Package org.jmol.adapter.readers.more

Class MdTopReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.more.ForceFieldReader

org.jmol.adapter.readers.more.MdTopReader

All Implemented Interfaces:

javajs.api.GenericLineReader

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

Fields

Modifier and Type	Field	Description
private int	ac
private String[]	atomTypes
(package private) String[]	group3s
private int	nAtoms

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors

Constructor	Description
MdTopReader()

Method Summary

Modifier and Type	Method	Description
protected boolean	checkLine()
protected void	finalizeSubclassReader()	optional reader-specific method run first.
private void	getAtomNames()
private void	getAtomTypes()
private void	getCharges()
private 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

addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

nAtoms

private int nAtoms

ac

private int ac

atomTypes

private String[] atomTypes

group3s

String[] group3s

Constructor Detail

MdTopReader

public MdTopReader()

Method Detail

initializeReader

protected void initializeReader()
                         throws Exception

Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

Exception

checkLine

protected boolean checkLine()
                     throws Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

finalizeSubclassReader

protected void finalizeSubclassReader()
                               throws Exception

Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

Exception

getDataBlock

private String[] getDataBlock()
                       throws Exception

Throws:

Exception

getPointers

private void getPointers()
                  throws Exception

Throws:

Exception

getAtomTypes

private void getAtomTypes()
                   throws Exception

Throws:

Exception

getCharges

private void getCharges()
                 throws Exception

Throws:

Exception

getResiduePointers

private void getResiduePointers()
                         throws Exception

Throws:

Exception

getResidueLabels

private void getResidueLabels()
                       throws Exception

Throws:

Exception

getAtomNames

private void getAtomNames()
                   throws Exception

Throws:

Exception

getMasses

private void getMasses()
                throws Exception

Throws:

Exception