Package org.jmol.adapter.readers.cif
Class TopoCifParser.TNode
java.lang.Object
javajs.util.T3
javajs.util.P3
org.jmol.adapter.smarter.Atom
org.jmol.adapter.readers.cif.TopoCifParser.TNode
- All Implemented Interfaces:
Serializable
,Cloneable
,javajs.api.JSONEncodable
,TopoCifParser.TPoint
- Enclosing class:
- TopoCifParser
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate Atom
(package private) javajs.util.BS
(package private) int
private boolean
(package private) String
private String
(package private) int
(package private) javajs.util.P3
private String
(package private) TopoCifParser.TNet
(package private) String
(package private) int
(package private) javajs.util.Lst<TopoCifParser.TAtom>
(package private) javajs.util.P3
Fields inherited from class org.jmol.adapter.smarter.Atom
altLoc, anisoBorU, atomName, atomSerial, atomSetIndex, atomSite, bfactor, bondingRadius, bsSymmetry, chainID, elementNumber, elementSymbol, foccupancy, formalCharge, group3, index, insertionCode, isHetero, isNegDisorder, partialCharge, radius, sequenceNumber, tensors, typeSymbol, vib
Fields inherited from class javajs.util.T3
x, y, z
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Constructor Summary
ConstructorsConstructorDescriptionTNode()
TNode
(int idx, Atom atom, TopoCifParser.TNet net, int op, javajs.util.P3 trans) Constructor from TLink -
Method Summary
Modifier and TypeMethodDescription(package private) void
addAtom
(TopoCifParser.TAtom atom) private void
addNode()
clone()
copy()
(package private) void
finalizeNode
(javajs.util.M4[] ops) getNet()
info()
private void
(package private) boolean
toString()
Returns a string that contains the values of this Tuple3f.Methods inherited from class org.jmol.adapter.smarter.Atom
addTensor, copyTo, getClone, getElementSymbol, isValidSym1, isValidSym2, isValidSymNoCase
Methods inherited from class javajs.util.P3
getUnlikely, new3, newA, newP
Methods inherited from class javajs.util.T3
add, add2, add3, ave, cross, distance, distanceSquared, dot, equals, floatToIntBits, hashCode, length, lengthSquared, normalize, scale, scaleAdd2, scaleT, set, setA, setT, sub, sub2, toJSON
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Field Details
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id
-
atomLabel
-
netID
String netID -
label
String label -
symop
int symop -
trans
javajs.util.P3 trans -
tatoms
javajs.util.Lst<TopoCifParser.TAtom> tatoms -
bsAtoms
javajs.util.BS bsAtoms -
linkSymop
int linkSymop -
linkTrans
javajs.util.P3 linkTrans -
net
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isFinalized
private boolean isFinalized -
idx
int idx -
atom
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line
-
mf
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Constructor Details
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TNode
TNode() -
TNode
TNode(int idx, Atom atom, TopoCifParser.TNet net, int op, javajs.util.P3 trans) Constructor from TLink- Parameters:
idx
-atom
-net
-op
-trans
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-
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Method Details
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getMolecularFormula
-
getNet
- Specified by:
getNet
in interfaceTopoCifParser.TPoint
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setNode
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addAtom
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finalizeNode
- Throws:
Exception
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addNode
private void addNode() -
setCentroid
private void setCentroid() -
info
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toString
Description copied from class:javajs.util.T3
Returns a string that contains the values of this Tuple3f. The form is (x,y,z).- Overrides:
toString
in classjavajs.util.T3
- Returns:
- the String representation
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copy
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clone
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