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

private class TopoCifParser.TNode extends Atom implements TopoCifParser.TPoint

Field Summary

Fields

Modifier and Type

Field

Description

private Atom

atom

String

atomLabel

(package private) javajs.util.BS

bsAtoms

String

id

(package private) int

idx

private boolean

isFinalized

(package private) String

label

private String

line

(package private) int

linkSymop

(package private) javajs.util.P3

linkTrans

private String

mf

(package private) TopoCifParser.TNet

net

(package private) 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, 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
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

Modifier and Type

Method

Description

(package private) void

addAtom(TopoCifParser.TAtom atom)

private void

addNode()

Object

clone()

TopoCifParser.TNode

copy()

(package private) void

finalizeNode(javajs.util.M4[] ops)

String

getMolecularFormula()

TopoCifParser.TNet

getNet()

String

info()

private void

setCentroid()

(package private) boolean

setNode(int[] a, String line)

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 Details
- id
  
  public String id
- atomLabel
  
  public String 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
  
  TopoCifParser.TNet net
- isFinalized
  
  private boolean isFinalized
- idx
  
  int idx
- atom
  
  private Atom atom
- line
  
  private String line
- mf
  
  private String mf
Constructor Details
- 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 Details
- getMolecularFormula
  
  public String getMolecularFormula()
- getNet
  
  public TopoCifParser.TNet getNet()
  
  Specified by:
  
  getNet in interface TopoCifParser.TPoint
- setNode
  
  boolean setNode(int[] a, String line)
- addAtom
  
  void addAtom(TopoCifParser.TAtom atom)
- finalizeNode
  
  void finalizeNode(javajs.util.M4[] ops) throws Exception
  
  Throws:
  
  Exception
- addNode
  
  private void addNode()
- setCentroid
  
  private void setCentroid()
- info
  
  public String info()
- toString
  
  public 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 Object clone()
  
  Overrides:
  
  clone in class Object

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 Details

id

atomLabel

netID

label

symop

trans

tatoms

bsAtoms

linkSymop

linkTrans

net

isFinalized

idx

atom

line

mf

Constructor Details

TNode

TNode

Method Details

getMolecularFormula

getNet

setNode

addAtom

finalizeNode

addNode

setCentroid

info

toString

copy

clone