org.jmol.adapter.readers.more
Class MdTopReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.FFReader
          extended by org.jmol.adapter.readers.more.MdTopReader

public class MdTopReader
extends FFReader

A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" file

PDB note: Note that topology format does not include chain designations, chain terminator, chain designator, or element symbol. Chains based on numbering reset just labeled A B C D .... Z a b c d .... z Element symbols based on reasoned guess and properties of hetero groups In principal we could use average atomic mass.


Field Summary
private  int atomCount
           
(package private)  java.lang.String[] group3s
           
private  int nAtoms
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount
 
Constructor Summary
MdTopReader()
           
 
Method Summary
private  void getAtomNames()
           
private  void getAtomTypes()
           
private  void getCharges()
           
private  java.lang.String getDataBlock()
           
private  void getMasses()
           
private  void getPointers()
           
private  void getResidueLabels()
           
private  void getResiduePointers()
           
 void readAtomSetCollection(java.io.BufferedReader reader)
           
 
Methods inherited from class org.jmol.adapter.readers.more.FFReader
getElementSymbol, setUserAtomTypes
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetryAndSetTrajectory, checkLineForScript, checkLineForScript, clearLatticeParameters, deducePdbElementSymbol, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, fillDataBlock, filterAtom, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readData, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

nAtoms

private int nAtoms

atomCount

private int atomCount

group3s

java.lang.String[] group3s
Constructor Detail

MdTopReader

public MdTopReader()
Method Detail

readAtomSetCollection

public void readAtomSetCollection(java.io.BufferedReader reader)
Specified by:
readAtomSetCollection in class AtomSetCollectionReader

getDataBlock

private java.lang.String getDataBlock()
                               throws java.lang.Exception
Throws:
java.lang.Exception

getMasses

private void getMasses()
                throws java.lang.Exception
Throws:
java.lang.Exception

getAtomTypes

private void getAtomTypes()
                   throws java.lang.Exception
Throws:
java.lang.Exception

getCharges

private void getCharges()
                 throws java.lang.Exception
Throws:
java.lang.Exception

getResiduePointers

private void getResiduePointers()
                         throws java.lang.Exception
Throws:
java.lang.Exception

getResidueLabels

private void getResidueLabels()
                       throws java.lang.Exception
Throws:
java.lang.Exception

getAtomNames

private void getAtomNames()
                   throws java.lang.Exception
Throws:
java.lang.Exception

getPointers

private void getPointers()
                  throws java.lang.Exception
Throws:
java.lang.Exception