Package org.jmol.adapter.readers.more
Class Mol2Reader
- 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.Mol2Reader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class Mol2Reader extends ForceFieldReader
A minimal multi-file reader for TRIPOS SYBYL mol2 files.http://www.tripos.com/data/support/mol2.pdf see also http://www.tripos.com/mol2/atom_types.html PDB note: Note that mol2 format of PDB files is quite minimal. All we get is the PDB atom name, coordinates, residue number, and residue name No chain terminator, not chain designator, no element symbol. Chains based on numbering reset just labeled A B C D .... Z a b c d .... z
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Field Summary
Fields Modifier and Type Field Description private intacprivate intchainIDprivate booleanisPDBprivate intlastSequenceNumberprivate 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 Mol2Reader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description booleancheckLine()private intgetPDBGroupLength(java.lang.String g3)protected voidinitializeReader()private booleanprocessMolecule()private voidreadAtoms(int ac)private voidreadBonds(int bondCount)private voidreadCrystalInfo()private voidreadResInfo(int resCount)-
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, finalizeSubclassReader, 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
public 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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processMolecule
private boolean processMolecule() throws java.lang.Exception- Throws:
java.lang.Exception
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readAtoms
private void readAtoms(int ac) throws java.lang.Exception- Throws:
java.lang.Exception
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getPDBGroupLength
private int getPDBGroupLength(java.lang.String g3)
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readBonds
private void readBonds(int bondCount) throws java.lang.Exception- Throws:
java.lang.Exception
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readResInfo
private void readResInfo(int resCount) throws java.lang.Exception- Throws:
java.lang.Exception
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readCrystalInfo
private void readCrystalInfo() throws java.lang.Exception- Throws:
java.lang.Exception
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