Class MMFFMolecule
- 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.forcefield.mmff.MMFFMolecule
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- All Implemented Interfaces:
java.io.Serializable
public final class MMFFMolecule extends StereoMolecule
MMFF molecule is a wrapper class for the ExtendedMolecule. It holds some additional data such as a cache of the atom types, whether the molecule is valid for MMFF and the ring mmff aromaticity property.- See Also:
- Serialized Form
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Field Summary
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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 MMFFMolecule(StereoMolecule mol)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getAtomType(int a)
Get the MMFF atom type of an atom.int[]
getHydrogenMap()
boolean
isSetRingMMFFAromaticity(int r)
Returns true if the given ring has had its MMFF aromaticity flag set.boolean
ringIsMMFFAromatic(int r)
Determine if a ring is aromatic according to MMFF criteria.-
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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Constructor Detail
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MMFFMolecule
public MMFFMolecule(StereoMolecule mol) throws BadAtomTypeException, BadRingAromException
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Method Detail
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getAtomType
public int getAtomType(int a)
Get the MMFF atom type of an atom. This returns the cached value.- Parameters:
a
- The atom index in the molecule.- Returns:
- The MMFF atom type.
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getHydrogenMap
public int[] getHydrogenMap()
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ringIsMMFFAromatic
public boolean ringIsMMFFAromatic(int r)
Determine if a ring is aromatic according to MMFF criteria. Only designed to work with rings of size 5 and 6. Returns the cached value.- Parameters:
r
- The ring index in the molecule.- Returns:
- True if the ring is aromatic, false otherwise.
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isSetRingMMFFAromaticity
public boolean isSetRingMMFFAromaticity(int r)
Returns true if the given ring has had its MMFF aromaticity flag set.- Parameters:
r
- The ring index in the molecule.- Returns:
- True if the ring has had its flag set, false otherwise.
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