Package org.jmol.adapter.readers.cif
Class TopoCifParser.TNode
- java.lang.Object
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- javajs.util.T3
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- javajs.util.P3
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- org.jmol.adapter.smarter.Atom
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- org.jmol.adapter.readers.cif.TopoCifParser.TNode
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,javajs.api.JSONEncodable
,TopoCifParser.TPoint
- Enclosing class:
- TopoCifParser
private class TopoCifParser.TNode extends Atom implements TopoCifParser.TPoint
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Field Summary
Fields Modifier and Type Field Description private Atom
atom
java.lang.String
atomLabel
(package private) javajs.util.BS
bsAtoms
java.lang.String
id
(package private) int
idx
private boolean
isFinalized
(package private) java.lang.String
label
private java.lang.String
line
(package private) int
linkSymop
(package private) javajs.util.P3
linkTrans
private java.lang.String
mf
(package private) TopoCifParser.TNet
net
(package private) java.lang.String
netID
(package private) int
symop
(package private) javajs.util.Lst<TopoCifParser.TAtom>
tatoms
(package private) javajs.util.P3
trans
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Fields inherited from class org.jmol.adapter.smarter.Atom
altLoc, anisoBorU, atomName, atomSerial, atomSetIndex, atomSite, bfactor, bondingRadius, bsSymmetry, chainID, elementNumber, elementSymbol, foccupancy, formalCharge, group3, ignoreSymmetry, index, insertionCode, isHetero, partialCharge, radius, sequenceNumber, tensors, typeSymbol, vib
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Constructor Summary
Constructors Constructor Description TNode()
TNode(int idx, Atom atom, TopoCifParser.TNet net, int op, javajs.util.P3 trans)
Constructor from TLink
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) void
addAtom(TopoCifParser.TAtom atom)
private void
addNode()
java.lang.Object
clone()
TopoCifParser.TNode
copy()
(package private) void
finalizeNode(javajs.util.M4[] ops)
java.lang.String
getMolecularFormula()
TopoCifParser.TNet
getNet()
java.lang.String
info()
private void
setCentroid()
(package private) boolean
setNode(int[] a, java.lang.String line)
java.lang.String
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
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Field Detail
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id
public java.lang.String id
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atomLabel
public java.lang.String atomLabel
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netID
java.lang.String netID
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label
java.lang.String label
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symop
int symop
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trans
javajs.util.P3 trans
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tatoms
javajs.util.Lst<TopoCifParser.TAtom> tatoms
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bsAtoms
javajs.util.BS bsAtoms
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linkSymop
int linkSymop
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linkTrans
javajs.util.P3 linkTrans
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net
TopoCifParser.TNet net
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isFinalized
private boolean isFinalized
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idx
int idx
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atom
private Atom atom
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line
private java.lang.String line
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mf
private java.lang.String mf
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Constructor Detail
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TNode
TNode()
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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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Method Detail
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getMolecularFormula
public java.lang.String getMolecularFormula()
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getNet
public TopoCifParser.TNet getNet()
- Specified by:
getNet
in interfaceTopoCifParser.TPoint
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setNode
boolean setNode(int[] a, java.lang.String line)
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addAtom
void addAtom(TopoCifParser.TAtom atom)
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finalizeNode
void finalizeNode(javajs.util.M4[] ops) throws java.lang.Exception
- Throws:
java.lang.Exception
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addNode
private void addNode()
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setCentroid
private void setCentroid()
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info
public java.lang.String info()
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toString
public java.lang.String 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
public TopoCifParser.TNode copy()
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clone
public java.lang.Object clone()
- Overrides:
clone
in classjava.lang.Object
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