Package org.jmol.adapter.readers.more
Class MdTopReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.more.ForceFieldReader
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- org.jmol.adapter.readers.more.MdTopReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class MdTopReader extends ForceFieldReader
A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" filePDB 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.
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Field Summary
Fields Modifier and Type Field Description private intacprivate java.lang.String[]atomTypes(package private) java.lang.String[]group3sprivate intnAtoms-
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, 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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description MdTopReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected booleancheckLine()protected voidfinalizeSubclassReader()optional reader-specific method run first.private voidgetAtomNames()private voidgetAtomTypes()private voidgetCharges()private java.lang.String[]getDataBlock()private voidgetMasses()private voidgetPointers()private voidgetResidueLabels()private voidgetResiduePointers()protected voidinitializeReader()-
Methods inherited from class org.jmol.adapter.readers.more.ForceFieldReader
deducePdbElementSymbol, getElementSymbol, setUserAtomTypes
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, 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
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Method Detail
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initializeReader
protected void initializeReader() throws java.lang.Exception- Overrides:
initializeReaderin classAtomSetCollectionReader- Throws:
java.lang.Exception
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checkLine
protected boolean checkLine() throws java.lang.Exception- Overrides:
checkLinein classAtomSetCollectionReader- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
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finalizeSubclassReader
protected void finalizeSubclassReader() throws java.lang.ExceptionDescription copied from class:AtomSetCollectionReaderoptional reader-specific method run first.- Overrides:
finalizeSubclassReaderin classAtomSetCollectionReader- Throws:
java.lang.Exception
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getDataBlock
private java.lang.String[] getDataBlock() throws java.lang.Exception- Throws:
java.lang.Exception
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getPointers
private void getPointers() throws java.lang.Exception- Throws:
java.lang.Exception
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getAtomTypes
private void getAtomTypes() throws java.lang.Exception- Throws:
java.lang.Exception
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getCharges
private void getCharges() throws java.lang.Exception- Throws:
java.lang.Exception
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getResiduePointers
private void getResiduePointers() throws java.lang.Exception- Throws:
java.lang.Exception
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getResidueLabels
private void getResidueLabels() throws java.lang.Exception- Throws:
java.lang.Exception
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getAtomNames
private void getAtomNames() throws java.lang.Exception- Throws:
java.lang.Exception
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getMasses
private void getMasses() throws java.lang.Exception- Throws:
java.lang.Exception
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