java.lang.Object

javajs.util.T3

javajs.util.P3

org.jmol.adapter.smarter.Atom

org.jmol.adapter.readers.cif.TopoCifParser.TAtom

All Implemented Interfaces:: Serializable, Cloneable, javajs.api.JSONEncodable, TopoCifParser.TPoint

Enclosing class:: TopoCifParser

private class TopoCifParser.TAtom extends Atom implements TopoCifParser.TPoint

Field Summary

Fields

Modifier and Type

Field

Description

(package private) String

atomLabel

(package private) String

id

(package private) int

idx

private boolean

isFinalized

(package private) String

line

(package private) String

linkID

(package private) TopoCifParser.TNet

net

(package private) String

nodeID

(package private) int

symop

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

TAtom()
Method Summary

Modifier and Type

Method

Description

(package private) void

finalizeAtom()

private TopoCifParser.TLink

getLinkById(String linkID)

TopoCifParser.TNet

getNet()

(package private) TopoCifParser.TAtom

getTClone()

(package private) boolean

setAtom(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
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Details
- id
  
  String id
- atomLabel
  
  String atomLabel
- nodeID
  
  String nodeID
- linkID
  
  String linkID
- symop
  
  int symop
- trans
  
  private javajs.util.P3 trans
- line
  
  String line
- isFinalized
  
  private boolean isFinalized
- idx
  
  int idx
- net
  
  TopoCifParser.TNet net
Constructor Details
- TAtom
  
  TAtom()
Method Details
- getTClone
  
  TopoCifParser.TAtom getTClone()
- getNet
  
  public TopoCifParser.TNet getNet()
  
  Specified by:
  
  getNet in interface TopoCifParser.TPoint
- setAtom
  
  boolean setAtom(int[] a, String line)
- finalizeAtom
  
  void finalizeAtom() throws Exception
  
  Throws:
  
  Exception
- getLinkById
  
  private TopoCifParser.TLink getLinkById(String linkID)
- 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

Class TopoCifParser.TAtom

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

nodeID

linkID

symop

trans

line

isFinalized

idx

net

Constructor Details

TAtom

Method Details

getTClone

getNet

setAtom

finalizeAtom

getLinkById

toString