Package org.jmol.adapter.readers.more
Class ForceFieldReader
- 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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- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
MdTopReader,Mol2Reader
public abstract class ForceFieldReader extends AtomSetCollectionReader
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Field Summary
Fields Modifier and Type Field Description private java.util.PropertiesatomTypesprivate static java.lang.StringffTypesprivate static java.lang.StringsecondCharOnlyprivate static java.lang.StringspecialTypesprivate static java.lang.StringtwoCharprivate java.lang.StringuserAtomTypes-
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 ForceFieldReader()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected static java.lang.StringdeducePdbElementSymbol(boolean isHetero, java.lang.String XX, java.lang.String group3)protected booleangetElementSymbol(Atom atom, java.lang.String atomType)protected voidsetUserAtomTypes()-
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeReader, 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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Field Detail
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ffTypes
private static final java.lang.String ffTypes
- See Also:
- Constant Field Values
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twoChar
private static final java.lang.String twoChar
- See Also:
- Constant Field Values
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specialTypes
private static final java.lang.String specialTypes
- See Also:
- Constant Field Values
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secondCharOnly
private static final java.lang.String secondCharOnly
- See Also:
- Constant Field Values
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userAtomTypes
private java.lang.String userAtomTypes
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atomTypes
private java.util.Properties atomTypes
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Method Detail
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setUserAtomTypes
protected void setUserAtomTypes()
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getElementSymbol
protected boolean getElementSymbol(Atom atom, java.lang.String atomType)
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deducePdbElementSymbol
protected static java.lang.String deducePdbElementSymbol(boolean isHetero, java.lang.String XX, java.lang.String group3)
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