org.jmol.adapter.readers.more
Class MdTopReader

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

public class MdTopReader
extends ForceFieldReader

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[] atomTypes
           
(package private)  java.lang.String[] group3s
           
private  int nAtoms
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer
 
Constructor Summary
MdTopReader()
           
 
Method Summary
protected  boolean checkLine()
           
protected  void finalizeReader()
           
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()
           
protected  void initializeReader()
           
 
Methods inherited from class org.jmol.adapter.readers.more.ForceFieldReader
deducePdbElementSymbol, getElementSymbol, setUserAtomTypes
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, 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

atomTypes

java.lang.String[] atomTypes

group3s

java.lang.String[] group3s
Constructor Detail

MdTopReader

public MdTopReader()
Method Detail

initializeReader

protected void initializeReader()
                         throws java.lang.Exception
Overrides:
initializeReader in class AtomSetCollectionReader
Throws:
java.lang.Exception

checkLine

protected boolean checkLine()
                     throws java.lang.Exception
Overrides:
checkLine in class AtomSetCollectionReader
Returns:
true if need to read new line
Throws:
java.lang.Exception

finalizeReader

protected void finalizeReader()
                       throws java.lang.Exception
Overrides:
finalizeReader in class AtomSetCollectionReader
Throws:
java.lang.Exception

getDataBlock

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

getPointers

private void getPointers()
                  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

getMasses

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