Package org.jmol.adapter.readers.molxyz
Class MolReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.molxyz.MolReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
JcampdxReader
,Mol3DReader
A reader for MDLI mol and sdf files.
http://www.mdli.com/downloads/public/ctfile/ctfile.jsp
also: http://www.mdl.com/downloads/public/ctfile/ctfile.pdf simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom, x, y, z) applySymmetryAndSetTrajectory() simple 2D-->3D conversion using load "xxx.mol" FILTER "2D" Jmol 14.8.2 adds bond type 15 (quintuple) and 16 (sextuple)
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected boolean
private int
private String[]
private javajs.util.BS
private boolean
fix charges for RN(=O)(O), =N(O)*, =Nprivate boolean
private int
(package private) boolean
(package private) boolean
private V3000Rdr
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, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, 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, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noPack, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addMolAtom
(int iAtom, int isotope, String elementSymbol, int charge, float x, float y, float z) void
addMolBond
(String iAtom1, String iAtom2, int order, int stereo) protected boolean
protected void
void
optional reader-specific method run first.(package private) int
fixOrder
(int order, int stereo) void
private void
processCtab
(boolean isMDL) private void
private void
readAtomsAndBonds
(int ac, int bc) private void
Read all V nnn lines as string data; user can adapt as needed.private void
Read all M ISO lines.private void
readMolData
(Map<String, Object> molData, javajs.util.Lst<String> _keyList) Read the SDF data with name in lower caseMethods 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, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, 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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Field Details
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optimize2D
boolean optimize2D -
haveAtomSerials
private boolean haveAtomSerials -
allow2D
protected boolean allow2D -
iatom0
private int iatom0 -
vr
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atomCount
private int atomCount -
atomData
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is2D
boolean is2D -
bsDeleted
private javajs.util.BS bsDeleted -
fixN
private boolean fixNfix charges for RN(=O)(O), =N(O)*, =N
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Constructor Details
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MolReader
public MolReader()
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Method Details
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initializeReader
- Overrides:
initializeReader
in classAtomSetCollectionReader
- Throws:
Exception
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checkLine
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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finalizeSubclassReader
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
Exception
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finalizeReaderMR
- Throws:
Exception
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processMolSdHeader
- Throws:
Exception
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processCtab
- Throws:
Exception
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readAtomsAndBonds
- Throws:
Exception
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readAtomValues
Read all V nnn lines as string data; user can adapt as needed.- Throws:
Exception
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readIsotopes
Read all M ISO lines. These are absolute isotope numbers.- Throws:
Exception
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readMolData
private void readMolData(Map<String, Object> molData, javajs.util.Lst<String> _keyList) throws ExceptionRead the SDF data with name in lower case- Parameters:
molData
-_keyList
-- Throws:
Exception
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addMolAtom
public void addMolAtom(int iAtom, int isotope, String elementSymbol, int charge, float x, float y, float z) -
fixOrder
int fixOrder(int order, int stereo) -
addMolBond
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