Package com.actelion.research.chem
Class SDFileMolecule
- java.lang.Object
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- com.actelion.research.chem.Molecule
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- com.actelion.research.chem.ExtendedMolecule
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- com.actelion.research.chem.StereoMolecule
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- com.actelion.research.chem.SDFileMolecule
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- All Implemented Interfaces:
java.io.Serializable
public class SDFileMolecule extends StereoMolecule implements java.io.Serializable
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
CMNT_FIELD
static java.lang.String
DENSITY_FIELD
static java.lang.String
ID_FIELD
static java.lang.String
NAME_FIELD
static java.lang.String
PURITY_FIELD
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Fields inherited from class com.actelion.research.chem.StereoMolecule
VALIDATION_ERROR_AMBIGUOUS_CONFIGURATION, VALIDATION_ERROR_ESR_CENTER_UNKNOWN, VALIDATION_ERROR_OVER_UNDER_SPECIFIED, VALIDATION_ERRORS_STEREO
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Fields inherited from class com.actelion.research.chem.ExtendedMolecule
cMaxConnAtoms, FISCHER_PROJECTION_LIMIT, FISCHER_PROJECTION_RING_LIMIT, STEREO_ANGLE_LIMIT
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Fields inherited from class com.actelion.research.chem.Molecule
cAtomCIPParityNone, cAtomCIPParityProblem, cAtomCIPParityRorM, cAtomCIPParitySorP, cAtomColorBlue, cAtomColorDarkGreen, cAtomColorDarkRed, cAtomColorGreen, cAtomColorMagenta, cAtomColorNone, cAtomColorOrange, cAtomColorRed, cAtomFlagAllylic, cAtomFlagAromatic, cAtomFlagConfigurationUnknown, cAtomFlagMarked, cAtomFlags2RingBonds, cAtomFlags3RingBonds, cAtomFlags4RingBonds, cAtomFlagsESR, cAtomFlagsHelper, cAtomFlagsHelper2, cAtomFlagsHelper3, cAtomFlagSmallRing, cAtomFlagsParity, cAtomFlagsRingBonds, cAtomFlagStabilized, cAtomFlagStereoProblem, cAtomFlagsValence, cAtomLabel, cAtomParity1, cAtomParity2, cAtomParityIsPseudo, cAtomParityNone, cAtomParityUnknown, cAtomQFAny, cAtomQFAromatic, cAtomQFAromState, cAtomQFAromStateBits, cAtomQFAromStateShift, cAtomQFCharge, cAtomQFChargeBits, cAtomQFChargeShift, cAtomQFExcludeGroup, cAtomQFFlatNitrogen, cAtomQFHydrogen, cAtomQFHydrogenBits, cAtomQFHydrogenShift, cAtomQFMatchStereo, cAtomQFMoreNeighbours, cAtomQFNarrowing, cAtomQFNeighbourBits, cAtomQFNeighbours, cAtomQFNeighbourShift, cAtomQFNoMoreNeighbours, cAtomQFNoOfBits, cAtomQFNot0Hydrogen, cAtomQFNot0Neighbours, cAtomQFNot0PiElectrons, cAtomQFNot1Hydrogen, cAtomQFNot1Neighbour, cAtomQFNot1PiElectron, cAtomQFNot2Hydrogen, cAtomQFNot2Neighbours, cAtomQFNot2PiElectrons, cAtomQFNot2RingBonds, cAtomQFNot3Hydrogen, cAtomQFNot3Neighbours, cAtomQFNot3RingBonds, cAtomQFNot4Neighbours, cAtomQFNot4RingBonds, cAtomQFNotAromatic, cAtomQFNotChain, cAtomQFNotCharge0, cAtomQFNotChargeNeg, cAtomQFNotChargePos, cAtomQFPiElectronBits, cAtomQFPiElectrons, cAtomQFPiElectronShift, cAtomQFRingSize, cAtomQFRingSizeBits, cAtomQFRingSizeShift, cAtomQFRingState, cAtomQFRingStateBits, cAtomQFRingStateShift, cAtomQFRxnParityBits, cAtomQFRxnParityHint, cAtomQFRxnParityInvert, cAtomQFRxnParityRacemize, cAtomQFRxnParityRetain, cAtomQFRxnParityShift, cAtomQFSimpleFeatures, cAtomRadicalState, cAtomRadicalStateD, cAtomRadicalStateNone, cAtomRadicalStateS, cAtomRadicalStateShift, cAtomRadicalStateT, cAtomValence, cBondCIPParityEorP, cBondCIPParityNone, cBondCIPParityProblem, cBondCIPParityZorM, cBondFlagAromatic, cBondFlagDelocalized, cBondFlagRing, cBondFlagsCIPParityShift, cBondFlagsESR, cBondFlagsHelper2, cBondFlagsHelper3, cBondFlagSmallRing, cBondFlagsParity, cBondParityEor1, cBondParityNone, cBondParityUnknown, cBondParityZor2, cBondQFAllFeatures, cBondQFAromatic, cBondQFAromState, cBondQFAromStateBits, cBondQFAromStateShift, cBondQFBondTypes, cBondQFBondTypesBits, cBondQFBondTypesShift, cBondQFBridge, cBondQFBridgeBits, cBondQFBridgeMin, cBondQFBridgeMinBits, cBondQFBridgeMinShift, cBondQFBridgeShift, cBondQFBridgeSpan, cBondQFBridgeSpanBits, cBondQFBridgeSpanShift, cBondQFDelocalized, cBondQFDouble, cBondQFMatchStereo, cBondQFMetalLigand, cBondQFNarrowing, cBondQFNoOfBits, cBondQFNotAromatic, cBondQFNotRing, cBondQFRing, cBondQFRingSize, cBondQFRingSizeBits, cBondQFRingSizeShift, cBondQFRingState, cBondQFRingStateBits, cBondQFRingStateShift, cBondQFSimpleFeatures, cBondQFSingle, cBondQFTriple, cBondTypeCross, cBondTypeDeleted, cBondTypeDelocalized, cBondTypeDouble, cBondTypeDown, cBondTypeIncreaseOrder, cBondTypeMaskSimple, cBondTypeMaskStereo, cBondTypeMetalLigand, cBondTypeSingle, cBondTypeTriple, cBondTypeUp, cChiralityDiastereomers, cChiralityEpimers, cChiralityIsomerCountMask, cChiralityKnownEnantiomer, cChiralityMeso, cChiralityNotChiral, cChiralityRacemic, cChiralityUnknown, cChiralityUnknownEnantiomer, cCommonOxidationState, cDefaultAtomValence, cESRGroupBits, cESRMaxGroups, cESRTypeAbs, cESRTypeAnd, cESRTypeOr, cHelperBitCIP, cHelperBitIncludeNitrogenParities, cHelperBitNeighbours, cHelperBitParities, cHelperBitRings, cHelperBitRingsSimple, cHelperBitsStereo, cHelperBitSymmetryDiastereotopic, cHelperBitSymmetryEnantiotopic, cHelperBitSymmetrySimple, cHelperCIP, cHelperNeighbours, cHelperNone, cHelperParities, cHelperRings, cHelperRingsSimple, cHelperSymmetryDiastereotopic, cHelperSymmetryEnantiotopic, cHelperSymmetrySimple, cMaxAtomicNo, cMoleculeColorDefault, cMoleculeColorNeutral, cRoundedMass, mAllAtoms, mAllBonds, mAtomCharge, mAtomCustomLabel, mAtomFlags, mAtomicNo, mAtomList, mAtomMapNo, mAtomMass, mAtomQueryFeatures, mBondAtom, mBondFlags, mBondQueryFeatures, mBondType, mChirality, mCoordinates, mIsFragment, mIsRacemate, mMaxAtoms, mMaxBonds, mProtectHydrogen, mValidHelperArrays
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Constructor Summary
Constructors Constructor Description SDFileMolecule()
SDFileMolecule(Molecule m)
SDFileMolecule(SDFileMolecule m)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getFieldData(java.lang.String field)
java.lang.String[]
getFields()
boolean
moveFieldToStart(java.lang.String field)
void
setFieldData(java.lang.String field, java.lang.String data)
java.lang.String
toString()
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Methods inherited from class com.actelion.research.chem.StereoMolecule
copyMoleculeProperties, createMolecule, ensureHelperArrays, getAbsoluteAtomParity, getAbsoluteBondParity, getCanonizer, getChiralText, getCompactCopy, getESRGroupMemberCounts, getFragments, getFragments, getIDCode, getIDCoordinates, getStereoCenterCount, getSymmetryRank, setAssignParitiesToNitrogen, setUnknownParitiesToExplicitlyUnknown, stripStereoInformation, translateTHParity, validate
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Methods inherited from class com.actelion.research.chem.ExtendedMolecule
addFragment, bondsAreParallel, canonizeCharge, canonizeCharge, convertStereoBondsToSingleBonds, copyMoleculeByAtoms, copyMoleculeByBonds, findAlleneCenterAtom, findAlleneEndAtom, findBINAPChiralityBond, findRingSystem, getAllConnAtoms, getAllConnAtomsPlusMetalBonds, getAllHydrogens, getAromaticRingCount, getAtomPi, getAtomPreferredStereoBond, getAtomRingBondCount, getAtomRingCount, getAtomRingSize, getAtoms, getAverageBondLength, getAverageTopologicalAtomDistance, getBond, getBondPreferredStereoBond, getBondRingSize, getBonds, getCenterGravity, getCenterGravity, getConnAtom, getConnAtoms, getConnBond, getConnBondOrder, getExcludedNeighbourCount, getExplicitHydrogens, getFisherProjectionParity, getFragmentAtoms, getFragmentAtoms, getFragmentNumbers, getFragmentNumbers, getFreeValence, getHandleHydrogenAtomMap, getHandleHydrogenBondMap, getHandleHydrogenMap, getHelperArrayStatus, getImplicitHigherValence, getImplicitHydrogens, getLowestFreeValence, getMetalBondedConnAtoms, getMolweight, getNonHydrogenNeighbourCount, getOccupiedValence, getPath, getPathBonds, getPathLength, getPathLength, getPlainHydrogens, getRingSet, getRingSetSimple, getRotatableBondCount, getStereoBond, getSubstituent, getSubstituentSize, getZNeighbour, isAlkaliMetal, isAllylicAtom, isAmideTypeBond, isAromaticAtom, isAromaticBond, isBINAPChiralityBond, isCentralAlleneAtom, isChalcogene, isDelocalizedBond, isEarthAlkaliMetal, isFlatNitrogen, isHalogene, isNitrogenFamily, isPseudoRotatableBond, isRingAtom, isRingBond, isSimpleHydrogen, isSmallRingAtom, isSmallRingBond, isStabilizedAtom, normalizeAmbiguousBonds, removeExplicitHydrogens, removeExplicitHydrogens, setParitiesValid, setStereoBondFromAtomParity, setStereoBondFromBondParity, setStereoBondsFromParity, shareSameFragment, stripSmallFragments, stripSmallFragments, supportsImplicitHydrogen, validateBondType
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Methods inherited from class com.actelion.research.chem.Molecule
addAtom, addAtom, addAtom, addAtom, addBond, addBond, addMolecule, addMolecule, addOrChangeAtom, addOrChangeBond, addRing, addRingToAtom, addRingToBond, addSubstituent, addSubstituent, calculateTorsion, center, changeAtom, changeAtomCharge, changeAtomCharge, changeBond, clear, compressMolTable, copyAtom, copyBond, copyBond, copyMolecule, deleteAtom, deleteAtomOrBond, deleteAtoms, deleteAtoms, deleteBond, deleteBondAndSurrounding, deleteMarkedAtomsAndBonds, deleteMolecule, deleteSelectedAtoms, findAtom, findBond, getAllAtoms, getAllBonds, getAllowedValences, getAngle, getAngleDif, getAtomAbnormalValence, getAtomCharge, getAtomCIPParity, getAtomColor, getAtomCoordinates, getAtomCustomLabel, getAtomCustomLabelBytes, getAtomESRGroup, getAtomESRType, getAtomicNo, getAtomicNoFromLabel, getAtomLabel, getAtomList, getAtomListString, getAtomMapNo, getAtomMass, getAtomParity, getAtomQueryFeatures, getAtomRadical, getAtomX, getAtomY, getAtomZ, getAverageBondLength, getAverageBondLength, getAverageBondLength, getAverageBondLength, getBondAngle, getBondAtom, getBondBridgeMaxSize, getBondBridgeMinSize, getBondCIPParity, getBondESRGroup, getBondESRType, getBondLength, getBondOrder, getBondParity, getBondQueryFeatures, getBondType, getBondTypeSimple, getBounds, getChirality, getCoordinates, getDefaultAverageBondLength, getDefaultMaxValenceUncharged, getDeleteAtomsBondMap, getDeleteAtomsBondMap, getElectronValenceCorrection, getMaxAtoms, getMaxBonds, getMaxValence, getMaxValenceUncharged, getMoleculeColor, getName, getStereoProblem, getUserData, invalidateHelperArrays, is3D, isAtomConfigurationUnknown, isAtomicNoElectronegative, isAtomicNoElectropositive, isAtomMarkedForDeletion, isAtomParityPseudo, isAtomStereoCenter, isAutoMappedAtom, isBondBackgroundHilited, isBondBridge, isBondForegroundHilited, isBondMarkedForDeletion, isBondParityPseudo, isBondParityUnknownOrNone, isElectronegative, isElectropositive, isFragment, isMarkedAtom, isMetalAtom, isNaturalAbundance, isOrganicAtom, isPurelyOrganic, isSelectedAtom, isSelectedBond, isStereoBond, isStereoBond, markAtomForDeletion, markBondForDeletion, removeAtomColors, removeAtomCustomLabels, removeAtomMapping, removeAtomMarkers, removeAtomSelection, removeBondHiliting, removeMappingNo, removeQueryFeatures, renumberESRGroups, scaleCoords, setAllAtoms, setAllBonds, setAtomAbnormalValence, setAtomCharge, setAtomCIPParity, setAtomColor, setAtomConfigurationUnknown, setAtomCustomLabel, setAtomCustomLabel, setAtomESR, setAtomicNo, setAtomList, setAtomList, setAtomMapNo, setAtomMarker, setAtomMass, setAtomParity, setAtomQueryFeature, setAtomRadical, setAtomSelection, setAtomStereoCenter, setAtomX, setAtomY, setAtomZ, setBondAtom, setBondBackgroundHiliting, setBondCIPParity, setBondESR, setBondForegroundHiliting, setBondOrder, setBondParity, setBondParityUnknownOrNone, setBondQueryFeature, setBondType, setChirality, setDefaultAverageBondLength, setFragment, setHelperValidity, setHydrogenProtection, setMaxAtoms, setMaxBonds, setMoleculeColor, setName, setStereoProblem, setToRacemate, setUserData, stripIsotopInfo, suggestBondType, swapAtoms, swapBonds, translate, translateCoords, zoomAndRotate, zoomAndRotateInit
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Field Detail
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NAME_FIELD
public static final transient java.lang.String NAME_FIELD
- See Also:
- Constant Field Values
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ID_FIELD
public static final transient java.lang.String ID_FIELD
- See Also:
- Constant Field Values
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CMNT_FIELD
public static final transient java.lang.String CMNT_FIELD
- See Also:
- Constant Field Values
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DENSITY_FIELD
public static final transient java.lang.String DENSITY_FIELD
- See Also:
- Constant Field Values
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PURITY_FIELD
public static final transient java.lang.String PURITY_FIELD
- See Also:
- Constant Field Values
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Constructor Detail
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SDFileMolecule
public SDFileMolecule()
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SDFileMolecule
public SDFileMolecule(Molecule m)
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SDFileMolecule
public SDFileMolecule(SDFileMolecule m)
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Method Detail
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setFieldData
public void setFieldData(java.lang.String field, java.lang.String data)
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getFieldData
public java.lang.String getFieldData(java.lang.String field)
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moveFieldToStart
public boolean moveFieldToStart(java.lang.String field)
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getFields
public java.lang.String[] getFields()
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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