Chemical Data Processing Library Python API - Version 1.2.3
Classes | Functions
CDPL.MolProp Package Reference

Contains classes and functions related to the calculation/preciction of physicochemical molecular properties. More...

Classes

class  AtomHydrophobicityCalculator
 Implements Greene's algorithm [CATA] for the calculation of atom hydrophobicities. More...
 
class  AtomProperty
 Provides keys for built-in MolProp.Atom properties. More...
 
class  AtomPropertyDefault
 Provides default values for built-in Chem.Atom properties. More...
 
class  BondProperty
 Provides keys for built-in MolProp.Bond properties. More...
 
class  CoordinationGeometry
 Provides constants used to specify the spatial geometry of atom arrangements around a common central atom. More...
 
class  ElementHistogram
 A data type for the storage of element histograms of chemical compounds. More...
 
class  HBondAcceptorAtomType
 Provides constants used to specify the structural class of H-bond acceptor atoms. More...
 
class  HBondAcceptorAtomTyper
 
class  HBondDonorAtomType
 Provides constants used to specify the structural class of H-bond donor atoms. More...
 
class  HBondDonorAtomTyper
 
class  LogSCalculator
 LogSCalculator. More...
 
class  MHMOPiChargeCalculator
 MHMOPiChargeCalculator. More...
 
class  MassComposition
 A data type for the storage of mass percent compositions of chemical compounds. More...
 
class  PEOESigmaChargeCalculator
 PEOESigmaChargeCalculator. More...
 
class  TPSACalculator
 TPSACalculator. More...
 
class  XLogPCalculator
 XLogPCalculator. More...
 

Functions

str generateExplicitMolecularFormula (Chem.AtomContainer cntnr)
 
int getNetFormalCharge (Chem.AtomContainer cntnr)
 
str generateExplicitMassCompositionString (Chem.AtomContainer cntnr)
 
None generateExplicitElementHistogram (Chem.AtomContainer cntnr, ElementHistogram hist, bool append=False)
 
None calcExplicitMassComposition (Chem.AtomContainer cntnr, MassComposition mass_comp)
 
float calcExplicitMass (Chem.AtomContainer cntnr)
 
bool calcDipoleMoment (Chem.AtomContainer cntnr, Math.Vector3D moment)
 
bool calcDipoleMoment (Chem.AtomContainer cntnr, Chem.Atom3DCoordinatesFunction coords_func, Math.Vector3D moment)
 
int getAromaticAtomCount (Chem.AtomContainer cntnr)
 
int getRingAtomCount (Chem.AtomContainer cntnr)
 
int getExplicitChainAtomCount (Chem.AtomContainer cntnr)
 
int getExplicitAtomCount (Chem.AtomContainer cntnr)
 
int getExplicitAtomCount (Chem.AtomContainer cntnr, int type, bool strict=True)
 
int getHeavyAtomCount (Chem.AtomContainer cntnr)
 
bool isBridgehead (Chem.Atom atom, Chem.MolecularGraph molgraph, bool bridged_only)
 
bool isUnsaturated (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getPeriod (Chem.Atom atom)
 
int calcValence (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int calcExplicitValence (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
None clearPEOESigmaCharge (Chem.Atom atom)
 
bool hasPEOESigmaCharge (Chem.Atom atom)
 
float getPEOESigmaCharge (Chem.Atom atom)
 
None setPEOESigmaCharge (Chem.Atom atom, float charge)
 
None clearMHMOPiCharge (Chem.Atom atom)
 
bool hasMHMOPiCharge (Chem.Atom atom)
 
float getMHMOPiCharge (Chem.Atom atom)
 
None setMHMOPiCharge (Chem.Atom atom, float charge)
 
float calcTotalPartialCharge (Chem.Atom atom)
 
bool isCarbonylLike (Chem.Atom atom, Chem.MolecularGraph molgraph, bool c_only=False, bool db_o_only=False)
 
str getElementName (Chem.Atom atom)
 
None clearHBondDonorType (Chem.Atom atom)
 
bool hasHBondDonorType (Chem.Atom atom)
 
int getHBondDonorType (Chem.Atom atom)
 
None setHBondDonorType (Chem.Atom atom, int type)
 
None clearHBondAcceptorType (Chem.Atom atom)
 
bool hasHBondAcceptorType (Chem.Atom atom)
 
int getHBondAcceptorType (Chem.Atom atom)
 
None setHBondAcceptorType (Chem.Atom atom, int type)
 
bool isInRingOfSize (Chem.Atom atom, Chem.MolecularGraph molgraph, int size)
 
bool isInRing (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
bool isSemiMetal (Chem.Atom atom)
 
bool isNonMetal (Chem.Atom atom)
 
bool isTransitionMetal (Chem.Atom atom)
 
bool isMetal (Chem.Atom atom)
 
bool isHalogen (Chem.Atom atom)
 
bool isOrdinaryHydrogen (Chem.Atom atom, Chem.MolecularGraph molgraph, int flags=2147483648)
 
bool isAmideNitrogen (Chem.Atom atom, Chem.MolecularGraph molgraph, bool c_only=False, bool db_o_only=False)
 
bool isInvertibleNitrogen (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
bool isPlanarNitrogen (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getIUPACGroup (Chem.Atom atom)
 
int calcStericNumber (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
bool isAmideCenter (Chem.Atom atom, Chem.MolecularGraph molgraph, bool c_only=False, bool db_o_only=False)
 
bool isSpiroCenter (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
bool isHBondDonor (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
bool isHBondAcceptor (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
bool isNobleGas (Chem.Atom atom)
 
int getNumContainingSSSRRings (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
float getVdWRadius (Chem.Atom atom)
 
float getCovalentRadius (Chem.Atom atom, int order=1)
 
float calcInductiveEffect (Chem.Atom atom, Chem.MolecularGraph molgraph, int num_bonds=10)
 
float getAtomicWeight (Chem.Atom atom)
 
bool isChemicalElement (Chem.Atom atom)
 
bool isMainGroupElement (Chem.Atom atom)
 
int getAromaticBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getRotatableBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, bool h_rotors=False, bool ring_bonds=False, bool amide_bonds=False)
 
int getRingBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getChainBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getExplicitChainBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int order)
 
int getBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int order, int type, bool strict=True)
 
int getExplicitBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getExplicitBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int order)
 
int getExplicitBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int order, int type, bool strict=True)
 
int getHeavyBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getAromaticAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getRingAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getChainAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getExplicitChainAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int type, bool strict=True)
 
int getExplicitAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int type, bool strict=True)
 
int getHeavyAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getOrdinaryHydrogenCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int flags=2147483648)
 
int calcValenceElectronCount (Chem.Atom atom)
 
int calcFreeValenceElectronCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getElementValenceElectronCount (Chem.Atom atom)
 
int getVSEPRCoordinationGeometry (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
int getVSEPRCoordinationGeometry (Chem.Atom atom, Chem.MolecularGraph molgraph, int steric_num)
 
None clearHydrophobicity (Chem.Atom atom)
 
bool hasHydrophobicity (Chem.Atom atom)
 
float getHydrophobicity (Chem.Atom atom)
 
None setHydrophobicity (Chem.Atom atom, float hyd)
 
float getHybridPolarizability (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
float calcEffectivePolarizability (Chem.Atom atom, Chem.MolecularGraph molgraph, float damping=0.75)
 
None clearPEOESigmaElectronegativity (Chem.Atom atom)
 
bool hasPEOESigmaElectronegativity (Chem.Atom atom)
 
float getPEOESigmaElectronegativity (Chem.Atom atom)
 
None setPEOESigmaElectronegativity (Chem.Atom atom, float e_neg)
 
float calcPiElectronegativity (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
float calcLonePairElectronegativity (Chem.Atom atom, Chem.MolecularGraph molgraph)
 
float getAllredRochowElectronegativity (Chem.Atom atom)
 
bool isHeavy (Chem.Atom atom)
 
int getAromaticBondCount (Chem.BondContainer cntnr)
 
int getRingBondCount (Chem.BondContainer cntnr)
 
int getExplicitHydrogenBondCount (Chem.BondContainer cntnr)
 
int getExplicitChainBondCount (Chem.BondContainer cntnr)
 
int getExplicitBondCount (Chem.BondContainer cntnr)
 
int getExplicitBondCount (Chem.BondContainer cntnr, int order, bool inc_aro=True)
 
int getHeavyBondCount (Chem.BondContainer cntnr)
 
bool isAmideBond (Chem.Bond bond, Chem.MolecularGraph molgraph, bool c_only=False, bool db_o_only=False)
 
bool isHydrogenBond (Chem.Bond bond)
 
bool isRotatable (Chem.Bond bond, Chem.MolecularGraph molgraph, bool h_rotors, bool ring_bonds, bool amide_bonds)
 
bool isInRingOfSize (Chem.Bond bond, Chem.MolecularGraph molgraph, int size)
 
bool isInRing (Chem.Bond bond, Chem.MolecularGraph molgraph)
 
None clearMHMOPiOrder (Chem.Bond bond)
 
bool hasMHMOPiOrder (Chem.Bond bond)
 
float getMHMOPiOrder (Chem.Bond bond)
 
None setMHMOPiOrder (Chem.Bond bond, float order)
 
bool isHeteroAtomHydrogenRotor (Chem.Bond bond, Chem.MolecularGraph molgraph)
 
bool isHydrogenRotor (Chem.Bond bond, Chem.MolecularGraph molgraph)
 
int getNumContainingSSSRRings (Chem.Bond bond, Chem.MolecularGraph molgraph)
 
float calcPolarizability (Chem.Bond bond, Chem.MolecularGraph molgraph, float damping=0.75)
 
float calcTPSA (Chem.MolecularGraph molgraph)
 
float calcXLogP (Chem.MolecularGraph molgraph)
 
float calcLogS (Chem.MolecularGraph molgraph)
 
object generateMolecularFormula (Chem.MolecularGraph molgraph, str sep='')
 
int getRuleOfFiveScore (Chem.MolecularGraph molgraph)
 
object generateMassCompositionString (Chem.MolecularGraph molgraph)
 
None generateElementHistogram (Chem.MolecularGraph molgraph, ElementHistogram hist, bool append=False)
 
None calcMassComposition (Chem.MolecularGraph molgraph, MassComposition comp)
 
int calcCyclomaticNumber (Chem.MolecularGraph molgraph)
 
None calcAtomHydrophobicities (Chem.MolecularGraph molgraph, bool overwrite, bool from_logp=False)
 
None calcPEOEProperties (Chem.MolecularGraph molgraph, bool overwrite, int num_iter=20, float damping=0.48)
 
None calcMHMOProperties (Chem.MolecularGraph molgraph, bool overwrite)
 
None perceiveHBondDonorAtomTypes (Chem.MolecularGraph molgraph, bool overwrite)
 
None perceiveHBondAcceptorAtomTypes (Chem.MolecularGraph molgraph, bool overwrite)
 
float calcMass (Chem.MolecularGraph molgraph)
 
int getRotatableBondCount (Chem.MolecularGraph molgraph, bool h_rotors=False, bool ring_bonds=False, bool amide_bonds=False)
 
int getHydrogenBondCount (Chem.MolecularGraph molgraph)
 
int getChainBondCount (Chem.MolecularGraph molgraph)
 
int getBondCount (Chem.MolecularGraph molgraph)
 
int getBondCount (Chem.MolecularGraph molgraph, int order, bool inc_aro=True)
 
int getChainAtomCount (Chem.MolecularGraph molgraph)
 
int getHBondDonorAtomCount (Chem.MolecularGraph molgraph)
 
int getHBondAcceptorAtomCount (Chem.MolecularGraph molgraph)
 
int getAtomCount (Chem.MolecularGraph molgraph)
 
int getAtomCount (Chem.MolecularGraph molgraph, int type, bool strict=True)
 
int getImplicitHydrogenCount (Chem.MolecularGraph molgraph)
 
int getOrdinaryHydrogenCount (Chem.MolecularGraph molgraph, int flags=2147483648)
 
int getExplicitOrdinaryHydrogenCount (Chem.MolecularGraph molgraph, int flags=2147483648)
 
int getComponentCount (Chem.MolecularGraph molgraph)
 
float calcMeanPolarizability (Chem.MolecularGraph molgraph)
 

Detailed Description

Contains classes and functions related to the calculation/preciction of physicochemical molecular properties.

Function Documentation

◆ generateExplicitMolecularFormula()

str CDPL.MolProp.generateExplicitMolecularFormula ( Chem.AtomContainer  cntnr)
Parameters
cntnr
Returns

◆ getNetFormalCharge()

int CDPL.MolProp.getNetFormalCharge ( Chem.AtomContainer  cntnr)
Parameters
cntnr
Returns

◆ generateExplicitMassCompositionString()

str CDPL.MolProp.generateExplicitMassCompositionString ( Chem.AtomContainer  cntnr)
Parameters
cntnr
Returns

◆ generateExplicitElementHistogram()

None CDPL.MolProp.generateExplicitElementHistogram ( Chem.AtomContainer  cntnr,
ElementHistogram  hist,
bool   append = False 
)
Parameters
cntnr
hist
append

◆ calcExplicitMassComposition()

None CDPL.MolProp.calcExplicitMassComposition ( Chem.AtomContainer  cntnr,
MassComposition  mass_comp 
)
Parameters
cntnr
mass_comp

◆ calcExplicitMass()

float CDPL.MolProp.calcExplicitMass ( Chem.AtomContainer  cntnr)
Parameters
cntnr
Returns

◆ calcDipoleMoment() [1/2]

bool CDPL.MolProp.calcDipoleMoment ( Chem.AtomContainer  cntnr,
Math.Vector3D  moment 
)
Parameters
cntnr
moment
Returns

◆ calcDipoleMoment() [2/2]

bool CDPL.MolProp.calcDipoleMoment ( Chem.AtomContainer  cntnr,
Chem.Atom3DCoordinatesFunction  coords_func,
Math.Vector3D  moment 
)
Parameters
cntnr
coords_func
moment
Returns

◆ getAromaticAtomCount() [1/2]

int CDPL.MolProp.getAromaticAtomCount ( Chem.AtomContainer  cntnr)
Parameters
cntnr
Returns

◆ getRingAtomCount() [1/2]

int CDPL.MolProp.getRingAtomCount ( Chem.AtomContainer  cntnr)
Parameters
cntnr
Returns

◆ getExplicitChainAtomCount() [1/2]

int CDPL.MolProp.getExplicitChainAtomCount ( Chem.AtomContainer  cntnr)
Parameters
cntnr
Returns

◆ getExplicitAtomCount() [1/3]

int CDPL.MolProp.getExplicitAtomCount ( Chem.AtomContainer  cntnr)
Parameters
cntnr
Returns

◆ getExplicitAtomCount() [2/3]

int CDPL.MolProp.getExplicitAtomCount ( Chem.AtomContainer  cntnr,
int  type,
bool   strict = True 
)
Parameters
cntnr
type
strict
Returns

◆ getHeavyAtomCount() [1/2]

int CDPL.MolProp.getHeavyAtomCount ( Chem.AtomContainer  cntnr)
Parameters
cntnr
Returns

◆ isBridgehead()

bool CDPL.MolProp.isBridgehead ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
bool  bridged_only 
)
Parameters
atom
molgraph
bridged_only
Returns

◆ isUnsaturated()

bool CDPL.MolProp.isUnsaturated ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getPeriod()

int CDPL.MolProp.getPeriod ( Chem.Atom  atom)
Parameters
atom
Returns

◆ calcValence()

int CDPL.MolProp.calcValence ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ calcExplicitValence()

int CDPL.MolProp.calcExplicitValence ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ clearPEOESigmaCharge()

None CDPL.MolProp.clearPEOESigmaCharge ( Chem.Atom  atom)
Parameters
atom

◆ hasPEOESigmaCharge()

bool CDPL.MolProp.hasPEOESigmaCharge ( Chem.Atom  atom)
Parameters
atom
Returns

◆ getPEOESigmaCharge()

float CDPL.MolProp.getPEOESigmaCharge ( Chem.Atom  atom)
Parameters
atom
Returns

◆ setPEOESigmaCharge()

None CDPL.MolProp.setPEOESigmaCharge ( Chem.Atom  atom,
float  charge 
)
Parameters
atom
charge

◆ clearMHMOPiCharge()

None CDPL.MolProp.clearMHMOPiCharge ( Chem.Atom  atom)
Parameters
atom

◆ hasMHMOPiCharge()

bool CDPL.MolProp.hasMHMOPiCharge ( Chem.Atom  atom)
Parameters
atom
Returns

◆ getMHMOPiCharge()

float CDPL.MolProp.getMHMOPiCharge ( Chem.Atom  atom)
Parameters
atom
Returns

◆ setMHMOPiCharge()

None CDPL.MolProp.setMHMOPiCharge ( Chem.Atom  atom,
float  charge 
)
Parameters
atom
charge

◆ calcTotalPartialCharge()

float CDPL.MolProp.calcTotalPartialCharge ( Chem.Atom  atom)
Parameters
atom
Returns

◆ isCarbonylLike()

bool CDPL.MolProp.isCarbonylLike ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
bool   c_only = False,
bool   db_o_only = False 
)
Parameters
atom
molgraph
c_only
db_o_only
Returns

◆ getElementName()

str CDPL.MolProp.getElementName ( Chem.Atom  atom)
Parameters
atom
Returns

◆ clearHBondDonorType()

None CDPL.MolProp.clearHBondDonorType ( Chem.Atom  atom)
Parameters
atom

◆ hasHBondDonorType()

bool CDPL.MolProp.hasHBondDonorType ( Chem.Atom  atom)
Parameters
atom
Returns

◆ getHBondDonorType()

int CDPL.MolProp.getHBondDonorType ( Chem.Atom  atom)
Parameters
atom
Returns

◆ setHBondDonorType()

None CDPL.MolProp.setHBondDonorType ( Chem.Atom  atom,
int  type 
)
Parameters
atom
type

◆ clearHBondAcceptorType()

None CDPL.MolProp.clearHBondAcceptorType ( Chem.Atom  atom)
Parameters
atom

◆ hasHBondAcceptorType()

bool CDPL.MolProp.hasHBondAcceptorType ( Chem.Atom  atom)
Parameters
atom
Returns

◆ getHBondAcceptorType()

int CDPL.MolProp.getHBondAcceptorType ( Chem.Atom  atom)
Parameters
atom
Returns

◆ setHBondAcceptorType()

None CDPL.MolProp.setHBondAcceptorType ( Chem.Atom  atom,
int  type 
)
Parameters
atom
type

◆ isInRingOfSize() [1/2]

bool CDPL.MolProp.isInRingOfSize ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
int  size 
)
Parameters
atom
molgraph
size
Returns

◆ isInRing() [1/2]

bool CDPL.MolProp.isInRing ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ isSemiMetal()

bool CDPL.MolProp.isSemiMetal ( Chem.Atom  atom)
Parameters
atom
Returns

◆ isNonMetal()

bool CDPL.MolProp.isNonMetal ( Chem.Atom  atom)
Parameters
atom
Returns

◆ isTransitionMetal()

bool CDPL.MolProp.isTransitionMetal ( Chem.Atom  atom)
Parameters
atom
Returns

◆ isMetal()

bool CDPL.MolProp.isMetal ( Chem.Atom  atom)
Parameters
atom
Returns

◆ isHalogen()

bool CDPL.MolProp.isHalogen ( Chem.Atom  atom)
Parameters
atom
Returns

◆ isOrdinaryHydrogen()

bool CDPL.MolProp.isOrdinaryHydrogen ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
int   flags = 2147483648 
)
Parameters
atom
molgraph
flags
Returns

◆ isAmideNitrogen()

bool CDPL.MolProp.isAmideNitrogen ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
bool   c_only = False,
bool   db_o_only = False 
)
Parameters
atom
molgraph
c_only
db_o_only
Returns

◆ isInvertibleNitrogen()

bool CDPL.MolProp.isInvertibleNitrogen ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ isPlanarNitrogen()

bool CDPL.MolProp.isPlanarNitrogen ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getIUPACGroup()

int CDPL.MolProp.getIUPACGroup ( Chem.Atom  atom)
Parameters
atom
Returns

◆ calcStericNumber()

int CDPL.MolProp.calcStericNumber ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ isAmideCenter()

bool CDPL.MolProp.isAmideCenter ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
bool   c_only = False,
bool   db_o_only = False 
)
Parameters
atom
molgraph
c_only
db_o_only
Returns

◆ isSpiroCenter()

bool CDPL.MolProp.isSpiroCenter ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ isHBondDonor()

bool CDPL.MolProp.isHBondDonor ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ isHBondAcceptor()

bool CDPL.MolProp.isHBondAcceptor ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ isNobleGas()

bool CDPL.MolProp.isNobleGas ( Chem.Atom  atom)
Parameters
atom
Returns

◆ getNumContainingSSSRRings() [1/2]

int CDPL.MolProp.getNumContainingSSSRRings ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getVdWRadius()

float CDPL.MolProp.getVdWRadius ( Chem.Atom  atom)
Parameters
atom
Returns

◆ getCovalentRadius()

float CDPL.MolProp.getCovalentRadius ( Chem.Atom  atom,
int   order = 1 
)
Parameters
atom
order
Returns

◆ calcInductiveEffect()

float CDPL.MolProp.calcInductiveEffect ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
int   num_bonds = 10 
)
Parameters
atom
molgraph
num_bonds
Returns

◆ getAtomicWeight()

float CDPL.MolProp.getAtomicWeight ( Chem.Atom  atom)
Parameters
atom
Returns

◆ isChemicalElement()

bool CDPL.MolProp.isChemicalElement ( Chem.Atom  atom)
Parameters
atom
Returns

◆ isMainGroupElement()

bool CDPL.MolProp.isMainGroupElement ( Chem.Atom  atom)
Parameters
atom
Returns

◆ getAromaticBondCount() [1/2]

int CDPL.MolProp.getAromaticBondCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getRotatableBondCount() [1/2]

int CDPL.MolProp.getRotatableBondCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
bool   h_rotors = False,
bool   ring_bonds = False,
bool   amide_bonds = False 
)
Parameters
atom
molgraph
h_rotors
ring_bonds
amide_bonds
Returns

◆ getRingBondCount() [1/2]

int CDPL.MolProp.getRingBondCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getChainBondCount() [1/2]

int CDPL.MolProp.getChainBondCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getExplicitChainBondCount() [1/2]

int CDPL.MolProp.getExplicitChainBondCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getBondCount() [1/5]

int CDPL.MolProp.getBondCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getBondCount() [2/5]

int CDPL.MolProp.getBondCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
int  order 
)
Parameters
atom
molgraph
order
Returns

◆ getBondCount() [3/5]

int CDPL.MolProp.getBondCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
int  order,
int  type,
bool   strict = True 
)
Parameters
atom
molgraph
order
type
strict
Returns

◆ getExplicitBondCount() [1/5]

int CDPL.MolProp.getExplicitBondCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getExplicitBondCount() [2/5]

int CDPL.MolProp.getExplicitBondCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
int  order 
)
Parameters
atom
molgraph
order
Returns

◆ getExplicitBondCount() [3/5]

int CDPL.MolProp.getExplicitBondCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
int  order,
int  type,
bool   strict = True 
)
Parameters
atom
molgraph
order
type
strict
Returns

◆ getHeavyBondCount() [1/2]

int CDPL.MolProp.getHeavyBondCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getAromaticAtomCount() [2/2]

int CDPL.MolProp.getAromaticAtomCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getRingAtomCount() [2/2]

int CDPL.MolProp.getRingAtomCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getChainAtomCount() [1/2]

int CDPL.MolProp.getChainAtomCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getExplicitChainAtomCount() [2/2]

int CDPL.MolProp.getExplicitChainAtomCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getAtomCount() [1/3]

int CDPL.MolProp.getAtomCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
int  type,
bool   strict = True 
)
Parameters
atom
molgraph
type
strict
Returns

◆ getExplicitAtomCount() [3/3]

int CDPL.MolProp.getExplicitAtomCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
int  type,
bool   strict = True 
)
Parameters
atom
molgraph
type
strict
Returns

◆ getHeavyAtomCount() [2/2]

int CDPL.MolProp.getHeavyAtomCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getOrdinaryHydrogenCount() [1/2]

int CDPL.MolProp.getOrdinaryHydrogenCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
int   flags = 2147483648 
)
Parameters
atom
molgraph
flags
Returns

◆ calcValenceElectronCount()

int CDPL.MolProp.calcValenceElectronCount ( Chem.Atom  atom)
Parameters
atom
Returns

◆ calcFreeValenceElectronCount()

int CDPL.MolProp.calcFreeValenceElectronCount ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getElementValenceElectronCount()

int CDPL.MolProp.getElementValenceElectronCount ( Chem.Atom  atom)
Parameters
atom
Returns

◆ getVSEPRCoordinationGeometry() [1/2]

int CDPL.MolProp.getVSEPRCoordinationGeometry ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getVSEPRCoordinationGeometry() [2/2]

int CDPL.MolProp.getVSEPRCoordinationGeometry ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
int  steric_num 
)
Parameters
atom
molgraph
steric_num
Returns

◆ clearHydrophobicity()

None CDPL.MolProp.clearHydrophobicity ( Chem.Atom  atom)
Parameters
atom

◆ hasHydrophobicity()

bool CDPL.MolProp.hasHydrophobicity ( Chem.Atom  atom)
Parameters
atom
Returns

◆ getHydrophobicity()

float CDPL.MolProp.getHydrophobicity ( Chem.Atom  atom)
Parameters
atom
Returns

◆ setHydrophobicity()

None CDPL.MolProp.setHydrophobicity ( Chem.Atom  atom,
float  hyd 
)
Parameters
atom
hyd

◆ getHybridPolarizability()

float CDPL.MolProp.getHybridPolarizability ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ calcEffectivePolarizability()

float CDPL.MolProp.calcEffectivePolarizability ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph,
float   damping = 0.75 
)
Parameters
atom
molgraph
damping
Returns

◆ clearPEOESigmaElectronegativity()

None CDPL.MolProp.clearPEOESigmaElectronegativity ( Chem.Atom  atom)
Parameters
atom

◆ hasPEOESigmaElectronegativity()

bool CDPL.MolProp.hasPEOESigmaElectronegativity ( Chem.Atom  atom)
Parameters
atom
Returns

◆ getPEOESigmaElectronegativity()

float CDPL.MolProp.getPEOESigmaElectronegativity ( Chem.Atom  atom)
Parameters
atom
Returns

◆ setPEOESigmaElectronegativity()

None CDPL.MolProp.setPEOESigmaElectronegativity ( Chem.Atom  atom,
float  e_neg 
)
Parameters
atom
e_neg

◆ calcPiElectronegativity()

float CDPL.MolProp.calcPiElectronegativity ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ calcLonePairElectronegativity()

float CDPL.MolProp.calcLonePairElectronegativity ( Chem.Atom  atom,
Chem.MolecularGraph  molgraph 
)
Parameters
atom
molgraph
Returns

◆ getAllredRochowElectronegativity()

float CDPL.MolProp.getAllredRochowElectronegativity ( Chem.Atom  atom)
Parameters
atom
Returns

◆ isHeavy()

bool CDPL.MolProp.isHeavy ( Chem.Atom  atom)
Parameters
atom
Returns

◆ getAromaticBondCount() [2/2]

int CDPL.MolProp.getAromaticBondCount ( Chem.BondContainer  cntnr)
Parameters
cntnr
Returns

◆ getRingBondCount() [2/2]

int CDPL.MolProp.getRingBondCount ( Chem.BondContainer  cntnr)
Parameters
cntnr
Returns

◆ getExplicitHydrogenBondCount()

int CDPL.MolProp.getExplicitHydrogenBondCount ( Chem.BondContainer  cntnr)
Parameters
cntnr
Returns

◆ getExplicitChainBondCount() [2/2]

int CDPL.MolProp.getExplicitChainBondCount ( Chem.BondContainer  cntnr)
Parameters
cntnr
Returns

◆ getExplicitBondCount() [4/5]

int CDPL.MolProp.getExplicitBondCount ( Chem.BondContainer  cntnr)
Parameters
cntnr
Returns

◆ getExplicitBondCount() [5/5]

int CDPL.MolProp.getExplicitBondCount ( Chem.BondContainer  cntnr,
int  order,
bool   inc_aro = True 
)
Parameters
cntnr
order
inc_aro
Returns

◆ getHeavyBondCount() [2/2]

int CDPL.MolProp.getHeavyBondCount ( Chem.BondContainer  cntnr)
Parameters
cntnr
Returns

◆ isAmideBond()

bool CDPL.MolProp.isAmideBond ( Chem.Bond  bond,
Chem.MolecularGraph  molgraph,
bool   c_only = False,
bool   db_o_only = False 
)
Parameters
bond
molgraph
c_only
db_o_only
Returns

◆ isHydrogenBond()

bool CDPL.MolProp.isHydrogenBond ( Chem.Bond  bond)
Parameters
bond
Returns

◆ isRotatable()

bool CDPL.MolProp.isRotatable ( Chem.Bond  bond,
Chem.MolecularGraph  molgraph,
bool  h_rotors,
bool  ring_bonds,
bool  amide_bonds 
)
Parameters
bond
molgraph
h_rotors
ring_bonds
amide_bonds
Returns

◆ isInRingOfSize() [2/2]

bool CDPL.MolProp.isInRingOfSize ( Chem.Bond  bond,
Chem.MolecularGraph  molgraph,
int  size 
)
Parameters
bond
molgraph
size
Returns

◆ isInRing() [2/2]

bool CDPL.MolProp.isInRing ( Chem.Bond  bond,
Chem.MolecularGraph  molgraph 
)
Parameters
bond
molgraph
Returns

◆ clearMHMOPiOrder()

None CDPL.MolProp.clearMHMOPiOrder ( Chem.Bond  bond)
Parameters
bond

◆ hasMHMOPiOrder()

bool CDPL.MolProp.hasMHMOPiOrder ( Chem.Bond  bond)
Parameters
bond
Returns

◆ getMHMOPiOrder()

float CDPL.MolProp.getMHMOPiOrder ( Chem.Bond  bond)
Parameters
bond
Returns

◆ setMHMOPiOrder()

None CDPL.MolProp.setMHMOPiOrder ( Chem.Bond  bond,
float  order 
)
Parameters
bond
order

◆ isHeteroAtomHydrogenRotor()

bool CDPL.MolProp.isHeteroAtomHydrogenRotor ( Chem.Bond  bond,
Chem.MolecularGraph  molgraph 
)
Parameters
bond
molgraph
Returns

◆ isHydrogenRotor()

bool CDPL.MolProp.isHydrogenRotor ( Chem.Bond  bond,
Chem.MolecularGraph  molgraph 
)
Parameters
bond
molgraph
Returns

◆ getNumContainingSSSRRings() [2/2]

int CDPL.MolProp.getNumContainingSSSRRings ( Chem.Bond  bond,
Chem.MolecularGraph  molgraph 
)
Parameters
bond
molgraph
Returns

◆ calcPolarizability()

float CDPL.MolProp.calcPolarizability ( Chem.Bond  bond,
Chem.MolecularGraph  molgraph,
float   damping = 0.75 
)
Parameters
bond
molgraph
damping
Returns

◆ calcTPSA()

float CDPL.MolProp.calcTPSA ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ calcXLogP()

float CDPL.MolProp.calcXLogP ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ calcLogS()

float CDPL.MolProp.calcLogS ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ generateMolecularFormula()

object CDPL.MolProp.generateMolecularFormula ( Chem.MolecularGraph  molgraph,
str   sep = '' 
)
Parameters
molgraph
sep
Returns

◆ getRuleOfFiveScore()

int CDPL.MolProp.getRuleOfFiveScore ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ generateMassCompositionString()

object CDPL.MolProp.generateMassCompositionString ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ generateElementHistogram()

None CDPL.MolProp.generateElementHistogram ( Chem.MolecularGraph  molgraph,
ElementHistogram  hist,
bool   append = False 
)
Parameters
molgraph
hist
append

◆ calcMassComposition()

None CDPL.MolProp.calcMassComposition ( Chem.MolecularGraph  molgraph,
MassComposition  comp 
)
Parameters
molgraph
comp

◆ calcCyclomaticNumber()

int CDPL.MolProp.calcCyclomaticNumber ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ calcAtomHydrophobicities()

None CDPL.MolProp.calcAtomHydrophobicities ( Chem.MolecularGraph  molgraph,
bool  overwrite,
bool   from_logp = False 
)
Parameters
molgraph
overwrite
from_logp

◆ calcPEOEProperties()

None CDPL.MolProp.calcPEOEProperties ( Chem.MolecularGraph  molgraph,
bool  overwrite,
int   num_iter = 20,
float   damping = 0.48 
)
Parameters
molgraph
overwrite
num_iter
damping

◆ calcMHMOProperties()

None CDPL.MolProp.calcMHMOProperties ( Chem.MolecularGraph  molgraph,
bool  overwrite 
)
Parameters
molgraph
overwrite

◆ perceiveHBondDonorAtomTypes()

None CDPL.MolProp.perceiveHBondDonorAtomTypes ( Chem.MolecularGraph  molgraph,
bool  overwrite 
)
Parameters
molgraph
overwrite

◆ perceiveHBondAcceptorAtomTypes()

None CDPL.MolProp.perceiveHBondAcceptorAtomTypes ( Chem.MolecularGraph  molgraph,
bool  overwrite 
)
Parameters
molgraph
overwrite

◆ calcMass()

float CDPL.MolProp.calcMass ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ getRotatableBondCount() [2/2]

int CDPL.MolProp.getRotatableBondCount ( Chem.MolecularGraph  molgraph,
bool   h_rotors = False,
bool   ring_bonds = False,
bool   amide_bonds = False 
)
Parameters
molgraph
h_rotors
ring_bonds
amide_bonds
Returns

◆ getHydrogenBondCount()

int CDPL.MolProp.getHydrogenBondCount ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ getChainBondCount() [2/2]

int CDPL.MolProp.getChainBondCount ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ getBondCount() [4/5]

int CDPL.MolProp.getBondCount ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ getBondCount() [5/5]

int CDPL.MolProp.getBondCount ( Chem.MolecularGraph  molgraph,
int  order,
bool   inc_aro = True 
)
Parameters
molgraph
order
inc_aro
Returns

◆ getChainAtomCount() [2/2]

int CDPL.MolProp.getChainAtomCount ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ getHBondDonorAtomCount()

int CDPL.MolProp.getHBondDonorAtomCount ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ getHBondAcceptorAtomCount()

int CDPL.MolProp.getHBondAcceptorAtomCount ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ getAtomCount() [2/3]

int CDPL.MolProp.getAtomCount ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ getAtomCount() [3/3]

int CDPL.MolProp.getAtomCount ( Chem.MolecularGraph  molgraph,
int  type,
bool   strict = True 
)
Parameters
molgraph
type
strict
Returns

◆ getImplicitHydrogenCount()

int CDPL.MolProp.getImplicitHydrogenCount ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ getOrdinaryHydrogenCount() [2/2]

int CDPL.MolProp.getOrdinaryHydrogenCount ( Chem.MolecularGraph  molgraph,
int   flags = 2147483648 
)
Parameters
molgraph
flags
Returns

◆ getExplicitOrdinaryHydrogenCount()

int CDPL.MolProp.getExplicitOrdinaryHydrogenCount ( Chem.MolecularGraph  molgraph,
int   flags = 2147483648 
)
Parameters
molgraph
flags
Returns

◆ getComponentCount()

int CDPL.MolProp.getComponentCount ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ calcMeanPolarizability()

float CDPL.MolProp.calcMeanPolarizability ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns
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