org.jmol.adapter.readers.more
Class MdTopReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.FFReader
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.
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 |
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 |
nAtoms
private int nAtoms
atomCount
private int atomCount
group3s
java.lang.String[] group3s
MdTopReader
public MdTopReader()
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