Package com.actelion.research.chem

Class SDFileMolecule

java.lang.Object

com.actelion.research.chem.Molecule

com.actelion.research.chem.ExtendedMolecule

com.actelion.research.chem.StereoMolecule

com.actelion.research.chem.SDFileMolecule

All Implemented Interfaces:

java.io.Serializable

public class SDFileMolecule
extends StereoMolecule
implements java.io.Serializable

See Also:

Serialized Form

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

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

Fields inherited from class com.actelion.research.chem.ExtendedMolecule

cMaxConnAtoms, FISCHER_PROJECTION_LIMIT, STEREO_ANGLE_LIMIT

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

Constructor Summary

Constructors

Constructor	Description
SDFileMolecule()
SDFileMolecule(Molecule m)
SDFileMolecule(SDFileMolecule m)

Method Summary

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()

Methods inherited from class com.actelion.research.chem.StereoMolecule

copyMoleculeProperties, createMolecule, ensureHelperArrays, getAbsoluteAtomParity, getAbsoluteBondParity, getCanonizer, getChiralText, getCompactCopy, getERSGroupMemberCounts, getFragments, getFragments, getIDCode, getIDCoordinates, getStereoCenterCount, getSymmetryRank, setAssignParitiesToNitrogen, setUnknownParitiesToExplicitlyUnknown, stripStereoInformation, translateTHParity, validate

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

Methods inherited from class com.actelion.research.chem.Molecule

addAtom, addAtom, addAtom, addAtom, addBond, addBond, 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, 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, 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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

NAME_FIELD

public static final transient java.lang.String NAME_FIELD

See Also:

Constant Field Values

ID_FIELD

public static final transient java.lang.String ID_FIELD

See Also:

Constant Field Values

CMNT_FIELD

public static final transient java.lang.String CMNT_FIELD

See Also:

Constant Field Values

DENSITY_FIELD

public static final transient java.lang.String DENSITY_FIELD

See Also:

Constant Field Values

PURITY_FIELD

public static final transient java.lang.String PURITY_FIELD

See Also:

Constant Field Values

Constructor Detail

SDFileMolecule

public SDFileMolecule()

SDFileMolecule

public SDFileMolecule(Molecule m)

SDFileMolecule

public SDFileMolecule(SDFileMolecule m)

Method Detail

setFieldData

public void setFieldData(java.lang.String field,
                         java.lang.String data)

getFieldData

public java.lang.String getFieldData(java.lang.String field)

moveFieldToStart

public boolean moveFieldToStart(java.lang.String field)

getFields

public java.lang.String[] getFields()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object