java.lang.Object
- javajs.util.T3
- - javajs.util.P3
  - - org.jmol.adapter.smarter.Atom
    - - org.jmol.adapter.readers.cif.TopoCifParser.TNode

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
```

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`

Fields inherited from class org.jmol.adapter.smarter.Atom
altLoc, anisoBorU, atomName, atomSerial, atomSetIndex, atomSite, bfactor, bondRadius, bsSymmetry, chainID, elementNumber, elementSymbol, foccupancy, formalCharge, group3, ignoreSymmetry, index, insertionCode, isHetero, partialCharge, radius, sequenceNumber, tensors, typeSymbol, vib

Fields inherited from class javajs.util.T3
x, y, z

Constructor Summary

Constructors
Constructor Description

TNode()

TNode(int idx, Atom atom, TopoCifParser.TNet net, int op, javajs.util.P3 trans)
Constructor from TLink

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

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

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

id
```
public java.lang.String id
```

atomLabel
```
public java.lang.String atomLabel
```

netID
```
java.lang.String netID
```

label
```
java.lang.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
```
TopoCifParser.TNet net
```

isFinalized
```
private boolean isFinalized
```

idx
```
int idx
```

atom
```
private Atom atom
```

line
```
private java.lang.String line
```

mf
```
private java.lang.String mf
```

Constructor Detail

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 -

Method Detail

getMolecularFormula

public java.lang.String getMolecularFormula()

getNet
```
public TopoCifParser.TNet getNet()
```
Specified by:

getNet in interface TopoCifParser.TPoint

setNode

boolean setNode(int[] a,
                java.lang.String line)

addAtom

void addAtom(TopoCifParser.TAtom atom)

finalizeNode

void finalizeNode(javajs.util.M4[] ops)
           throws java.lang.Exception

Throws:: java.lang.Exception

addNode
```
private void addNode()
```

setCentroid
```
private void setCentroid()
```

info
```
public java.lang.String info()
```

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 class javajs.util.T3

Returns:

the String representation

copy
```
public TopoCifParser.TNode copy()
```

clone
```
public java.lang.Object clone()
```
Overrides:

clone in class java.lang.Object

Constructor	Description
`TNode()`
`TNode(int idx, Atom atom, TopoCifParser.TNet net, int op, javajs.util.P3 trans)`	Constructor from TLink

Class TopoCifParser.TNode

Field Summary

Fields inherited from class org.jmol.adapter.smarter.Atom

Fields inherited from class javajs.util.T3

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.smarter.Atom

Methods inherited from class javajs.util.P3

Methods inherited from class javajs.util.T3

Methods inherited from class java.lang.Object

Field Detail

id

atomLabel

netID

label

symop

trans

tatoms

bsAtoms

linkSymop

linkTrans

net

isFinalized

idx

atom

line

mf

Constructor Detail

TNode

TNode

Method Detail

getMolecularFormula

getNet

setNode

addAtom

finalizeNode

addNode

setCentroid

info

toString

copy

clone