
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finalizeLink
Take all actions prior to applying symmetry. Specifically, create any nodes and atoms- Throws:
Exception
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finalizeLinkNode
- Parameters:
index
- 0 or 1- Throws:
Exception
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getNodeWithSym
private TopoCifParser.TNode getNodeWithSym(String nodeID, 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
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info
String info() -
toString
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