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 int
ac
private int
chainID
private boolean
isPDB
private int
lastSequenceNumber
private int
nAtoms
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Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, 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, paramsCentroid, paramsLattice, 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
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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 boolean
checkLine()
private int
getPDBGroupLength(java.lang.String g3)
protected void
initializeReader()
private boolean
processMolecule()
private void
readAtoms(int ac)
private void
readBonds(int bondCount)
private void
readCrystalInfo()
private void
readResInfo(int resCount)
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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, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, 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, 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:
initializeReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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checkLine
public boolean checkLine() throws java.lang.Exception
- Overrides:
checkLine
in 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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