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.Properties
atomTypes
private static java.lang.String
ffTypes
private static java.lang.String
secondCharOnly
private static java.lang.String
specialTypes
private static java.lang.String
twoChar
private java.lang.String
userAtomTypes
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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, 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, 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.String
deducePdbElementSymbol(boolean isHetero, java.lang.String XX, java.lang.String group3)
protected boolean
getElementSymbol(Atom atom, java.lang.String atomType)
protected void
setUserAtomTypes()
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, 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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