Chemical Data Processing Library Python API - Version 1.4.0
Classes | Functions
CDPL.MolProp Package Reference

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

Classes

class  AtomHydrophobicityCalculator
 Implementation of Greene's algorithm [CATA] for the calculation of atom hydrophobicities. More...
 
class  AtomProperty
 Provides keys for built-in Chem.Atom properties. More...
 
class  AtomPropertyDefault
 Provides default values for built-in Chem.Atom properties. More...
 
class  BondProperty
 Provides keys for built-in Chem.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  FunctionalGroupList
 Implementation of Ertl's algorithm [FGPE] for the identification of functional groups in organic molecules. 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  MolecularGraphProperty
 Provides keys for built-in Chem.MolecularGraph properties. More...
 
class  PEOESigmaChargeCalculator
 PEOESigmaChargeCalculator. More...
 
class  TPSACalculator
 Calculation of the topological polar surface area (TPSA) of molecular graphs based on fragment contributions. More...
 
class  XLogPCalculator
 Calculation of the octanol/water partition coefficient ( \( \log P \)) of molecular graphs using the atom-additive method of Wang, Gao and Lai. More...
 

Functions

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

Detailed Description

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

Function Documentation

◆ getAllredRochowElectronegativity()

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

◆ getAromaticAtomCount() [1/2]

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

◆ getAromaticAtomCount() [2/2]

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

◆ getAromaticBondCount() [1/2]

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

◆ getAromaticBondCount() [2/2]

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

◆ 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

◆ getAtomicWeight()

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

◆ 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() [1/2]

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

◆ getChainAtomCount() [2/2]

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

◆ getChainBondCount() [1/2]

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

◆ getChainBondCount() [2/2]

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

◆ getComponentCount()

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

◆ getCovalentRadius()

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

◆ getElementName()

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

◆ getElementValenceElectronCount()

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

◆ getExplicitAtomCount() [1/3]

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

◆ getExplicitAtomCount() [2/3]

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

◆ getExplicitAtomCount() [3/3]

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

◆ 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

◆ getExplicitChainAtomCount() [1/2]

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

◆ getExplicitChainAtomCount() [2/2]

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

◆ getExplicitChainBondCount() [1/2]

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

◆ getExplicitChainBondCount() [2/2]

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

◆ getExplicitHydrogenBondCount()

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

◆ getExplicitOrdinaryHydrogenCount()

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

◆ setFunctionalGroups()

None CDPL.MolProp.setFunctionalGroups ( Chem.MolecularGraph  molgraph,
Chem.FragmentList  fg_list 
)
Parameters
molgraph
fg_list

◆ hasFunctionalGroups()

bool CDPL.MolProp.hasFunctionalGroups ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ getFunctionalGroups()

Chem.FragmentList CDPL.MolProp.getFunctionalGroups ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ clearFunctionalGroups()

None CDPL.MolProp.clearFunctionalGroups ( Chem.MolecularGraph  molgraph)
Parameters
molgraph

◆ getHBondAcceptorAtomCount()

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

◆ setHBondAcceptorType()

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

◆ hasHBondAcceptorType()

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

◆ getHBondAcceptorType()

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

◆ clearHBondAcceptorType()

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

◆ getHBondDonorAtomCount()

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

◆ setHBondDonorType()

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

◆ hasHBondDonorType()

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

◆ getHBondDonorType()

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

◆ clearHBondDonorType()

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

◆ getHeavyAtomCount() [1/2]

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

◆ getHeavyAtomCount() [2/2]

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

◆ getHeavyBondCount() [1/2]

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

◆ getHeavyBondCount() [2/2]

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

◆ getHybridPolarizability()

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

◆ getHydrogenBondCount()

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

◆ setHydrophobicity()

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

◆ hasHydrophobicity()

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

◆ getHydrophobicity()

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

◆ clearHydrophobicity()

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

◆ getIUPACGroup()

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

◆ getImplicitHydrogenCount()

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

◆ setMHMOPiCharge()

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

◆ hasMHMOPiCharge()

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

◆ getMHMOPiCharge()

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

◆ clearMHMOPiCharge()

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

◆ setMHMOPiOrder()

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

◆ hasMHMOPiOrder()

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

◆ getMHMOPiOrder()

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

◆ clearMHMOPiOrder()

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

◆ getNetFormalCharge()

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

◆ getNumContainingSSSRRings() [1/2]

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

◆ getNumContainingSSSRRings() [2/2]

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

◆ getOrdinaryHydrogenCount() [1/2]

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

◆ getOrdinaryHydrogenCount() [2/2]

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

◆ setPEOESigmaCharge()

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

◆ hasPEOESigmaCharge()

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

◆ getPEOESigmaCharge()

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

◆ clearPEOESigmaCharge()

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

◆ setPEOESigmaElectronegativity()

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

◆ hasPEOESigmaElectronegativity()

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

◆ getPEOESigmaElectronegativity()

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

◆ clearPEOESigmaElectronegativity()

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

◆ getPeriod()

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

◆ getRingAtomCount() [1/2]

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

◆ getRingAtomCount() [2/2]

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

◆ getRingBondCount() [1/2]

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

◆ getRingBondCount() [2/2]

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

◆ 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

◆ getRuleOfFiveScore()

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

◆ getVdWRadius()

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

◆ calcAtomHydrophobicities()

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

◆ calcCyclomaticNumber()

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

◆ calcEffectivePolarizability()

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

◆ calcExplicitMass()

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

◆ calcExplicitMassComposition()

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

◆ calcExplicitValence()

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

◆ calcFreeValenceElectronCount()

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

◆ calcInductiveEffect()

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

◆ calcLogS()

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

◆ calcLonePairElectronegativity()

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

◆ calcMHMOProperties()

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

◆ calcMassComposition()

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

◆ calcMass()

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

◆ calcMeanPolarizability()

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

◆ calcPEOEProperties()

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

◆ calcPiElectronegativity()

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

◆ calcPolarizability()

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

◆ calcStericNumber()

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

◆ calcTPSA()

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

◆ calcTotalPartialCharge()

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

◆ calcValence()

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

◆ calcValenceElectronCount()

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

◆ calcXLogP()

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

◆ generateElementHistogram()

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

◆ generateExplicitElementHistogram()

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

◆ generateExplicitMassCompositionString()

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

◆ generateExplicitMolecularFormula()

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

◆ generateMassCompositionString()

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

◆ generateMolecularFormula()

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

◆ 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

◆ 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

◆ isBridgehead()

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

◆ isChemicalElement()

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

◆ isHBondAcceptor()

bool CDPL.MolProp.isHBondAcceptor ( 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

◆ isHalogen()

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

◆ isHeavy()

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

◆ isHeteroAtomHydrogenRotor()

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

◆ isHydrogenBond()

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

◆ isHydrogenRotor()

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

◆ isInRing() [1/2]

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

◆ isInRing() [2/2]

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

◆ isInRingOfSize() [1/2]

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

◆ isInRingOfSize() [2/2]

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

◆ isInvertibleNitrogen()

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

◆ isMainGroupElement()

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

◆ isMetal()

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

◆ isNobleGas()

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

◆ isNonMetal()

bool CDPL.MolProp.isNonMetal ( 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

◆ isPlanarNitrogen()

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

◆ isSemiMetal()

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

◆ isSpiroCenter()

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

◆ isTransitionMetal()

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

◆ isUnsaturated()

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

◆ perceiveFunctionalGroups() [1/2]

Chem.FragmentList CDPL.MolProp.perceiveFunctionalGroups ( Chem.MolecularGraph  molgraph)
Parameters
molgraph
Returns

◆ perceiveFunctionalGroups() [2/2]

Chem.FragmentList CDPL.MolProp.perceiveFunctionalGroups ( Chem.MolecularGraph  molgraph,
bool  overwrite 
)
Parameters
molgraph
overwrite
Returns

◆ perceiveHBondAcceptorAtomTypes()

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

◆ perceiveHBondDonorAtomTypes()

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