rdkit.Chem.rdchem module — The RDKit 2025.09.6 documentation

# rdkit.Chem.rdchem module

Module containing the core chemistry functionality of the RDKit

rdkit.Chem.rdchem.AddMolSubstanceGroup((Mol)mol, (SubstanceGroup)sgroup) → SubstanceGroup :

  adds a copy of a SubstanceGroup to a molecule, returns the new SubstanceGroup

  C++ signature :

    RDKit::SubstanceGroup* AddMolSubstanceGroup(RDKit::ROMol {lvalue},RDKit::SubstanceGroup)

class rdkit.Chem.rdchem.Atom((object)self, (str)what) → None :

  Bases: `instance`

  The class to store Atoms. Note that, though it is possible to create one, having an Atom on its own (i.e not associated with a molecule) is not particularly useful.

  > C++ signature :

  >   void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  __init__( (object)self, (Atom)other) -> None :

  > C++ signature :

  >   void __init__(_object*,RDKit::Atom)

  __init__( (object)self, (int)num) -> None :

    Constructor, takes the atomic number

    C++ signature :

      void __init__(_object*,unsigned int)

  ClearProp((Atom)self, (str)key) → None :

    Removes a particular property from an Atom (does nothing if not already set).

    > ARGUMENTS:

    >   - key: the name of the property to be removed.

    C++ signature :

      void ClearProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  ClearPropertyCache((Atom)self) → None :

    Clears implicit and explicit valence information.

    C++ signature :

      void ClearPropertyCache(RDKit::Atom {lvalue})

  DescribeQuery((Atom)self) → str :

    returns a text description of the query. Primarily intended for debugging purposes.

    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > DescribeQuery(RDKit::Atom const*)

  GetAtomMapNum((Atom)self) → int :

    Gets the atoms map number, returns 0 if not set

    C++ signature :

      int GetAtomMapNum(RDKit::Atom {lvalue})

  GetAtomicNum((Atom)self) → int :

    Returns the atomic number.

    C++ signature :

      int GetAtomicNum(RDKit::Atom {lvalue})

  GetBonds((Atom)self) → tuple :

    Returns a read-only sequence of the atom’s bonds

    C++ signature :

      boost::python::tuple GetBonds(RDKit::Atom*)

  GetBoolProp((Atom)self, (str)key) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (a bool).

    > RETURNS: a bool

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetBoolProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetChiralTag((Atom)self) → ChiralType :
    C++ signature :

      RDKit::Atom::ChiralType GetChiralTag(RDKit::Atom {lvalue})

  GetDegree((Atom)self) → int :

    Returns the degree of the atom in the molecule.

    > The degree of an atom is defined to be its number of directly-bonded neighbors. The degree is independent of bond orders, but is dependent

    > > on whether or not Hs are explicit in the graph.

    C++ signature :

      unsigned int GetDegree(RDKit::Atom {lvalue})

  GetDoubleProp((Atom)self, (str)key) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (a double).

    > RETURNS: a double

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetDoubleProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetExplicitBitVectProp((Atom)self, (str)key) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (a ExplicitBitVect).

    > RETURNS: an ExplicitBitVect

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetExplicitBitVectProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetExplicitValence((Atom)self) → int :

    DEPRECATED, please use GetValence(Chem.ValenceType.EXPLICIT) instead. Returns the explicit valence of the atom.

    C++ signature :

      int GetExplicitValence(RDKit::Atom const*)

  GetFormalCharge((Atom)self) → int :
    C++ signature :

      int GetFormalCharge(RDKit::Atom {lvalue})

  GetHybridization((Atom)self) → HybridizationType :

    Returns the atom’s hybridization.

    C++ signature :

      RDKit::Atom::HybridizationType GetHybridization(RDKit::Atom {lvalue})

  GetIdx((Atom)self) → int :

    Returns the atom’s index (ordering in the molecule)

    C++ signature :

      unsigned int GetIdx(RDKit::Atom {lvalue})

  GetImplicitValence((Atom)self) → int :

    DEPRECATED, please use GetValence(Chem.ValenceType.IMPLICIT) instead. Returns the number of implicit Hs on the atom.

    C++ signature :

      int GetImplicitValence(RDKit::Atom const*)

  GetIntProp((Atom)self, (str)key) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (an int).

    > RETURNS: an int

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetIntProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetIsAromatic((Atom)self) → bool :
    C++ signature :

      bool GetIsAromatic(RDKit::Atom {lvalue})

  GetIsotope((Atom)self) → int :
    C++ signature :

      unsigned int GetIsotope(RDKit::Atom {lvalue})

  GetMass((Atom)self) → float :
    C++ signature :

      double GetMass(RDKit::Atom {lvalue})

  GetMonomerInfo((Atom)self) → AtomMonomerInfo :

    Returns the atom’s MonomerInfo object, if there is one.

    C++ signature :

      RDKit::AtomMonomerInfo* GetMonomerInfo(RDKit::Atom*)

  GetNeighbors((Atom)self) → tuple :

    Returns a read-only sequence of the atom’s neighbors

    C++ signature :

      boost::python::tuple GetNeighbors(RDKit::Atom*)

  GetNoImplicit((Atom)self) → bool :

    Returns whether or not the atom is allowed to have implicit Hs.

    C++ signature :

      bool GetNoImplicit(RDKit::Atom {lvalue})

  GetNumExplicitHs((Atom)self) → int :
    C++ signature :

      unsigned int GetNumExplicitHs(RDKit::Atom {lvalue})

  GetNumImplicitHs((Atom)self) → int :

    Returns the total number of implicit Hs on the atom.

    C++ signature :

      unsigned int GetNumImplicitHs(RDKit::Atom {lvalue})

  GetNumRadicalElectrons((Atom)self) → int :
    C++ signature :

      unsigned int GetNumRadicalElectrons(RDKit::Atom {lvalue})

  GetOwningMol((Atom)self) → Mol :

    Returns the Mol that owns this atom.

    C++ signature :

      RDKit::ROMol {lvalue} GetOwningMol(RDKit::Atom {lvalue})

  GetPDBResidueInfo((Atom)self) → AtomPDBResidueInfo :

    Returns the atom’s MonomerInfo object, if there is one.

    C++ signature :

      RDKit::AtomPDBResidueInfo* GetPDBResidueInfo(RDKit::Atom*)

  GetProp((Atom)self, (str)key[, (bool)autoConvert=False]) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    >   - autoConvert: if True attempt to convert the property into a python object

    > RETURNS: a string

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > [,bool=False])

  GetPropNames((Atom)self[, (bool)includePrivate=False[, (bool)includeComputed=False]]) → rdkit.rdBase._vectNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE :

    Returns a list of the properties set on the Atom.

    C++ signature :

      std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > GetPropNames(RDKit::Atom {lvalue} [,bool=False [,bool=False]])

  GetPropsAsDict((Atom)self[, (bool)includePrivate=True[, (bool)includeComputed=True[, (bool)autoConvertStrings=True]]]) → dict :

    Returns a dictionary populated with properties. When possible, string values will be converted to integers or doubles (trimming if necessary)

    > n.b. Some properties are not able to be converted to python types.

    > > ARGUMENTS:
    > >   - includePrivate: (optional) toggles inclusion of private properties in the result set.

    > >       Defaults to False.

    > >   - includeComputed: (optional) toggles inclusion of computed properties in the result set.

    > >       Defaults to False.

    > >   - autoConvertStrings: (optional) toggles automatic conversion of string properties to integers or doubles.

    > >       Defaults to True.

    > > RETURNS: a dictionary

    C++ signature :

      boost::python::dict GetPropsAsDict(RDKit::Atom [,bool=True [,bool=True [,bool=True]]])

  GetQueryType((Atom)self) → str :
    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetQueryType(RDKit::Atom {lvalue})

  GetSmarts((Atom)self[, (bool)doKekule=False[, (bool)allHsExplicit=False[, (bool)isomericSmiles=True]]]) → str :

    returns the SMARTS (or SMILES) string for an Atom

    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetSmarts(RDKit::Atom const* [,bool=False [,bool=False [,bool=True]]])

  GetSymbol((Atom)self) → str :

    Returns the atomic symbol (a string)

    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetSymbol(RDKit::Atom {lvalue})

  GetTotalDegree((Atom)self) → int :

    Returns the degree of the atom in the molecule including Hs.

    > The degree of an atom is defined to be its number of directly-bonded neighbors. The degree is independent of bond orders.

    C++ signature :

      unsigned int GetTotalDegree(RDKit::Atom {lvalue})

  GetTotalNumHs((Atom)self[, (bool)includeNeighbors=False]) → int :

    Returns the total number of Hs (explicit and implicit) on the atom.

    > ARGUMENTS:

    > > - includeNeighbors: (optional) toggles inclusion of neighboring H atoms in the sum. Defaults to 0.

    C++ signature :

      unsigned int GetTotalNumHs(RDKit::Atom {lvalue} [,bool=False])

  GetTotalValence((Atom)self) → int :

    Returns the total valence (explicit + implicit) of the atom.

    C++ signature :

      unsigned int GetTotalValence(RDKit::Atom {lvalue})

  GetUnsignedProp((Atom)self, (str)key) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (an unsigned integer).

    > RETURNS: an integer (Python has no unsigned type)

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetUnsignedProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetValence((Atom)self, (ValenceType)which) → int :

    Returns the valence (Chem.ValenceType.EXPLICIT or Chem.ValenceType.IMPLICIT) of the atom.

    C++ signature :

      unsigned int GetValence(RDKit::Atom {lvalue},RDKit::Atom::ValenceType)

  HasOwningMol((Atom)self) → bool :

    Returns whether or not this instance belongs to a molecule.

    C++ signature :

      bool HasOwningMol(RDKit::Atom {lvalue})

  HasProp((Atom)self, (str)key) → int :

    Queries a Atom to see if a particular property has been assigned.

    > ARGUMENTS:

    >   - key: the name of the property to check for (a string).

    C++ signature :

      int HasProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  HasQuery((Atom)self) → bool :

    Returns whether or not the atom has an associated query

    C++ signature :

      bool HasQuery(RDKit::Atom {lvalue})

  HasValenceViolation((Atom)arg1) → bool :

    Returns whether the atom has a valence violation or not.

    C++ signature :

      bool HasValenceViolation(RDKit::Atom {lvalue})

  InvertChirality((Atom)self) → bool :
    C++ signature :

      bool InvertChirality(RDKit::Atom {lvalue})

  IsInRing((Atom)self) → bool :

    Returns whether or not the atom is in a ring

    C++ signature :

      bool IsInRing(RDKit::Atom const*)

  IsInRingSize((Atom)self, (int)size) → bool :

    Returns whether or not the atom is in a ring of a particular size.

    > ARGUMENTS:

    >   - size: the ring size to look for

    C++ signature :

      bool IsInRingSize(RDKit::Atom const*,int)

  Match((Atom)self, (Atom)what) → bool :

    Returns whether or not this atom matches another Atom.

    > Each Atom (or query Atom) has a query function which is used for this type of matching.

    > ARGUMENTS:

    >   - other: the other Atom to which to compare

    C++ signature :

      bool Match(RDKit::Atom {lvalue},RDKit::Atom const*)

  NOATOM = 4294967295
  NeedsUpdatePropertyCache((Atom)self) → bool :

    Returns true or false depending on whether implicit and explicit valence of the molecule have already been calculated.

    C++ signature :

      bool NeedsUpdatePropertyCache(RDKit::Atom {lvalue})

  SetAtomMapNum((Atom)self, (int)mapno[, (bool)strict=False]) → None :

    Sets the atoms map number, a value of 0 clears the atom map

    C++ signature :

      void SetAtomMapNum(RDKit::Atom {lvalue},int [,bool=False])

  SetAtomicNum((Atom)self, (int)newNum) → None :

    Sets the atomic number, takes an integer value as an argument

    C++ signature :

      void SetAtomicNum(RDKit::Atom {lvalue},int)

  SetBoolProp((Atom)self, (str)key, (bool)val) → None :

    Sets an atomic property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a bool).

    >   - value: the property value (a bool).

    C++ signature :

      void SetBoolProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,bool)

  SetChiralTag((Atom)self, (ChiralType)what) → None :
    C++ signature :

      void SetChiralTag(RDKit::Atom {lvalue},RDKit::Atom::ChiralType)

  SetDoubleProp((Atom)self, (str)key, (float)val) → None :

    Sets an atomic property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a double).

    >   - value: the property value (a double).

    C++ signature :

      void SetDoubleProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,double)

  SetExplicitBitVectProp((Atom)self, (str)key, (rdkit.DataStructs.cDataStructs.ExplicitBitVect)val) → None :

    Sets an atomic property

    > ARGUMENTS:

    >   - key: the name of the property to be set (an ExplicitBitVect).

    >   - value: the property value (an ExplicitBitVect).

    C++ signature :

      void SetExplicitBitVectProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,ExplicitBitVect)

  SetFormalCharge((Atom)self, (int)what) → None :
    C++ signature :

      void SetFormalCharge(RDKit::Atom {lvalue},int)

  SetHybridization((Atom)self, (HybridizationType)what) → None :
    Sets the hybridization of the atom.

      The argument should be a HybridizationType

    C++ signature :

      void SetHybridization(RDKit::Atom {lvalue},RDKit::Atom::HybridizationType)

  SetIntProp((Atom)self, (str)key, (int)val) → None :

    Sets an atomic property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a int).

    >   - value: the property value (a int).

    C++ signature :

      void SetIntProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,int)

  SetIsAromatic((Atom)self, (bool)what) → None :
    C++ signature :

      void SetIsAromatic(RDKit::Atom {lvalue},bool)

  SetIsotope((Atom)self, (int)what) → None :
    C++ signature :

      void SetIsotope(RDKit::Atom {lvalue},unsigned int)

  SetMonomerInfo((Atom)self, (AtomMonomerInfo)info) → None :

    Sets the atom’s MonomerInfo object.

    C++ signature :

      void SetMonomerInfo(RDKit::Atom*,RDKit::AtomMonomerInfo const*)

  SetNoImplicit((Atom)self, (bool)what) → None :
    Sets a marker on the atom that disallows implicit Hs.

      This holds even if the atom would otherwise have implicit Hs added.

    C++ signature :

      void SetNoImplicit(RDKit::Atom {lvalue},bool)

  SetNumExplicitHs((Atom)self, (int)what) → None :
    C++ signature :

      void SetNumExplicitHs(RDKit::Atom {lvalue},unsigned int)

  SetNumRadicalElectrons((Atom)self, (int)num) → None :
    C++ signature :

      void SetNumRadicalElectrons(RDKit::Atom {lvalue},unsigned int)

  SetPDBResidueInfo((Atom)self, (AtomMonomerInfo)info) → None :

    Sets the atom’s MonomerInfo object.

    C++ signature :

      void SetPDBResidueInfo(RDKit::Atom*,RDKit::AtomMonomerInfo const*)

  SetProp((Atom)self, (str)key, (str)val) → None :

    Sets an atomic property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value (a string).

    C++ signature :

      void SetProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  SetUnsignedProp((Atom)self, (str)key, (int)val) → None :

    Sets an atomic property

    > ARGUMENTS:

    >   - key: the name of the property to be set (an unsigned integer).

    >   - value: the property value (a int >= 0).

    C++ signature :

      void SetUnsignedProp(RDKit::Atom const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,unsigned int)

  UpdatePropertyCache((Atom)self[, (bool)strict=True]) → None :

    Regenerates computed properties like implicit valence and ring information.

    C++ signature :

      void UpdatePropertyCache(RDKit::Atom {lvalue} [,bool=True])

class rdkit.Chem.rdchem.AtomCoordsMatcher((object)self) → None :

  Bases: `instance`

  Allows using atom coordinates as part of substructure matching

  > C++ signature :

  >   void __init__(_object*)

  __init__( (object)self [, (int)refConfId=-1 [, (int)queryConfId=-1 [, (float)tol=0.0001]]]) -> None :

    constructor taking reference and query conformer IDs and a distance tolerance

    C++ signature :

      void __init__(_object* [,int=-1 [,int=-1 [,double=0.0001]]])

  property queryConfId

    query conformer ID

  property refConfId

    reference conformer ID

  property tol2

    squared distance tolerance

exception rdkit.Chem.rdchem.AtomKekulizeException

  Bases: `AtomSanitizeException`

class rdkit.Chem.rdchem.AtomMonomerInfo((object)self) → None :

  Bases: `instance`

  The class to store monomer information attached to Atoms

  > C++ signature :

  >   void __init__(_object*)

  __init__( (object)self, (AtomMonomerType)type [, (str)name=’’]) -> None :

  > C++ signature :

  >   void __init__(_object*,RDKit::AtomMonomerInfo::AtomMonomerType [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’])

  GetMonomerType((AtomMonomerInfo)self) → AtomMonomerType :
    C++ signature :

      RDKit::AtomMonomerInfo::AtomMonomerType GetMonomerType(RDKit::AtomMonomerInfo {lvalue})

  GetName((AtomMonomerInfo)self) → str :
    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetName(RDKit::AtomMonomerInfo {lvalue})

  SetMonomerType((AtomMonomerInfo)self, (AtomMonomerType)typ) → None :
    C++ signature :

      void SetMonomerType(RDKit::AtomMonomerInfo {lvalue},RDKit::AtomMonomerInfo::AtomMonomerType)

  SetName((AtomMonomerInfo)self, (str)nm) → None :
    C++ signature :

      void SetName(RDKit::AtomMonomerInfo {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

class rdkit.Chem.rdchem.AtomMonomerType

  Bases: `enum`

  OTHER = rdkit.Chem.rdchem.AtomMonomerType.OTHER
  PDBRESIDUE = rdkit.Chem.rdchem.AtomMonomerType.PDBRESIDUE
  UNKNOWN = rdkit.Chem.rdchem.AtomMonomerType.UNKNOWN
  names = {'OTHER': rdkit.Chem.rdchem.AtomMonomerType.OTHER, 'PDBRESIDUE': rdkit.Chem.rdchem.AtomMonomerType.PDBRESIDUE, 'UNKNOWN': rdkit.Chem.rdchem.AtomMonomerType.UNKNOWN}
  values = {0: rdkit.Chem.rdchem.AtomMonomerType.UNKNOWN, 1: rdkit.Chem.rdchem.AtomMonomerType.PDBRESIDUE, 2: rdkit.Chem.rdchem.AtomMonomerType.OTHER}

class rdkit.Chem.rdchem.AtomPDBResidueInfo((object)self) → None :

  Bases: `AtomMonomerInfo`

  The class to store PDB residue information attached to Atoms

  > C++ signature :

  >   void __init__(_object*)

  __init__( (object)self, (str)atomName [, (int)serialNumber=1 [, (str)altLoc=’’ [, (str)residueName=’’ [, (int)residueNumber=0 [, (str)chainId=’’ [, (str)insertionCode=’’ [, (float)occupancy=1.0 [, (float)tempFactor=0.0 [, (bool)isHeteroAtom=False [, (int)secondaryStructure=0 [, (int)segmentNumber=0]]]]]]]]]]]) -> None :

  > C++ signature :

  >   void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > [,int=1 [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’ [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’ [,int=0 [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’ [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’ [,double=1.0 [,double=0.0 [,bool=False [,unsigned int=0 [,unsigned int=0]]]]]]]]]]])

  GetAltLoc((AtomPDBResidueInfo)self) → str :
    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetAltLoc(RDKit::AtomPDBResidueInfo {lvalue})

  GetChainId((AtomPDBResidueInfo)self) → str :
    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetChainId(RDKit::AtomPDBResidueInfo {lvalue})

  GetInsertionCode((AtomPDBResidueInfo)self) → str :
    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetInsertionCode(RDKit::AtomPDBResidueInfo {lvalue})

  GetIsHeteroAtom((AtomPDBResidueInfo)self) → bool :
    C++ signature :

      bool GetIsHeteroAtom(RDKit::AtomPDBResidueInfo {lvalue})

  GetOccupancy((AtomPDBResidueInfo)self) → float :
    C++ signature :

      double GetOccupancy(RDKit::AtomPDBResidueInfo {lvalue})

  GetResidueName((AtomPDBResidueInfo)self) → str :
    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetResidueName(RDKit::AtomPDBResidueInfo {lvalue})

  GetResidueNumber((AtomPDBResidueInfo)self) → int :
    C++ signature :

      int GetResidueNumber(RDKit::AtomPDBResidueInfo {lvalue})

  GetSecondaryStructure((AtomPDBResidueInfo)self) → int :
    C++ signature :

      unsigned int GetSecondaryStructure(RDKit::AtomPDBResidueInfo {lvalue})

  GetSegmentNumber((AtomPDBResidueInfo)self) → int :
    C++ signature :

      unsigned int GetSegmentNumber(RDKit::AtomPDBResidueInfo {lvalue})

  GetSerialNumber((AtomPDBResidueInfo)self) → int :
    C++ signature :

      int GetSerialNumber(RDKit::AtomPDBResidueInfo {lvalue})

  GetTempFactor((AtomPDBResidueInfo)self) → float :
    C++ signature :

      double GetTempFactor(RDKit::AtomPDBResidueInfo {lvalue})

  SetAltLoc((AtomPDBResidueInfo)self, (str)val) → None :
    C++ signature :

      void SetAltLoc(RDKit::AtomPDBResidueInfo {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  SetChainId((AtomPDBResidueInfo)self, (str)val) → None :
    C++ signature :

      void SetChainId(RDKit::AtomPDBResidueInfo {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  SetInsertionCode((AtomPDBResidueInfo)self, (str)val) → None :
    C++ signature :

      void SetInsertionCode(RDKit::AtomPDBResidueInfo {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  SetIsHeteroAtom((AtomPDBResidueInfo)self, (bool)val) → None :
    C++ signature :

      void SetIsHeteroAtom(RDKit::AtomPDBResidueInfo {lvalue},bool)

  SetOccupancy((AtomPDBResidueInfo)self, (float)val) → None :
    C++ signature :

      void SetOccupancy(RDKit::AtomPDBResidueInfo {lvalue},double)

  SetResidueName((AtomPDBResidueInfo)self, (str)val) → None :
    C++ signature :

      void SetResidueName(RDKit::AtomPDBResidueInfo {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  SetResidueNumber((AtomPDBResidueInfo)self, (int)val) → None :
    C++ signature :

      void SetResidueNumber(RDKit::AtomPDBResidueInfo {lvalue},int)

  SetSecondaryStructure((AtomPDBResidueInfo)self, (int)val) → None :
    C++ signature :

      void SetSecondaryStructure(RDKit::AtomPDBResidueInfo {lvalue},unsigned int)

  SetSegmentNumber((AtomPDBResidueInfo)self, (int)val) → None :
    C++ signature :

      void SetSegmentNumber(RDKit::AtomPDBResidueInfo {lvalue},unsigned int)

  SetSerialNumber((AtomPDBResidueInfo)self, (int)val) → None :
    C++ signature :

      void SetSerialNumber(RDKit::AtomPDBResidueInfo {lvalue},int)

  SetTempFactor((AtomPDBResidueInfo)self, (float)val) → None :
    C++ signature :

      void SetTempFactor(RDKit::AtomPDBResidueInfo {lvalue},double)

exception rdkit.Chem.rdchem.AtomSanitizeException

  Bases: `MolSanitizeException`

exception rdkit.Chem.rdchem.AtomValenceException

  Bases: `AtomSanitizeException`

class rdkit.Chem.rdchem.Bond

  Bases: `instance`

  The class to store Bonds. Note: unlike Atoms, is it currently impossible to construct Bonds from Python.

  Raises an exception This class cannot be instantiated from Python

  ClearProp((Bond)self, (str)key) → None :

    Removes a particular property from an Bond (does nothing if not already set).

    > ARGUMENTS:

    >   - key: the name of the property to be removed.

    C++ signature :

      void ClearProp(RDKit::Bond const*,char const*)

  DescribeQuery((Bond)self) → str :

    returns a text description of the query. Primarily intended for debugging purposes.

    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > DescribeQuery(RDKit::Bond const*)

  GetBeginAtom((Bond)self) → Atom :

    Returns the bond’s first atom.

    C++ signature :

      RDKit::Atom* GetBeginAtom(RDKit::Bond {lvalue})

  GetBeginAtomIdx((Bond)self) → int :

    Returns the index of the bond’s first atom.

    C++ signature :

      unsigned int GetBeginAtomIdx(RDKit::Bond {lvalue})

  GetBondDir((Bond)self) → BondDir :

    Returns the type of the bond as a BondDir

    C++ signature :

      RDKit::Bond::BondDir GetBondDir(RDKit::Bond {lvalue})

  GetBondType((Bond)self) → BondType :

    Returns the type of the bond as a BondType

    C++ signature :

      RDKit::Bond::BondType GetBondType(RDKit::Bond {lvalue})

  GetBondTypeAsDouble((Bond)self) → float :

    Returns the type of the bond as a double (i.e. 1.0 for SINGLE, 1.5 for AROMATIC, 2.0 for DOUBLE)

    C++ signature :

      double GetBondTypeAsDouble(RDKit::Bond {lvalue})

  GetBoolProp((Bond)self, (str)key) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (a boolean).

    > RETURNS: a boolean

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetBoolProp(RDKit::Bond const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetDoubleProp((Bond)self, (str)key) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (a double).

    > RETURNS: a double

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetDoubleProp(RDKit::Bond const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetEndAtom((Bond)self) → Atom :

    Returns the bond’s second atom.

    C++ signature :

      RDKit::Atom* GetEndAtom(RDKit::Bond {lvalue})

  GetEndAtomIdx((Bond)self) → int :

    Returns the index of the bond’s first atom.

    C++ signature :

      unsigned int GetEndAtomIdx(RDKit::Bond {lvalue})

  GetIdx((Bond)self) → int :

    Returns the bond’s index (ordering in the molecule)

    C++ signature :

      unsigned int GetIdx(RDKit::Bond {lvalue})

  GetIntProp((Bond)self, (str)key) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (an int).

    > RETURNS: an int

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetIntProp(RDKit::Bond const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetIsAromatic((Bond)self) → bool :
    C++ signature :

      bool GetIsAromatic(RDKit::Bond {lvalue})

  GetIsConjugated((Bond)self) → bool :

    Returns whether or not the bond is considered to be conjugated.

    C++ signature :

      bool GetIsConjugated(RDKit::Bond {lvalue})

  GetOtherAtom((Bond)self, (Atom)what) → Atom :

    Given one of the bond’s atoms, returns the other one.

    C++ signature :

      RDKit::Atom* GetOtherAtom(RDKit::Bond {lvalue},RDKit::Atom const*)

  GetOtherAtomIdx((Bond)self, (int)thisIdx) → int :

    Given the index of one of the bond’s atoms, returns the index of the other.

    C++ signature :

      unsigned int GetOtherAtomIdx(RDKit::Bond {lvalue},unsigned int)

  GetOwningMol((Bond)self) → Mol :

    Returns the Mol that owns this bond.

    C++ signature :

      RDKit::ROMol {lvalue} GetOwningMol(RDKit::Bond {lvalue})

  GetProp((Bond)self, (str)key[, (bool)autoConvert=False]) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    >   - autoConvert: if True attempt to convert the property into a python object

    > RETURNS: a string

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetProp(RDKit::Bond const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > [,bool=False])

  GetPropNames((Bond)self[, (bool)includePrivate=False[, (bool)includeComputed=False]]) → rdkit.rdBase._vectNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE :

    Returns a list of the properties set on the Bond.

    C++ signature :

      std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > GetPropNames(RDKit::Bond {lvalue} [,bool=False [,bool=False]])

  GetPropsAsDict((Bond)self[, (bool)includePrivate=True[, (bool)includeComputed=True[, (bool)autoConvertStrings=True]]]) → dict :

    Returns a dictionary populated with properties. When possible, string values will be converted to integers or doubles (trimming if necessary)

    > n.b. Some properties are not able to be converted to python types.

    > > ARGUMENTS:
    > >   - includePrivate: (optional) toggles inclusion of private properties in the result set.

    > >       Defaults to False.

    > >   - includeComputed: (optional) toggles inclusion of computed properties in the result set.

    > >       Defaults to False.

    > >   - autoConvertStrings: (optional) toggles automatic conversion of string properties to integers or doubles.

    > >       Defaults to True.

    > > RETURNS: a dictionary

    C++ signature :

      boost::python::dict GetPropsAsDict(RDKit::Bond [,bool=True [,bool=True [,bool=True]]])

  GetSmarts((Bond)bond[, (bool)allBondsExplicit=False]) → str :

    returns the SMARTS (or SMILES) string for a Bond

    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetSmarts(RDKit::Bond const* [,bool=False])

  GetStereo((Bond)self) → BondStereo :

    Returns the stereo configuration of the bond as a BondStereo

    C++ signature :

      RDKit::Bond::BondStereo GetStereo(RDKit::Bond {lvalue})

  GetStereoAtoms((Bond)self) → rdkit.rdBase._vecti :

    Returns the indices of the atoms setting this bond’s stereochemistry.

    C++ signature :

      std::vector<int, std::allocator<int> > GetStereoAtoms(RDKit::Bond const*)

  GetUnsignedProp((Bond)self, (str)key) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (an unsigned integer).

    > RETURNS: an int (Python has no unsigned type)

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetUnsignedProp(RDKit::Bond const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetValenceContrib((Bond)self, (Atom)at) → float :

    Returns the contribution of the bond to the valence of an Atom.

    > ARGUMENTS:

    > > - atom: the Atom to consider.

    C++ signature :

      double GetValenceContrib(RDKit::Bond {lvalue},RDKit::Atom const*)

  HasOwningMol((Bond)self) → bool :

    Returns whether or not this instance belongs to a molecule.

    C++ signature :

      bool HasOwningMol(RDKit::Bond {lvalue})

  HasProp((Bond)self, (str)key) → int :

    Queries a Bond to see if a particular property has been assigned.

    > ARGUMENTS:

    >   - key: the name of the property to check for (a string).

    C++ signature :

      int HasProp(RDKit::Bond const*,char const*)

  HasQuery((Bond)self) → bool :

    Returns whether or not the bond has an associated query

    C++ signature :

      bool HasQuery(RDKit::Bond {lvalue})

  InvertChirality((Bond)self) → bool :
    C++ signature :

      bool InvertChirality(RDKit::Bond {lvalue})

  IsInRing((Bond)self) → bool :

    Returns whether or not the bond is in a ring of any size.

    C++ signature :

      bool IsInRing(RDKit::Bond const*)

  IsInRingSize((Bond)self, (int)size) → bool :

    Returns whether or not the bond is in a ring of a particular size.

    > ARGUMENTS:

    >   - size: the ring size to look for

    C++ signature :

      bool IsInRingSize(RDKit::Bond const*,int)

  Match((Bond)self, (Bond)what) → bool :

    Returns whether or not this bond matches another Bond.

    > Each Bond (or query Bond) has a query function which is used for this type of matching.

    > ARGUMENTS:

    >   - other: the other Bond to which to compare

    C++ signature :

      bool Match(RDKit::Bond {lvalue},RDKit::Bond const*)

  SetBondDir((Bond)self, (BondDir)what) → None :

    Set the type of the bond as a BondDir

    C++ signature :

      void SetBondDir(RDKit::Bond {lvalue},RDKit::Bond::BondDir)

  SetBondType((Bond)self, (BondType)bT) → None :

    Set the type of the bond as a BondType

    C++ signature :

      void SetBondType(RDKit::Bond {lvalue},RDKit::Bond::BondType)

  SetBoolProp((Bond)self, (str)key, (bool)val) → None :

    Sets a bond property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value (a boolean).

    C++ signature :

      void SetBoolProp(RDKit::Bond const*,char const*,bool)

  SetDoubleProp((Bond)self, (str)key, (float)val) → None :

    Sets a bond property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value (a double).

    C++ signature :

      void SetDoubleProp(RDKit::Bond const*,char const*,double)

  SetIntProp((Bond)self, (str)key, (int)val) → None :

    Sets a bond property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value (an int).

    C++ signature :

      void SetIntProp(RDKit::Bond const*,char const*,int)

  SetIsAromatic((Bond)self, (bool)what) → None :
    C++ signature :

      void SetIsAromatic(RDKit::Bond {lvalue},bool)

  SetIsConjugated((Bond)self, (bool)what) → None :
    C++ signature :

      void SetIsConjugated(RDKit::Bond {lvalue},bool)

  SetProp((Bond)self, (str)key, (str)val) → None :

    Sets a bond property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value (a string).

    C++ signature :

      void SetProp(RDKit::Bond const*,char const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  SetStereo((Bond)self, (BondStereo)what) → None :

    Set the stereo configuration of the bond as a BondStereo

    C++ signature :

      void SetStereo(RDKit::Bond {lvalue},RDKit::Bond::BondStereo)

  SetStereoAtoms((Bond)self, (int)bgnIdx, (int)endIdx) → None :

    Set the indices of the atoms setting this bond’s stereochemistry.

    C++ signature :

      void SetStereoAtoms(RDKit::Bond {lvalue},unsigned int,unsigned int)

  SetUnsignedProp((Bond)self, (str)key, (int)val) → None :

    Sets a bond property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value (an int >= 0).

    C++ signature :

      void SetUnsignedProp(RDKit::Bond const*,char const*,unsigned int)

class rdkit.Chem.rdchem.BondDir

  Bases: `enum`

  BEGINDASH = rdkit.Chem.rdchem.BondDir.BEGINDASH
  BEGINWEDGE = rdkit.Chem.rdchem.BondDir.BEGINWEDGE
  EITHERDOUBLE = rdkit.Chem.rdchem.BondDir.EITHERDOUBLE
  ENDDOWNRIGHT = rdkit.Chem.rdchem.BondDir.ENDDOWNRIGHT
  ENDUPRIGHT = rdkit.Chem.rdchem.BondDir.ENDUPRIGHT
  NONE = rdkit.Chem.rdchem.BondDir.NONE
  UNKNOWN = rdkit.Chem.rdchem.BondDir.UNKNOWN
  names = {'BEGINDASH': rdkit.Chem.rdchem.BondDir.BEGINDASH, 'BEGINWEDGE': rdkit.Chem.rdchem.BondDir.BEGINWEDGE, 'EITHERDOUBLE': rdkit.Chem.rdchem.BondDir.EITHERDOUBLE, 'ENDDOWNRIGHT': rdkit.Chem.rdchem.BondDir.ENDDOWNRIGHT, 'ENDUPRIGHT': rdkit.Chem.rdchem.BondDir.ENDUPRIGHT, 'NONE': rdkit.Chem.rdchem.BondDir.NONE, 'UNKNOWN': rdkit.Chem.rdchem.BondDir.UNKNOWN}
  values = {0: rdkit.Chem.rdchem.BondDir.NONE, 1: rdkit.Chem.rdchem.BondDir.BEGINWEDGE, 2: rdkit.Chem.rdchem.BondDir.BEGINDASH, 3: rdkit.Chem.rdchem.BondDir.ENDDOWNRIGHT, 4: rdkit.Chem.rdchem.BondDir.ENDUPRIGHT, 5: rdkit.Chem.rdchem.BondDir.EITHERDOUBLE, 6: rdkit.Chem.rdchem.BondDir.UNKNOWN}

class rdkit.Chem.rdchem.BondStereo

  Bases: `enum`

  STEREOANY = rdkit.Chem.rdchem.BondStereo.STEREOANY
  STEREOATROPCCW = rdkit.Chem.rdchem.BondStereo.STEREOATROPCCW
  STEREOATROPCW = rdkit.Chem.rdchem.BondStereo.STEREOATROPCW
  STEREOCIS = rdkit.Chem.rdchem.BondStereo.STEREOCIS
  STEREOE = rdkit.Chem.rdchem.BondStereo.STEREOE
  STEREONONE = rdkit.Chem.rdchem.BondStereo.STEREONONE
  STEREOTRANS = rdkit.Chem.rdchem.BondStereo.STEREOTRANS
  STEREOZ = rdkit.Chem.rdchem.BondStereo.STEREOZ
  names = {'STEREOANY': rdkit.Chem.rdchem.BondStereo.STEREOANY, 'STEREOATROPCCW': rdkit.Chem.rdchem.BondStereo.STEREOATROPCCW, 'STEREOATROPCW': rdkit.Chem.rdchem.BondStereo.STEREOATROPCW, 'STEREOCIS': rdkit.Chem.rdchem.BondStereo.STEREOCIS, 'STEREOE': rdkit.Chem.rdchem.BondStereo.STEREOE, 'STEREONONE': rdkit.Chem.rdchem.BondStereo.STEREONONE, 'STEREOTRANS': rdkit.Chem.rdchem.BondStereo.STEREOTRANS, 'STEREOZ': rdkit.Chem.rdchem.BondStereo.STEREOZ}
  values = {0: rdkit.Chem.rdchem.BondStereo.STEREONONE, 1: rdkit.Chem.rdchem.BondStereo.STEREOANY, 2: rdkit.Chem.rdchem.BondStereo.STEREOZ, 3: rdkit.Chem.rdchem.BondStereo.STEREOE, 4: rdkit.Chem.rdchem.BondStereo.STEREOCIS, 5: rdkit.Chem.rdchem.BondStereo.STEREOTRANS, 6: rdkit.Chem.rdchem.BondStereo.STEREOATROPCW, 7: rdkit.Chem.rdchem.BondStereo.STEREOATROPCCW}

class rdkit.Chem.rdchem.BondType

  Bases: `enum`

  AROMATIC = rdkit.Chem.rdchem.BondType.AROMATIC
  DATIVE = rdkit.Chem.rdchem.BondType.DATIVE
  DATIVEL = rdkit.Chem.rdchem.BondType.DATIVEL
  DATIVEONE = rdkit.Chem.rdchem.BondType.DATIVEONE
  DATIVER = rdkit.Chem.rdchem.BondType.DATIVER
  DOUBLE = rdkit.Chem.rdchem.BondType.DOUBLE
  FIVEANDAHALF = rdkit.Chem.rdchem.BondType.FIVEANDAHALF
  FOURANDAHALF = rdkit.Chem.rdchem.BondType.FOURANDAHALF
  HEXTUPLE = rdkit.Chem.rdchem.BondType.HEXTUPLE
  HYDROGEN = rdkit.Chem.rdchem.BondType.HYDROGEN
  IONIC = rdkit.Chem.rdchem.BondType.IONIC
  ONEANDAHALF = rdkit.Chem.rdchem.BondType.ONEANDAHALF
  OTHER = rdkit.Chem.rdchem.BondType.OTHER
  QUADRUPLE = rdkit.Chem.rdchem.BondType.QUADRUPLE
  QUINTUPLE = rdkit.Chem.rdchem.BondType.QUINTUPLE
  SINGLE = rdkit.Chem.rdchem.BondType.SINGLE
  THREEANDAHALF = rdkit.Chem.rdchem.BondType.THREEANDAHALF
  THREECENTER = rdkit.Chem.rdchem.BondType.THREECENTER
  TRIPLE = rdkit.Chem.rdchem.BondType.TRIPLE
  TWOANDAHALF = rdkit.Chem.rdchem.BondType.TWOANDAHALF
  UNSPECIFIED = rdkit.Chem.rdchem.BondType.UNSPECIFIED
  ZERO = rdkit.Chem.rdchem.BondType.ZERO
  names = {'AROMATIC': rdkit.Chem.rdchem.BondType.AROMATIC, 'DATIVE': rdkit.Chem.rdchem.BondType.DATIVE, 'DATIVEL': rdkit.Chem.rdchem.BondType.DATIVEL, 'DATIVEONE': rdkit.Chem.rdchem.BondType.DATIVEONE, 'DATIVER': rdkit.Chem.rdchem.BondType.DATIVER, 'DOUBLE': rdkit.Chem.rdchem.BondType.DOUBLE, 'FIVEANDAHALF': rdkit.Chem.rdchem.BondType.FIVEANDAHALF, 'FOURANDAHALF': rdkit.Chem.rdchem.BondType.FOURANDAHALF, 'HEXTUPLE': rdkit.Chem.rdchem.BondType.HEXTUPLE, 'HYDROGEN': rdkit.Chem.rdchem.BondType.HYDROGEN, 'IONIC': rdkit.Chem.rdchem.BondType.IONIC, 'ONEANDAHALF': rdkit.Chem.rdchem.BondType.ONEANDAHALF, 'OTHER': rdkit.Chem.rdchem.BondType.OTHER, 'QUADRUPLE': rdkit.Chem.rdchem.BondType.QUADRUPLE, 'QUINTUPLE': rdkit.Chem.rdchem.BondType.QUINTUPLE, 'SINGLE': rdkit.Chem.rdchem.BondType.SINGLE, 'THREEANDAHALF': rdkit.Chem.rdchem.BondType.THREEANDAHALF, 'THREECENTER': rdkit.Chem.rdchem.BondType.THREECENTER, 'TRIPLE': rdkit.Chem.rdchem.BondType.TRIPLE, 'TWOANDAHALF': rdkit.Chem.rdchem.BondType.TWOANDAHALF, 'UNSPECIFIED': rdkit.Chem.rdchem.BondType.UNSPECIFIED, 'ZERO': rdkit.Chem.rdchem.BondType.ZERO}
  values = {0: rdkit.Chem.rdchem.BondType.UNSPECIFIED, 1: rdkit.Chem.rdchem.BondType.SINGLE, 2: rdkit.Chem.rdchem.BondType.DOUBLE, 3: rdkit.Chem.rdchem.BondType.TRIPLE, 4: rdkit.Chem.rdchem.BondType.QUADRUPLE, 5: rdkit.Chem.rdchem.BondType.QUINTUPLE, 6: rdkit.Chem.rdchem.BondType.HEXTUPLE, 7: rdkit.Chem.rdchem.BondType.ONEANDAHALF, 8: rdkit.Chem.rdchem.BondType.TWOANDAHALF, 9: rdkit.Chem.rdchem.BondType.THREEANDAHALF, 10: rdkit.Chem.rdchem.BondType.FOURANDAHALF, 11: rdkit.Chem.rdchem.BondType.FIVEANDAHALF, 12: rdkit.Chem.rdchem.BondType.AROMATIC, 13: rdkit.Chem.rdchem.BondType.IONIC, 14: rdkit.Chem.rdchem.BondType.HYDROGEN, 15: rdkit.Chem.rdchem.BondType.THREECENTER, 16: rdkit.Chem.rdchem.BondType.DATIVEONE, 17: rdkit.Chem.rdchem.BondType.DATIVE, 18: rdkit.Chem.rdchem.BondType.DATIVEL, 19: rdkit.Chem.rdchem.BondType.DATIVER, 20: rdkit.Chem.rdchem.BondType.OTHER, 21: rdkit.Chem.rdchem.BondType.ZERO}

class rdkit.Chem.rdchem.ChiralType

  Bases: `enum`

  CHI_ALLENE = rdkit.Chem.rdchem.ChiralType.CHI_ALLENE
  CHI_OCTAHEDRAL = rdkit.Chem.rdchem.ChiralType.CHI_OCTAHEDRAL
  CHI_OTHER = rdkit.Chem.rdchem.ChiralType.CHI_OTHER
  CHI_SQUAREPLANAR = rdkit.Chem.rdchem.ChiralType.CHI_SQUAREPLANAR
  CHI_TETRAHEDRAL = rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL
  CHI_TETRAHEDRAL_CCW = rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW
  CHI_TETRAHEDRAL_CW = rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW
  CHI_TRIGONALBIPYRAMIDAL = rdkit.Chem.rdchem.ChiralType.CHI_TRIGONALBIPYRAMIDAL
  CHI_UNSPECIFIED = rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED
  names = {'CHI_ALLENE': rdkit.Chem.rdchem.ChiralType.CHI_ALLENE, 'CHI_OCTAHEDRAL': rdkit.Chem.rdchem.ChiralType.CHI_OCTAHEDRAL, 'CHI_OTHER': rdkit.Chem.rdchem.ChiralType.CHI_OTHER, 'CHI_SQUAREPLANAR': rdkit.Chem.rdchem.ChiralType.CHI_SQUAREPLANAR, 'CHI_TETRAHEDRAL': rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL, 'CHI_TETRAHEDRAL_CCW': rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW, 'CHI_TETRAHEDRAL_CW': rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW, 'CHI_TRIGONALBIPYRAMIDAL': rdkit.Chem.rdchem.ChiralType.CHI_TRIGONALBIPYRAMIDAL, 'CHI_UNSPECIFIED': rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED}
  values = {0: rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED, 1: rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW, 2: rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW, 3: rdkit.Chem.rdchem.ChiralType.CHI_OTHER, 4: rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL, 5: rdkit.Chem.rdchem.ChiralType.CHI_ALLENE, 6: rdkit.Chem.rdchem.ChiralType.CHI_SQUAREPLANAR, 7: rdkit.Chem.rdchem.ChiralType.CHI_TRIGONALBIPYRAMIDAL, 8: rdkit.Chem.rdchem.ChiralType.CHI_OCTAHEDRAL}

rdkit.Chem.rdchem.ClearMolSubstanceGroups((Mol)mol) → None :

  removes all SubstanceGroups from a molecule (if any)

  C++ signature :

    void ClearMolSubstanceGroups(RDKit::ROMol {lvalue})

class rdkit.Chem.rdchem.CompositeQueryType

  Bases: `enum`

  COMPOSITE_AND = rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_AND
  COMPOSITE_OR = rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_OR
  COMPOSITE_XOR = rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_XOR
  names = {'COMPOSITE_AND': rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_AND, 'COMPOSITE_OR': rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_OR, 'COMPOSITE_XOR': rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_XOR}
  values = {0: rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_AND, 1: rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_OR, 2: rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_XOR}

class rdkit.Chem.rdchem.Conformer((object)self) → None :

  Bases: `instance`

  The class to store 2D or 3D conformation of a molecule

  > C++ signature :

  >   void __init__(_object*)

  __init__( (object)self, (int)numAtoms) -> None :

    Constructor with the number of atoms specified

    C++ signature :

      void __init__(_object*,unsigned int)

  __init__( (object)self, (Conformer)other) -> None :

  > C++ signature :

  >   void __init__(_object*,RDKit::Conformer)

  ClearComputedProps((Conformer)self) → None :

    Removes all computed properties from the conformer.

    C++ signature :

      void ClearComputedProps(RDKit::Conformer)

  ClearProp((Conformer)self, (str)key) → None :

    Removes a property from the conformer.

    > ARGUMENTS:

    >   - key: the name of the property to clear (a string).

    C++ signature :

      void ClearProp(RDKit::Conformer,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetAtomPosition((Conformer)self, (int)aid) → rdkit.Geometry.rdGeometry.Point3D :

    Get the posistion of an atom

    C++ signature :

      RDGeom::Point3D GetAtomPosition(RDKit::Conformer const*,unsigned int)

  GetBoolProp((Conformer)self, (str)key) → object :

    Returns the Bool value of the property if possible.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    > RETURNS: a bool

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetBoolProp(RDKit::Conformer const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetDoubleProp((Conformer)self, (str)key) → object :

    Returns the double value of the property if possible.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    > RETURNS: a double

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetDoubleProp(RDKit::Conformer const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetId((Conformer)self) → int :

    Get the ID of the conformer

    C++ signature :

      unsigned int GetId(RDKit::Conformer {lvalue})

  GetIntProp((Conformer)self, (str)key) → object :

    Returns the integer value of the property if possible.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    > RETURNS: an integer

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetIntProp(RDKit::Conformer const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetNumAtoms((Conformer)self) → int :

    Get the number of atoms in the conformer

    C++ signature :

      unsigned int GetNumAtoms(RDKit::Conformer {lvalue})

  GetOwningMol((Conformer)self) → Mol :

    Get the owning molecule

    C++ signature :

      RDKit::ROMol {lvalue} GetOwningMol(RDKit::Conformer {lvalue})

  GetPositions((Conformer)self) → object :

    Get positions of all the atoms

    C++ signature :

      _object* GetPositions(RDKit::Conformer const*)

  GetProp((Conformer)self, (str)key[, (bool)autoConvert=False]) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    >   - autoConvert: if True attempt to convert the property into a python object

    > RETURNS: a string

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetProp(RDKit::Conformer const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > [,bool=False])

  GetPropNames((Conformer)self[, (bool)includePrivate=False[, (bool)includeComputed=False]]) → rdkit.rdBase._vectNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE :

    Returns a tuple with all property names for this conformer.

    > ARGUMENTS:
    >   - includePrivate: (optional) toggles inclusion of private properties in the result set.

    >       Defaults to 0.

    >   - includeComputed: (optional) toggles inclusion of computed properties in the result set.

    >       Defaults to 0.

    > RETURNS: a tuple of strings

    C++ signature :

      std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > GetPropNames(RDKit::Conformer {lvalue} [,bool=False [,bool=False]])

  GetPropsAsDict((Conformer)self[, (bool)includePrivate=False[, (bool)includeComputed=False[, (bool)autoConvertStrings=True]]]) → dict :

    Returns a dictionary populated with properties. When possible, string values will be converted to integers or doubles (trimming if necessary)

    > n.b. Some properties are not able to be converted to python types.

    > > ARGUMENTS:
    > >   - includePrivate: (optional) toggles inclusion of private properties in the result set.

    > >       Defaults to False.

    > >   - includeComputed: (optional) toggles inclusion of computed properties in the result set.

    > >       Defaults to False.

    > >   - autoConvertStrings: (optional) toggles automatic conversion of string properties to integers or doubles.

    > >       Defaults to True.

    > > RETURNS: a dictionary

    C++ signature :

      boost::python::dict GetPropsAsDict(RDKit::Conformer [,bool=False [,bool=False [,bool=True]]])

  GetUnsignedProp((Conformer)self, (str)key) → object :

    Returns the unsigned int value of the property if possible.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    > RETURNS: an unsigned integer

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetUnsignedProp(RDKit::Conformer const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  HasOwningMol((Conformer)self) → bool :

    Returns whether or not this instance belongs to a molecule.

    C++ signature :

      bool HasOwningMol(RDKit::Conformer {lvalue})

  HasProp((Conformer)self, (str)key) → int :

    Queries a conformer to see if a particular property has been assigned.

    > ARGUMENTS:

    >   - key: the name of the property to check for (a string).

    C++ signature :

      int HasProp(RDKit::Conformer,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  Is3D((Conformer)self) → bool :

    returns the 3D flag of the conformer

    C++ signature :

      bool Is3D(RDKit::Conformer {lvalue})

  Set3D((Conformer)self, (bool)v) → None :

    Set the 3D flag of the conformer

    C++ signature :

      void Set3D(RDKit::Conformer {lvalue},bool)

  SetAtomPosition((Conformer)self, (int)aid, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)loc) → None :

    Set the position of the specified atom

    > C++ signature :

    >   void SetAtomPosition(RDKit::Conformer*,unsigned int,boost::python::api::object)

    SetAtomPosition( (Conformer)self, (int)atomId, (rdkit.Geometry.rdGeometry.Point3D)position) -> None :

      Set the position of the specified atom

      C++ signature :

        void SetAtomPosition(RDKit::Conformer {lvalue},unsigned int,RDGeom::Point3D)

  SetBoolProp((Conformer)self, (str)key, (bool)val[, (bool)computed=False]) → None :

    Sets a boolean valued molecular property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value as a bool.

    >   - computed: (optional) marks the property as being computed.

    >       Defaults to False.

    C++ signature :

      void SetBoolProp(RDKit::Conformer,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,bool [,bool=False])

  SetDoubleProp((Conformer)self, (str)key, (float)val[, (bool)computed=False]) → None :

    Sets a double valued molecular property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value as a double.

    >   - computed: (optional) marks the property as being computed.

    >       Defaults to 0.

    C++ signature :

      void SetDoubleProp(RDKit::Conformer,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,double [,bool=False])

  SetId((Conformer)self, (int)id) → None :

    Set the ID of the conformer

    C++ signature :

      void SetId(RDKit::Conformer {lvalue},unsigned int)

  SetIntProp((Conformer)self, (str)key, (int)val[, (bool)computed=False]) → None :

    Sets an integer valued molecular property

    > ARGUMENTS:

    >   - key: the name of the property to be set (an unsigned number).

    >   - value: the property value as an integer.

    >   - computed: (optional) marks the property as being computed.

    >       Defaults to False.

    C++ signature :

      void SetIntProp(RDKit::Conformer,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,int [,bool=False])

  SetPositions((Conformer)self, (object)positions) → None :

    Set positions of all the atoms given a 2D or 3D numpy array of type double

    C++ signature :

      void SetPositions(RDKit::Conformer*,boost::python::numpy::ndarray)

  SetProp((Conformer)self, (str)key, (str)val[, (bool)computed=False]) → None :

    Sets a molecular property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value (a string).

    >   - computed: (optional) marks the property as being computed.

    >       Defaults to False.

    C++ signature :

      void SetProp(RDKit::Conformer,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > [,bool=False])

  SetUnsignedProp((Conformer)self, (str)key, (int)val[, (bool)computed=False]) → None :

    Sets an unsigned integer valued molecular property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value as an unsigned integer.

    >   - computed: (optional) marks the property as being computed.

    >       Defaults to False.

    C++ signature :

      void SetUnsignedProp(RDKit::Conformer,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,unsigned int [,bool=False])

rdkit.Chem.rdchem.CreateMolDataSubstanceGroup((Mol)mol, (str)fieldName, (str)value) → SubstanceGroup :

  creates a new DATA SubstanceGroup associated with a molecule, returns the new SubstanceGroup

  C++ signature :

    RDKit::SubstanceGroup* CreateMolDataSubstanceGroup(RDKit::ROMol {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

rdkit.Chem.rdchem.CreateMolSubstanceGroup((Mol)mol, (str)type) → SubstanceGroup :

  creates a new SubstanceGroup associated with a molecule, returns the new SubstanceGroup

  C++ signature :

    RDKit::SubstanceGroup* CreateMolSubstanceGroup(RDKit::ROMol {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

rdkit.Chem.rdchem.CreateStereoGroup((StereoGroupType)stereoGroupType, (Mol)mol[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)atomIds=[][, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)bondIds=[][, (int)readId=0]]]) → StereoGroup :

  creates a StereoGroup associated with a molecule from a list of atom Ids

  C++ signature :

    RDKit::StereoGroup* CreateStereoGroup(RDKit::StereoGroupType,RDKit::ROMol {lvalue} [,boost::python::api::object=[] [,boost::python::api::object=[] [,unsigned int=0]]])

class rdkit.Chem.rdchem.EditableMol((object)self, (Mol)m) → None :

  Bases: `instance`

  an editable molecule class

  Construct from a Mol

  C++ signature :

    void __init__(_object*,RDKit::ROMol)

  AddAtom((EditableMol)self, (Atom)atom) → int :

    add an atom, returns the index of the newly added atom

    C++ signature :

      int AddAtom(RDKit::(anonymous namespace)::EditableMol {lvalue},RDKit::Atom*)

  AddBond((EditableMol)self, (int)beginAtomIdx, (int)endAtomIdx[, (BondType)order=rdkit.Chem.rdchem.BondType.UNSPECIFIED]) → int :

    add a bond, returns the total number of bonds

    C++ signature :

      int AddBond(RDKit::(anonymous namespace)::EditableMol {lvalue},unsigned int,unsigned int [,RDKit::Bond::BondType=rdkit.Chem.rdchem.BondType.UNSPECIFIED])

  BeginBatchEdit((EditableMol)self) → None :

    starts batch editing

    C++ signature :

      void BeginBatchEdit(RDKit::(anonymous namespace)::EditableMol {lvalue})

  CommitBatchEdit((EditableMol)self) → None :

    finishes batch editing and makes the actual edits

    C++ signature :

      void CommitBatchEdit(RDKit::(anonymous namespace)::EditableMol {lvalue})

  GetMol((EditableMol)self) → Mol :

    Returns a Mol (a normal molecule)

    C++ signature :

      RDKit::ROMol* GetMol(RDKit::(anonymous namespace)::EditableMol {lvalue})

  RemoveAtom((EditableMol)self, (int)idx) → None :

    Remove the specified atom from the molecule

    C++ signature :

      void RemoveAtom(RDKit::(anonymous namespace)::EditableMol {lvalue},unsigned int)

  RemoveBond((EditableMol)self, (int)idx1, (int)idx2) → None :

    Remove the specified bond from the molecule

    C++ signature :

      void RemoveBond(RDKit::(anonymous namespace)::EditableMol {lvalue},unsigned int,unsigned int)

  ReplaceAtom((EditableMol)self, (int)index, (Atom)newAtom[, (bool)updateLabel=False[, (bool)preserveProps=False]]) → None :

    replaces the specified atom with the provided one If updateLabel is True, the new atom becomes the active atom If preserveProps is True preserve keep the existing props unless explicit set on the new atom

    C++ signature :

      void ReplaceAtom(RDKit::(anonymous namespace)::EditableMol {lvalue},unsigned int,RDKit::Atom* [,bool=False [,bool=False]])

  ReplaceBond((EditableMol)self, (int)index, (Bond)newBond[, (bool)preserveProps=False]) → None :

    replaces the specified bond with the provided one. If preserveProps is True preserve keep the existing props unless explicit set on the new bond

    C++ signature :

      void ReplaceBond(RDKit::(anonymous namespace)::EditableMol {lvalue},unsigned int,RDKit::Bond* [,bool=False])

  RollbackBatchEdit((EditableMol)self) → None :

    cancels batch editing

    C++ signature :

      void RollbackBatchEdit(RDKit::(anonymous namespace)::EditableMol {lvalue})

class rdkit.Chem.rdchem.FixedMolSizeMolBundle((object)self) → None :

  Bases: `MolBundle`

  A class for storing groups of related molecules. Here related means that the molecules have to have the same number of atoms.

  C++ signature :

    void __init__(_object*)

rdkit.Chem.rdchem.ForwardStereoGroupIds((Mol)mol) → None :

  Forward the original Stereo Group IDs when exporting the Mol.

  C++ signature :

    void ForwardStereoGroupIds(RDKit::ROMol {lvalue})

rdkit.Chem.rdchem.GetAtomAlias((Atom)atom) → str :

  Returns the atom’s MDL alias text

  C++ signature :

    std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetAtomAlias(RDKit::Atom const*)

rdkit.Chem.rdchem.GetAtomRLabel((Atom)atom) → int :

  Returns the atom’s MDL AtomRLabel (this is an integer from 0 to 99)

  C++ signature :

    int GetAtomRLabel(RDKit::Atom const*)

rdkit.Chem.rdchem.GetAtomValue((Atom)atom) → str :

  Returns the atom’s MDL alias text

  C++ signature :

    std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetAtomValue(RDKit::Atom const*)

rdkit.Chem.rdchem.GetDefaultPickleProperties() → int :

  Get the current global mol pickler options.

  C++ signature :

    unsigned int GetDefaultPickleProperties()

rdkit.Chem.rdchem.GetMolSubstanceGroupWithIdx((Mol)mol, (int)idx) → SubstanceGroup :

  returns a particular SubstanceGroup from the molecule

  C++ signature :

    RDKit::SubstanceGroup* GetMolSubstanceGroupWithIdx(RDKit::ROMol {lvalue},unsigned int)

rdkit.Chem.rdchem.GetMolSubstanceGroups((Mol)mol) → SubstanceGroup_VECT :

  returns a copy of the molecule’s SubstanceGroups (if any)

  C++ signature :

    std::vector<RDKit::SubstanceGroup, std::allocator<RDKit::SubstanceGroup> > GetMolSubstanceGroups(RDKit::ROMol {lvalue})

rdkit.Chem.rdchem.GetNumPiElectrons((Atom)atom) → int :

  Returns the number of electrons an atom is using for pi bonding

  C++ signature :

    unsigned int GetNumPiElectrons(RDKit::Atom)

rdkit.Chem.rdchem.GetPeriodicTable() → PeriodicTable :

  Returns the application’s PeriodicTable instance.

  C++ signature :

    RDKit::PeriodicTable* GetPeriodicTable()

rdkit.Chem.rdchem.GetSupplementalSmilesLabel((Atom)atom) → str :

  Gets the supplemental smiles label on an atom, returns an empty string if not present.

  C++ signature :

    std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetSupplementalSmilesLabel(RDKit::Atom const*)

class rdkit.Chem.rdchem.HybridizationType

  Bases: `enum`

  OTHER = rdkit.Chem.rdchem.HybridizationType.OTHER
  S = rdkit.Chem.rdchem.HybridizationType.S
  SP = rdkit.Chem.rdchem.HybridizationType.SP
  SP2 = rdkit.Chem.rdchem.HybridizationType.SP2
  SP2D = rdkit.Chem.rdchem.HybridizationType.SP2D
  SP3 = rdkit.Chem.rdchem.HybridizationType.SP3
  SP3D = rdkit.Chem.rdchem.HybridizationType.SP3D
  SP3D2 = rdkit.Chem.rdchem.HybridizationType.SP3D2
  UNSPECIFIED = rdkit.Chem.rdchem.HybridizationType.UNSPECIFIED
  names = {'OTHER': rdkit.Chem.rdchem.HybridizationType.OTHER, 'S': rdkit.Chem.rdchem.HybridizationType.S, 'SP': rdkit.Chem.rdchem.HybridizationType.SP, 'SP2': rdkit.Chem.rdchem.HybridizationType.SP2, 'SP2D': rdkit.Chem.rdchem.HybridizationType.SP2D, 'SP3': rdkit.Chem.rdchem.HybridizationType.SP3, 'SP3D': rdkit.Chem.rdchem.HybridizationType.SP3D, 'SP3D2': rdkit.Chem.rdchem.HybridizationType.SP3D2, 'UNSPECIFIED': rdkit.Chem.rdchem.HybridizationType.UNSPECIFIED}
  values = {0: rdkit.Chem.rdchem.HybridizationType.UNSPECIFIED, 1: rdkit.Chem.rdchem.HybridizationType.S, 2: rdkit.Chem.rdchem.HybridizationType.SP, 3: rdkit.Chem.rdchem.HybridizationType.SP2, 4: rdkit.Chem.rdchem.HybridizationType.SP3, 5: rdkit.Chem.rdchem.HybridizationType.SP2D, 6: rdkit.Chem.rdchem.HybridizationType.SP3D, 7: rdkit.Chem.rdchem.HybridizationType.SP3D2, 8: rdkit.Chem.rdchem.HybridizationType.OTHER}

exception rdkit.Chem.rdchem.KekulizeException

  Bases: `MolSanitizeException`

class rdkit.Chem.rdchem.Mol((object)self) → None :

  Bases: `instance`

  The Molecule class.

  In addition to the expected Atoms and Bonds, molecules contain:
    - a collection of Atom and Bond bookmarks indexed with integers

        that can be used to flag and retrieve particular Atoms or Bonds using the {get|set}{Atom|Bond}Bookmark() methods.

    - a set of string-valued properties. These can have arbitrary string

        labels and can be set and retrieved using the {set|get}Prop() methods Molecular properties can be tagged as being computed, in which case

        > they will be automatically cleared under certain circumstances (when the molecule itself is modified, for example).

        Molecules also have the concept of private properties, which are tagged

          by beginning the property name with an underscore (_).

  Constructor, takes no arguments

  > C++ signature :

  >   void __init__(_object*)

  __init__( (object)self, (str)pklString) -> None :

  > C++ signature :

  >   void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  __init__( (object)self, (str)pklString, (int)propertyFlags) -> None :

  > C++ signature :

  >   void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,unsigned int)

  __init__( (object)self, (Mol)mol [, (bool)quickCopy=False [, (int)confId=-1]]) -> None :

  > C++ signature :

  >   void __init__(_object*,RDKit::ROMol [,bool=False [,int=-1]])

  AddConformer((Mol)self, (Conformer)conf[, (bool)assignId=False]) → int :

    Add a conformer to the molecule and return the conformer ID

    C++ signature :

      unsigned int AddConformer(RDKit::ROMol {lvalue},RDKit::Conformer* [,bool=False])

  ClearComputedProps((Mol)self[, (bool)includeRings=True]) → None :

    Removes all computed properties from the molecule.

    C++ signature :

      void ClearComputedProps(RDKit::ROMol [,bool=True])

  ClearProp((Mol)self, (str)key) → None :

    Removes a property from the molecule.

    > ARGUMENTS:

    >   - key: the name of the property to clear (a string).

    C++ signature :

      void ClearProp(RDKit::ROMol,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  ClearPropertyCache((Mol)self) → None :

    Clears implicit and explicit valence information from all atoms.

    C++ signature :

      void ClearPropertyCache(RDKit::ROMol {lvalue})

  Debug((Mol)self[, (bool)useStdout=True]) → None :

    Prints debugging information about the molecule.

    C++ signature :

      void Debug(RDKit::ROMol [,bool=True])

  GetAromaticAtoms((Mol)self) → _ROQAtomSeq :

    Returns a read-only sequence containing all of the molecule’s aromatic Atoms.

    C++ signature :

      RDKit::ReadOnlySeq<RDKit::QueryAtomIterator_<RDKit::Atom, RDKit::ROMol>, RDKit::Atom*, RDKit::AtomCountFunctor>* GetAromaticAtoms(boost::shared_ptr<RDKit::ROMol>)

  GetAtomWithIdx((Mol)self, (int)idx) → Atom :

    Returns a particular Atom.

    > ARGUMENTS:

    >   - idx: which Atom to return

    > NOTE: atom indices start at 0

    C++ signature :

      RDKit::Atom* GetAtomWithIdx(RDKit::ROMol {lvalue},unsigned int)

  GetAtoms()

    returns an iterator over the atoms in the molecule

  GetAtomsMatchingQuery((Mol)self, (QueryAtom)qa) → _ROQAtomSeq :

    Returns a read-only sequence containing all of the atoms in a molecule that match the query atom. Atom query options are defined in the rdkit.Chem.rdqueries module.

    C++ signature :

      RDKit::ReadOnlySeq<RDKit::QueryAtomIterator_<RDKit::Atom, RDKit::ROMol>, RDKit::Atom*, RDKit::AtomCountFunctor>* GetAtomsMatchingQuery(boost::shared_ptr<RDKit::ROMol>,RDKit::QueryAtom*)

  GetBondBetweenAtoms((Mol)self, (int)idx1, (int)idx2) → Bond :

    Returns the bond between two atoms, if there is one.

    > ARGUMENTS:

    >   - idx1,idx2: the Atom indices

    > Returns:

    >   The Bond between the two atoms, if such a bond exists. If there is no Bond between the atoms, None is returned instead.

    > NOTE: bond indices start at 0

    C++ signature :

      RDKit::Bond* GetBondBetweenAtoms(RDKit::ROMol {lvalue},unsigned int,unsigned int)

  GetBondWithIdx((Mol)self, (int)idx) → Bond :

    Returns a particular Bond.

    > ARGUMENTS:

    >   - idx: which Bond to return

    > NOTE: bond indices start at 0

    C++ signature :

      RDKit::Bond* GetBondWithIdx(RDKit::ROMol {lvalue},unsigned int)

  GetBonds()

    returns an iterator over the bonds in the molecule

  GetBoolProp((Mol)self, (str)key) → object :

    Returns the Bool value of the property if possible.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    > RETURNS: a bool

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetBoolProp(RDKit::ROMol const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetConformer((Mol)self[, (int)id=-1]) → Conformer :

    Get the conformer with a specified ID

    C++ signature :

      RDKit::Conformer* GetConformer(RDKit::ROMol {lvalue} [,int=-1])

  GetConformers((Mol)self) → _ROConformerSeq :

    Returns a read-only sequence containing all of the molecule’s Conformers.

    C++ signature :

      RDKit::ReadOnlySeq<std::_List_iterator<boost::shared_ptr<RDKit::Conformer> >, boost::shared_ptr<RDKit::Conformer>&, RDKit::ConformerCountFunctor>* GetConformers(boost::shared_ptr<RDKit::ROMol>)

  GetDoubleProp((Mol)self, (str)key) → object :

    Returns the double value of the property if possible.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    > RETURNS: a double

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetDoubleProp(RDKit::ROMol const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetIntProp((Mol)self, (str)key) → object :

    Returns the integer value of the property if possible.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    > RETURNS: an integer

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetIntProp(RDKit::ROMol const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetNumAtoms((Mol)self[, (int)onlyHeavy=-1[, (bool)onlyExplicit=True]]) → int :

    Returns the number of atoms in the molecule.

    > ARGUMENTS:
    >   - onlyExplicit: (optional) include only explicit atoms (atoms in the molecular graph)

    >       defaults to 1.

    > NOTE: the onlyHeavy argument is deprecated

    C++ signature :

      int GetNumAtoms(RDKit::ROMol [,int=-1 [,bool=True]])

  GetNumBonds((Mol)self[, (bool)onlyHeavy=True]) → int :

    Returns the number of Bonds in the molecule.

    > ARGUMENTS:
    >   - onlyHeavy: (optional) include only bonds to heavy atoms (not Hs)

    >       defaults to 1.

    C++ signature :

      unsigned int GetNumBonds(RDKit::ROMol {lvalue} [,bool=True])

  GetNumConformers((Mol)self) → int :

    Return the number of conformations on the molecule

    C++ signature :

      unsigned int GetNumConformers(RDKit::ROMol {lvalue})

  GetNumHeavyAtoms((Mol)self) → int :

    Returns the number of heavy atoms (atomic number >1) in the molecule.

    C++ signature :

      unsigned int GetNumHeavyAtoms(RDKit::ROMol {lvalue})

  GetProp((Mol)self, (str)key[, (bool)autoConvert=False]) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    >   - autoConvert: if True attempt to convert the property into a python object

    > RETURNS: a string

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetProp(RDKit::ROMol const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > [,bool=False])

  GetPropNames((Mol)self[, (bool)includePrivate=False[, (bool)includeComputed=False]]) → rdkit.rdBase._vectNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE :

    Returns a tuple with all property names for this molecule.

    > ARGUMENTS:
    >   - includePrivate: (optional) toggles inclusion of private properties in the result set.

    >       Defaults to 0.

    >   - includeComputed: (optional) toggles inclusion of computed properties in the result set.

    >       Defaults to 0.

    > RETURNS: a tuple of strings

    C++ signature :

      std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > GetPropNames(RDKit::ROMol {lvalue} [,bool=False [,bool=False]])

  GetPropsAsDict((Mol)self[, (bool)includePrivate=False[, (bool)includeComputed=False[, (bool)autoConvertStrings=True]]]) → dict :

    Returns a dictionary populated with properties. When possible, string values will be converted to integers or doubles (trimming if necessary)

    > n.b. Some properties are not able to be converted to python types.

    > > ARGUMENTS:
    > >   - includePrivate: (optional) toggles inclusion of private properties in the result set.

    > >       Defaults to False.

    > >   - includeComputed: (optional) toggles inclusion of computed properties in the result set.

    > >       Defaults to False.

    > >   - autoConvertStrings: (optional) toggles automatic conversion of string properties to integers or doubles.

    > >       Defaults to True.

    > > RETURNS: a dictionary

    C++ signature :

      boost::python::dict GetPropsAsDict(RDKit::ROMol [,bool=False [,bool=False [,bool=True]]])

  GetRingInfo((Mol)self) → RingInfo :

    Returns the number of molecule’s RingInfo object.

    C++ signature :

      RDKit::RingInfo* GetRingInfo(RDKit::ROMol {lvalue})

  GetStereoGroups((Mol)self) → StereoGroup_vect :

    Returns a list of StereoGroups defining the relative stereochemistry of the atoms.

    C++ signature :

      std::vector<RDKit::StereoGroup, std::allocator<RDKit::StereoGroup> > GetStereoGroups(RDKit::ROMol {lvalue})

  GetSubstructMatch((Mol)self, (Mol)query[, (bool)useChirality=False[, (bool)useQueryQueryMatches=False]]) → object :

    Returns the indices of the molecule’s atoms that match a substructure query.

    > > ARGUMENTS:

    > >   - query: a Molecule

    > >   - useChirality: enables the use of stereochemistry in the matching

    > >   - useQueryQueryMatches: use query-query matching logic

    > > RETURNS: a tuple of integers

    > > NOTES:

    > >   - only a single match is returned

    > >   - the ordering of the indices corresponds to the atom ordering

    > >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

    > C++ signature :

    >   _object* GetSubstructMatch(RDKit::ROMol,RDKit::ROMol [,bool=False [,bool=False]])

    GetSubstructMatch( (Mol)self, (MolBundle)query [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]) -> object :

    > C++ signature :

    >   _object* GetSubstructMatch(RDKit::ROMol,RDKit::MolBundle [,bool=False [,bool=False]])

    GetSubstructMatch( (Mol)self, (Mol)query, (SubstructMatchParameters)params) -> object :

      Returns the indices of the molecule’s atoms that match a substructure query.

      > ARGUMENTS:

      >   - query: a Molecule

      >   - params: parameters controlling the substructure match

      > RETURNS: a tuple of integers

      > NOTES:

      >   - only a single match is returned

      >   - the ordering of the indices corresponds to the atom ordering

      >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

      C++ signature :

        _object* GetSubstructMatch(RDKit::ROMol,RDKit::ROMol,RDKit::SubstructMatchParameters)

    GetSubstructMatch( (Mol)self, (MolBundle)query, (SubstructMatchParameters)params) -> object :

    > C++ signature :

    >   _object* GetSubstructMatch(RDKit::ROMol,RDKit::MolBundle,RDKit::SubstructMatchParameters)

  GetSubstructMatches((Mol)self, (Mol)query[, (bool)uniquify=True[, (bool)useChirality=False[, (bool)useQueryQueryMatches=False[, (int)maxMatches=1000]]]]) → object :

    Returns tuples of the indices of the molecule’s atoms that match a substructure query.

    > > ARGUMENTS:

    > >   - query: a Molecule.

    > >   - uniquify: (optional) determines whether or not the matches are uniquified.

    > >       Defaults to 1.

    > >   - useChirality: enables the use of stereochemistry in the matching

    > >   - useQueryQueryMatches: use query-query matching logic

    > >   - maxMatches: The maximum number of matches that will be returned.

    > >       In high-symmetry cases with medium-sized molecules, it is very easy to end up with a combinatorial explosion in the number of possible matches. This argument prevents that from having unintended consequences

    > > RETURNS: a tuple of tuples of integers

    > > NOTE:
    > >   - the ordering of the indices corresponds to the atom ordering

    > >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

    > C++ signature :

    >   _object* GetSubstructMatches(RDKit::ROMol,RDKit::ROMol [,bool=True [,bool=False [,bool=False [,unsigned int=1000]]]])

    GetSubstructMatches( (Mol)self, (MolBundle)query [, (bool)uniquify=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False [, (int)maxMatches=1000]]]]) -> object :

    > C++ signature :

    >   _object* GetSubstructMatches(RDKit::ROMol,RDKit::MolBundle [,bool=True [,bool=False [,bool=False [,unsigned int=1000]]]])

    GetSubstructMatches( (Mol)self, (Mol)query, (SubstructMatchParameters)params) -> object :

      Returns tuples of the indices of the molecule’s atoms that match a substructure query.

      > ARGUMENTS:

      >   - query: a Molecule.

      >   - params: parameters controlling the substructure match

      > RETURNS: a tuple of tuples of integers

      > NOTE:
      >   - the ordering of the indices corresponds to the atom ordering

      >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

      C++ signature :

        _object* GetSubstructMatches(RDKit::ROMol,RDKit::ROMol,RDKit::SubstructMatchParameters)

    GetSubstructMatches( (Mol)self, (MolBundle)query, (SubstructMatchParameters)params) -> object :

    > C++ signature :

    >   _object* GetSubstructMatches(RDKit::ROMol,RDKit::MolBundle,RDKit::SubstructMatchParameters)

  GetUnsignedProp((Mol)self, (str)key) → object :

    Returns the unsigned int value of the property if possible.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    > RETURNS: an unsigned integer

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetUnsignedProp(RDKit::ROMol const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  HasProp((Mol)self, (str)key) → int :

    Queries a molecule to see if a particular property has been assigned.

    > ARGUMENTS:

    >   - key: the name of the property to check for (a string).

    C++ signature :

      int HasProp(RDKit::ROMol,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  HasQuery((Mol)self) → bool :

    Returns if any atom or bond in molecule has a query

    C++ signature :

      bool HasQuery(RDKit::ROMol {lvalue})

  HasSubstructMatch((Mol)self, (Mol)query[, (bool)recursionPossible=True[, (bool)useChirality=False[, (bool)useQueryQueryMatches=False]]]) → bool :

    Queries whether or not the molecule contains a particular substructure.

    > > ARGUMENTS:

    > >   - query: a Molecule

    > >   - recursionPossible: (optional)

    > >   - useChirality: enables the use of stereochemistry in the matching

    > >   - useQueryQueryMatches: use query-query matching logic

    > > RETURNS: True or False

    > C++ signature :

    >   bool HasSubstructMatch(RDKit::ROMol,RDKit::ROMol [,bool=True [,bool=False [,bool=False]]])

    HasSubstructMatch( (Mol)self, (MolBundle)query [, (bool)recursionPossible=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]]) -> bool :

    > C++ signature :

    >   bool HasSubstructMatch(RDKit::ROMol,RDKit::MolBundle [,bool=True [,bool=False [,bool=False]]])

    HasSubstructMatch( (Mol)self, (Mol)query, (SubstructMatchParameters)params) -> bool :

      Queries whether or not the molecule contains a particular substructure.

      > ARGUMENTS:

      >   - query: a Molecule

      >   - params: parameters controlling the substructure match

      > RETURNS: True or False

      C++ signature :

        bool HasSubstructMatch(RDKit::ROMol,RDKit::ROMol,RDKit::SubstructMatchParameters)

    HasSubstructMatch( (Mol)self, (MolBundle)query [, (SubstructMatchParameters)params=True]) -> bool :

    > C++ signature :

    >   bool HasSubstructMatch(RDKit::ROMol,RDKit::MolBundle [,RDKit::SubstructMatchParameters=True])

  NeedsUpdatePropertyCache((Mol)self) → bool :

    Returns true or false depending on whether implicit and explicit valence of the molecule have already been calculated.

    C++ signature :

      bool NeedsUpdatePropertyCache(RDKit::ROMol {lvalue})

  RemoveAllConformers((Mol)self) → None :

    Remove all the conformations on the molecule

    C++ signature :

      void RemoveAllConformers(RDKit::ROMol {lvalue})

  RemoveConformer((Mol)self, (int)id) → None :

    Remove the conformer with the specified ID

    C++ signature :

      void RemoveConformer(RDKit::ROMol {lvalue},unsigned int)

  SetBoolProp((Mol)self, (str)key, (bool)val[, (bool)computed=False]) → None :

    Sets a boolean valued molecular property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value as a bool.

    >   - computed: (optional) marks the property as being computed.

    >       Defaults to False.

    C++ signature :

      void SetBoolProp(RDKit::ROMol,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,bool [,bool=False])

  SetDoubleProp((Mol)self, (str)key, (float)val[, (bool)computed=False]) → None :

    Sets a double valued molecular property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value as a double.

    >   - computed: (optional) marks the property as being computed.

    >       Defaults to 0.

    C++ signature :

      void SetDoubleProp(RDKit::ROMol,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,double [,bool=False])

  SetIntProp((Mol)self, (str)key, (int)val[, (bool)computed=False]) → None :

    Sets an integer valued molecular property

    > ARGUMENTS:

    >   - key: the name of the property to be set (an unsigned number).

    >   - value: the property value as an integer.

    >   - computed: (optional) marks the property as being computed.

    >       Defaults to False.

    C++ signature :

      void SetIntProp(RDKit::ROMol,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,int [,bool=False])

  SetProp((Mol)self, (str)key, (str)val[, (bool)computed=False]) → None :

    Sets a molecular property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value (a string).

    >   - computed: (optional) marks the property as being computed.

    >       Defaults to False.

    C++ signature :

      void SetProp(RDKit::ROMol,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > [,bool=False])

  SetUnsignedProp((Mol)self, (str)key, (int)val[, (bool)computed=False]) → None :

    Sets an unsigned integer valued molecular property

    > ARGUMENTS:

    >   - key: the name of the property to be set (a string).

    >   - value: the property value as an unsigned integer.

    >   - computed: (optional) marks the property as being computed.

    >       Defaults to False.

    C++ signature :

      void SetUnsignedProp(RDKit::ROMol,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,unsigned int [,bool=False])

  ToBinary((Mol)self) → object :

    Returns a binary string representation of the molecule.

    > C++ signature :

    >   boost::python::api::object ToBinary(RDKit::ROMol)

    ToBinary( (Mol)self, (int)propertyFlags) -> object :

      Returns a binary string representation of the molecule pickling the specified properties.

      C++ signature :

        boost::python::api::object ToBinary(RDKit::ROMol,unsigned int)

  UpdatePropertyCache((Mol)self[, (bool)strict=True]) → None :

    Regenerates computed properties like implicit valence and ring information.

    C++ signature :

      void UpdatePropertyCache(RDKit::ROMol {lvalue} [,bool=True])

class rdkit.Chem.rdchem.MolBundle((object)self) → None :

  Bases: `instance`

  A class for storing groups of related molecules.

  > C++ signature :

  >   void __init__(_object*)

  __init__( (object)self, (str)pkl) -> None :

  > C++ signature :

  >   void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  AddMol((MolBundle)self, (Mol)nmol) → int :
    C++ signature :

      unsigned long AddMol(RDKit::MolBundle {lvalue},boost::shared_ptr<RDKit::ROMol>)

  GetMol((MolBundle)self, (int)idx) → Mol :
    C++ signature :

      boost::shared_ptr<RDKit::ROMol> GetMol(RDKit::MolBundle {lvalue},unsigned long)

  GetSubstructMatch((MolBundle)self, (Mol)query[, (bool)useChirality=False[, (bool)useQueryQueryMatches=False]]) → object :

    Returns the indices of the atoms from the first molecule in a bundle that matches a substructure query.

    > > ARGUMENTS:

    > >   - query: a Molecule

    > >   - useChirality: enables the use of stereochemistry in the matching

    > >   - useQueryQueryMatches: use query-query matching logic

    > > RETURNS: a tuple of integers

    > > NOTES:

    > >   - only a single match is returned

    > >   - the ordering of the indices corresponds to the atom ordering

    > >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

    > C++ signature :

    >   _object* GetSubstructMatch(RDKit::MolBundle,RDKit::ROMol [,bool=False [,bool=False]])

    GetSubstructMatch( (MolBundle)self, (MolBundle)query [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]) -> object :

      Returns the indices of the atoms from the first molecule in a bundle that matches a substructure query from a bundle.

      > ARGUMENTS:

      >   - query: a MolBundle

      >   - useChirality: enables the use of stereochemistry in the matching

      >   - useQueryQueryMatches: use query-query matching logic

      > RETURNS: a tuple of integers

      > NOTES:

      >   - only a single match is returned

      >   - the ordering of the indices corresponds to the atom ordering

      >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

      C++ signature :

        _object* GetSubstructMatch(RDKit::MolBundle,RDKit::MolBundle [,bool=False [,bool=False]])

    GetSubstructMatch( (MolBundle)self, (Mol)query, (SubstructMatchParameters)params) -> object :

      Returns the indices of the atoms from the first molecule in a bundle that matches a substructure query.

      > ARGUMENTS:

      >   - query: a Molecule

      >   - params: parameters controlling the substructure match

      > RETURNS: a tuple of integers

      > NOTES:

      >   - only a single match is returned

      >   - the ordering of the indices corresponds to the atom ordering

      >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

      C++ signature :

        _object* GetSubstructMatch(RDKit::MolBundle,RDKit::ROMol,RDKit::SubstructMatchParameters)

    GetSubstructMatch( (MolBundle)self, (MolBundle)query, (SubstructMatchParameters)params) -> object :

      Returns the indices of the atoms from the first molecule in a bundle that matches a substructure query from a bundle.

      > ARGUMENTS:

      >   - query: a MolBundle

      >   - params: parameters controlling the substructure match

      > RETURNS: a tuple of integers

      > NOTES:

      >   - only a single match is returned

      >   - the ordering of the indices corresponds to the atom ordering

      >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

      C++ signature :

        _object* GetSubstructMatch(RDKit::MolBundle,RDKit::MolBundle,RDKit::SubstructMatchParameters)

  GetSubstructMatches((MolBundle)self, (Mol)query[, (bool)uniquify=True[, (bool)useChirality=False[, (bool)useQueryQueryMatches=False[, (int)maxMatches=1000]]]]) → object :

    Returns tuple of all indices of the atoms from the first molecule in a bundle that matches a substructure query.

    > > ARGUMENTS:

    > >   - query: a molecule.

    > >   - uniquify: (optional) determines whether or not the matches are uniquified.

    > >       Defaults to 1.

    > >   - useChirality: enables the use of stereochemistry in the matching

    > >   - useQueryQueryMatches: use query-query matching logic

    > >   - maxMatches: The maximum number of matches that will be returned.

    > >       In high-symmetry cases with medium-sized molecules, it is very easy to end up with a combinatorial explosion in the number of possible matches. This argument prevents that from having unintended consequences

    > > RETURNS: a tuple of tuples of integers

    > > NOTE:
    > >   - the ordering of the indices corresponds to the atom ordering

    > >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

    > C++ signature :

    >   _object* GetSubstructMatches(RDKit::MolBundle,RDKit::ROMol [,bool=True [,bool=False [,bool=False [,unsigned int=1000]]]])

    GetSubstructMatches( (MolBundle)self, (MolBundle)query [, (bool)uniquify=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False [, (int)maxMatches=1000]]]]) -> object :

      Returns tuple of all indices of the atoms from the first molecule in a bundle that matches a substructure query from the second bundle.

      > ARGUMENTS:

      >   - query: a MolBundle.

      >   - uniquify: (optional) determines whether or not the matches are uniquified.

      >       Defaults to 1.

      >   - useChirality: enables the use of stereochemistry in the matching

      >   - useQueryQueryMatches: use query-query matching logic

      >   - maxMatches: The maximum number of matches that will be returned.

      >       In high-symmetry cases with medium-sized molecules, it is very easy to end up with a combinatorial explosion in the number of possible matches. This argument prevents that from having unintended consequences

      > RETURNS: a tuple of tuples of integers

      > NOTE:
      >   - the ordering of the indices corresponds to the atom ordering

      >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

      C++ signature :

        _object* GetSubstructMatches(RDKit::MolBundle,RDKit::MolBundle [,bool=True [,bool=False [,bool=False [,unsigned int=1000]]]])

    GetSubstructMatches( (MolBundle)self, (Mol)query, (SubstructMatchParameters)params) -> object :

      Returns tuple of all indices of the atoms from the first molecule in a bundle that matches a substructure query.

      > ARGUMENTS:

      >   - query: a molecule.

      >   - params: parameters controlling the substructure match

      > RETURNS: a tuple of tuples of integers

      > NOTE:
      >   - the ordering of the indices corresponds to the atom ordering

      >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

      C++ signature :

        _object* GetSubstructMatches(RDKit::MolBundle,RDKit::ROMol,RDKit::SubstructMatchParameters)

    GetSubstructMatches( (MolBundle)self, (MolBundle)query, (SubstructMatchParameters)params) -> object :

      Returns tuple of all indices of the atoms from the first molecule in a bundle that matches a substructure query from the second bundle.

      > ARGUMENTS:

      >   - query: a MolBundle.

      >   - params: parameters controlling the substructure match

      > RETURNS: a tuple of tuples of integers

      > NOTE:
      >   - the ordering of the indices corresponds to the atom ordering

      >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

      C++ signature :

        _object* GetSubstructMatches(RDKit::MolBundle,RDKit::MolBundle,RDKit::SubstructMatchParameters)

  HasSubstructMatch((MolBundle)self, (Mol)query[, (bool)recursionPossible=True[, (bool)useChirality=False[, (bool)useQueryQueryMatches=False]]]) → bool :

    Queries whether or not any molecule in the bundle contains a particular substructure.

    > > ARGUMENTS:

    > >   - query: a Molecule

    > >   - recursionPossible: (optional)

    > >   - useChirality: enables the use of stereochemistry in the matching

    > >   - useQueryQueryMatches: use query-query matching logic

    > > RETURNS: True or False

    > C++ signature :

    >   bool HasSubstructMatch(RDKit::MolBundle,RDKit::ROMol [,bool=True [,bool=False [,bool=False]]])

    HasSubstructMatch( (MolBundle)self, (MolBundle)query [, (bool)recursionPossible=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]]) -> bool :

      Queries whether or not any molecule in the first bundle matches any molecule in the second bundle.

      > ARGUMENTS:

      >   - query: a MolBundle

      >   - recursionPossible: (optional)

      >   - useChirality: enables the use of stereochemistry in the matching

      >   - useQueryQueryMatches: use query-query matching logic

      > RETURNS: True or False

      C++ signature :

        bool HasSubstructMatch(RDKit::MolBundle,RDKit::MolBundle [,bool=True [,bool=False [,bool=False]]])

    HasSubstructMatch( (MolBundle)self, (Mol)query, (SubstructMatchParameters)params) -> bool :

      Queries whether or not any molecule in the bundle contains a particular substructure.

      > ARGUMENTS:

      >   - query: a Molecule

      >   - params: parameters controlling the substructure match

      matching

      > > - useQueryQueryMatches: use query-query matching logic

      > RETURNS: True or False

      C++ signature :

        bool HasSubstructMatch(RDKit::MolBundle,RDKit::ROMol,RDKit::SubstructMatchParameters)

    HasSubstructMatch( (MolBundle)self, (MolBundle)query, (SubstructMatchParameters)params) -> bool :

      Queries whether or not any molecule in the first bundle matches any molecule in the second bundle.

      > ARGUMENTS:

      >   - query: a MolBundle

      >   - params: parameters controlling the substructure match

      > RETURNS: True or False

      C++ signature :

        bool HasSubstructMatch(RDKit::MolBundle,RDKit::MolBundle,RDKit::SubstructMatchParameters)

  Size((MolBundle)self) → int :
    C++ signature :

      unsigned long Size(RDKit::MolBundle {lvalue})

  ToBinary((MolBundle)self) → object :

    Returns a binary string representation of the MolBundle.

    C++ signature :

      boost::python::api::object ToBinary(RDKit::MolBundle)

rdkit.Chem.rdchem.MolBundleCanSerialize() → bool :

  Returns True if the MolBundle is serializable (requires boost serialization

  C++ signature :

    bool MolBundleCanSerialize()

exception rdkit.Chem.rdchem.MolSanitizeException

  Bases: `ValueError`

class rdkit.Chem.rdchem.PeriodicTable

  Bases: `instance`

  A class which stores information from the Periodic Table.

  It is not possible to create a PeriodicTable object directly from Python, use GetPeriodicTable() to get the global table.

  The PeriodicTable object can be queried for a variety of properties:

  > - GetAtomicWeight

  > - GetAtomicNumber

  > - GetElementSymbol

  > - GetElementName

  > - GetRow

  > - GetRvdw (van der Waals radius)

  > - GetRCovalent (covalent radius)

  > - GetDefaultValence

  > - GetValenceList

  > - GetNOuterElecs (number of valence electrons)

  > - GetMostCommonIsotope

  > - GetMostCommonIsotopeMass

  > - GetRb0

  > - GetAbundanceForIsotope

  > - GetMassForIsotope

  When it makes sense, these can be queried using either an atomic number (integer) or an atomic symbol (string)

  Raises an exception This class cannot be instantiated from Python

  GetAbundanceForIsotope((PeriodicTable)self, (int)atomicNumber, (int)isotope) → float :

    > C++ signature :

    >   double GetAbundanceForIsotope(RDKit::PeriodicTable {lvalue},unsigned int,unsigned int)

    GetAbundanceForIsotope( (PeriodicTable)self, (str)elementSymbol, (int)isotope) -> float :

    > C++ signature :

    >   double GetAbundanceForIsotope(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,unsigned int)

  GetAtomicNumber((PeriodicTable)self, (str)elementSymbol) → int :
    C++ signature :

      int GetAtomicNumber(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetAtomicWeight((PeriodicTable)self, (int)atomicNumber) → float :

    > C++ signature :

    >   double GetAtomicWeight(RDKit::PeriodicTable {lvalue},unsigned int)

    GetAtomicWeight( (PeriodicTable)self, (str)elementSymbol) -> float :

    > C++ signature :

    >   double GetAtomicWeight(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetDefaultValence((PeriodicTable)self, (int)atomicNumber) → int :

    > C++ signature :

    >   int GetDefaultValence(RDKit::PeriodicTable {lvalue},unsigned int)

    GetDefaultValence( (PeriodicTable)self, (str)elementSymbol) -> int :

    > C++ signature :

    >   int GetDefaultValence(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetElementName((PeriodicTable)self, (int)atomicNumber) → str :
    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetElementName(RDKit::PeriodicTable {lvalue},unsigned int)

  GetElementSymbol((PeriodicTable)self, (int)atomicNumber) → str :
    C++ signature :

      std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetElementSymbol(RDKit::PeriodicTable {lvalue},unsigned int)

  GetMassForIsotope((PeriodicTable)self, (int)atomicNumber, (int)isotope) → float :

    > C++ signature :

    >   double GetMassForIsotope(RDKit::PeriodicTable {lvalue},unsigned int,unsigned int)

    GetMassForIsotope( (PeriodicTable)self, (str)elementSymbol, (int)isotope) -> float :

    > C++ signature :

    >   double GetMassForIsotope(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,unsigned int)

  GetMaxAtomicNumber((PeriodicTable)self) → int :
    C++ signature :

      unsigned int GetMaxAtomicNumber(RDKit::PeriodicTable {lvalue})

  GetMostCommonIsotope((PeriodicTable)self, (int)atomicNumber) → int :

    > C++ signature :

    >   int GetMostCommonIsotope(RDKit::PeriodicTable {lvalue},unsigned int)

    GetMostCommonIsotope( (PeriodicTable)self, (str)elementSymbol) -> int :

    > C++ signature :

    >   int GetMostCommonIsotope(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetMostCommonIsotopeMass((PeriodicTable)self, (int)atomicNumber) → float :

    > C++ signature :

    >   double GetMostCommonIsotopeMass(RDKit::PeriodicTable {lvalue},unsigned int)

    GetMostCommonIsotopeMass( (PeriodicTable)self, (str)elementSymbol) -> float :

    > C++ signature :

    >   double GetMostCommonIsotopeMass(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetNOuterElecs((PeriodicTable)self, (int)atomicNumber) → int :

    > C++ signature :

    >   int GetNOuterElecs(RDKit::PeriodicTable {lvalue},unsigned int)

    GetNOuterElecs( (PeriodicTable)self, (str)elementSymbol) -> int :

    > C++ signature :

    >   int GetNOuterElecs(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetRb0((PeriodicTable)self, (int)atomicNumber) → float :

    > C++ signature :

    >   double GetRb0(RDKit::PeriodicTable {lvalue},unsigned int)

    GetRb0( (PeriodicTable)self, (str)elementSymbol) -> float :

    > C++ signature :

    >   double GetRb0(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetRcovalent((PeriodicTable)self, (int)atomicNumber) → float :

    > C++ signature :

    >   double GetRcovalent(RDKit::PeriodicTable {lvalue},unsigned int)

    GetRcovalent( (PeriodicTable)self, (str)elementSymbol) -> float :

    > C++ signature :

    >   double GetRcovalent(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetRow((PeriodicTable)self, (int)atomicNumber) → int :

    > C++ signature :

    >   unsigned int GetRow(RDKit::PeriodicTable {lvalue},unsigned int)

    GetRow( (PeriodicTable)self, (str)elementSymbol) -> int :

    > C++ signature :

    >   unsigned int GetRow(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetRvdw((PeriodicTable)self, (int)atomicNumber) → float :

    > C++ signature :

    >   double GetRvdw(RDKit::PeriodicTable {lvalue},unsigned int)

    GetRvdw( (PeriodicTable)self, (str)elementSymbol) -> float :

    > C++ signature :

    >   double GetRvdw(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetValenceList((PeriodicTable)self, (int)atomicNumber) → rdkit.rdBase._vecti :

    > C++ signature :

    >   std::vector<int, std::allocator<int> > GetValenceList(RDKit::PeriodicTable {lvalue},unsigned int)

    GetValenceList( (PeriodicTable)self, (str)elementSymbol) -> rdkit.rdBase._vecti :

    > C++ signature :

    >   std::vector<int, std::allocator<int> > GetValenceList(RDKit::PeriodicTable {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

class rdkit.Chem.rdchem.PropertyPickleOptions

  Bases: `enum`

  AllProps = rdkit.Chem.rdchem.PropertyPickleOptions.AllProps
  AtomProps = rdkit.Chem.rdchem.PropertyPickleOptions.AtomProps
  BondProps = rdkit.Chem.rdchem.PropertyPickleOptions.BondProps
  ComputedProps = rdkit.Chem.rdchem.PropertyPickleOptions.ComputedProps
  CoordsAsDouble = rdkit.Chem.rdchem.PropertyPickleOptions.CoordsAsDouble
  MolProps = rdkit.Chem.rdchem.PropertyPickleOptions.MolProps
  NoConformers = rdkit.Chem.rdchem.PropertyPickleOptions.NoConformers
  NoProps = rdkit.Chem.rdchem.PropertyPickleOptions.NoProps
  PrivateProps = rdkit.Chem.rdchem.PropertyPickleOptions.PrivateProps
  QueryAtomData = rdkit.Chem.rdchem.PropertyPickleOptions.QueryAtomData
  names = {'AllProps': rdkit.Chem.rdchem.PropertyPickleOptions.AllProps, 'AtomProps': rdkit.Chem.rdchem.PropertyPickleOptions.AtomProps, 'BondProps': rdkit.Chem.rdchem.PropertyPickleOptions.BondProps, 'ComputedProps': rdkit.Chem.rdchem.PropertyPickleOptions.ComputedProps, 'CoordsAsDouble': rdkit.Chem.rdchem.PropertyPickleOptions.CoordsAsDouble, 'MolProps': rdkit.Chem.rdchem.PropertyPickleOptions.MolProps, 'NoConformers': rdkit.Chem.rdchem.PropertyPickleOptions.NoConformers, 'NoProps': rdkit.Chem.rdchem.PropertyPickleOptions.NoProps, 'PrivateProps': rdkit.Chem.rdchem.PropertyPickleOptions.PrivateProps, 'QueryAtomData': rdkit.Chem.rdchem.PropertyPickleOptions.QueryAtomData}
  values = {0: rdkit.Chem.rdchem.PropertyPickleOptions.NoProps, 1: rdkit.Chem.rdchem.PropertyPickleOptions.MolProps, 2: rdkit.Chem.rdchem.PropertyPickleOptions.QueryAtomData, 4: rdkit.Chem.rdchem.PropertyPickleOptions.BondProps, 16: rdkit.Chem.rdchem.PropertyPickleOptions.PrivateProps, 32: rdkit.Chem.rdchem.PropertyPickleOptions.ComputedProps, 65535: rdkit.Chem.rdchem.PropertyPickleOptions.AllProps, 65536: rdkit.Chem.rdchem.PropertyPickleOptions.CoordsAsDouble, 131072: rdkit.Chem.rdchem.PropertyPickleOptions.NoConformers}

class rdkit.Chem.rdchem.QueryAtom

  Bases: `Atom`

  The class to store QueryAtoms. These cannot currently be constructed directly from Python

  Raises an exception This class cannot be instantiated from Python

  ExpandQuery((QueryAtom)self, (QueryAtom)other[, (CompositeQueryType)how=rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_AND[, (bool)maintainOrder=True]]) → None :

    combines the query from other with ours

    C++ signature :

      void ExpandQuery(RDKit::QueryAtom*,RDKit::QueryAtom const* [,Queries::CompositeQueryType=rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_AND [,bool=True]])

  SetQuery((QueryAtom)self, (QueryAtom)other) → None :

    Replace our query with a copy of the other query

    C++ signature :

      void SetQuery(RDKit::QueryAtom*,RDKit::QueryAtom const*)

class rdkit.Chem.rdchem.QueryBond

  Bases: `Bond`

  The class to store QueryBonds. These cannot currently be constructed directly from Python

  Raises an exception This class cannot be instantiated from Python

  ExpandQuery((QueryBond)self, (QueryBond)other[, (CompositeQueryType)how=rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_AND[, (bool)maintainOrder=True]]) → None :

    combines the query from other with ours

    C++ signature :

      void ExpandQuery(RDKit::QueryBond*,RDKit::QueryBond const* [,Queries::CompositeQueryType=rdkit.Chem.rdchem.CompositeQueryType.COMPOSITE_AND [,bool=True]])

  SetQuery((QueryBond)self, (QueryBond)other) → None :

    Replace our query with a copy of the other query

    C++ signature :

      void SetQuery(RDKit::QueryBond*,RDKit::QueryBond const*)

class rdkit.Chem.rdchem.RWMol((object)self, (Mol)m) → None :

  Bases: `Mol`

  The RW molecule class (read/write)

  This class is a more-performant version of the EditableMolecule class in that it is a ‘live’ molecule and shares the interface from the Mol class. All changes are performed without the need to create a copy of the molecule using GetMol() (this is still available, however).

  n.b. Eventually this class may become a direct replacement for EditableMol

  Construct from a Mol

  > C++ signature :

  >   void __init__(_object*,RDKit::ROMol)

  __init__( (object)self) -> None :

  > C++ signature :

  >   void __init__(_object*)

  __init__( (object)self, (str)pklString) -> None :

  > C++ signature :

  >   void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  __init__( (object)self, (str)pklString, (int)propertyFlags) -> None :

  > C++ signature :

  >   void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,unsigned int)

  __init__( (object)self, (Mol)mol [, (bool)quickCopy=False [, (int)confId=-1]]) -> None :

  > C++ signature :

  >   void __init__(_object*,RDKit::ROMol [,bool=False [,int=-1]])

  AddAtom((RWMol)self, (Atom)atom) → int :

    add an atom, returns the index of the newly added atom

    C++ signature :

      int AddAtom(RDKit::ReadWriteMol {lvalue},RDKit::Atom*)

  AddBond((RWMol)self, (int)beginAtomIdx, (int)endAtomIdx[, (BondType)order=rdkit.Chem.rdchem.BondType.UNSPECIFIED]) → int :

    add a bond, returns the new number of bonds

    C++ signature :

      int AddBond(RDKit::ReadWriteMol {lvalue},unsigned int,unsigned int [,RDKit::Bond::BondType=rdkit.Chem.rdchem.BondType.UNSPECIFIED])

  BeginBatchEdit((RWMol)self) → None :

    starts batch editing

    C++ signature :

      void BeginBatchEdit(RDKit::ReadWriteMol {lvalue})

  CommitBatchEdit((RWMol)self) → None :

    finishes batch editing and makes the actual changes

    C++ signature :

      void CommitBatchEdit(RDKit::ReadWriteMol {lvalue})

  GetMol((RWMol)self) → Mol :

    Returns a Mol (a normal molecule)

    C++ signature :

      RDKit::ROMol* GetMol(RDKit::ReadWriteMol {lvalue})

  InsertMol((RWMol)self, (Mol)mol) → None :

    Insert (add) the given molecule into this one

    C++ signature :

      void InsertMol(RDKit::ReadWriteMol {lvalue},RDKit::ROMol)

  RemoveAtom((RWMol)self, (int)idx) → None :

    Remove the specified atom from the molecule

    C++ signature :

      void RemoveAtom(RDKit::ReadWriteMol {lvalue},unsigned int)

  RemoveBond((RWMol)self, (int)idx1, (int)idx2) → None :

    Remove the specified bond from the molecule

    C++ signature :

      void RemoveBond(RDKit::ReadWriteMol {lvalue},unsigned int,unsigned int)

  ReplaceAtom((RWMol)self, (int)index, (Atom)newAtom[, (bool)updateLabel=False[, (bool)preserveProps=False]]) → None :

    replaces the specified atom with the provided one If updateLabel is True, the new atom becomes the active atom If preserveProps is True preserve keep the existing props unless explicit set on the new atom

    C++ signature :

      void ReplaceAtom(RDKit::ReadWriteMol {lvalue},unsigned int,RDKit::Atom* [,bool=False [,bool=False]])

  ReplaceBond((RWMol)self, (int)index, (Bond)newBond[, (bool)preserveProps=False[, (bool)keepSGroups=True]]) → None :

    replaces the specified bond with the provided one. If preserveProps is True preserve keep the existing props unless explicit set on the new bond. If keepSGroups is False, allSubstance Groups referencing the bond will be dropped.

    C++ signature :

      void ReplaceBond(RDKit::ReadWriteMol {lvalue},unsigned int,RDKit::Bond* [,bool=False [,bool=True]])

  RollbackBatchEdit((RWMol)self) → None :

    cancels batch editing

    C++ signature :

      void RollbackBatchEdit(RDKit::ReadWriteMol {lvalue})

  SetStereoGroups((RWMol)self, (list)stereo_groups) → None :

    Set the stereo groups

    C++ signature :

      void SetStereoGroups(RDKit::ReadWriteMol {lvalue},boost::python::list {lvalue})

class rdkit.Chem.rdchem.ResonanceFlags

  Bases: `enum`

  ALLOW_CHARGE_SEPARATION = rdkit.Chem.rdchem.ResonanceFlags.ALLOW_CHARGE_SEPARATION
  ALLOW_INCOMPLETE_OCTETS = rdkit.Chem.rdchem.ResonanceFlags.ALLOW_INCOMPLETE_OCTETS
  KEKULE_ALL = rdkit.Chem.rdchem.ResonanceFlags.KEKULE_ALL
  UNCONSTRAINED_ANIONS = rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_ANIONS
  UNCONSTRAINED_CATIONS = rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_CATIONS
  names = {'ALLOW_CHARGE_SEPARATION': rdkit.Chem.rdchem.ResonanceFlags.ALLOW_CHARGE_SEPARATION, 'ALLOW_INCOMPLETE_OCTETS': rdkit.Chem.rdchem.ResonanceFlags.ALLOW_INCOMPLETE_OCTETS, 'KEKULE_ALL': rdkit.Chem.rdchem.ResonanceFlags.KEKULE_ALL, 'UNCONSTRAINED_ANIONS': rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_ANIONS, 'UNCONSTRAINED_CATIONS': rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_CATIONS}
  values = {1: rdkit.Chem.rdchem.ResonanceFlags.ALLOW_INCOMPLETE_OCTETS, 2: rdkit.Chem.rdchem.ResonanceFlags.ALLOW_CHARGE_SEPARATION, 4: rdkit.Chem.rdchem.ResonanceFlags.KEKULE_ALL, 8: rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_CATIONS, 16: rdkit.Chem.rdchem.ResonanceFlags.UNCONSTRAINED_ANIONS}

class rdkit.Chem.rdchem.ResonanceMolSupplier((object)self, (Mol)mol[, (int)flags=0[, (int)maxStructs=1000]]) → None :

  Bases: `instance`

  A class which supplies resonance structures (as mols) from a mol.

  Usage examples:

  > 1. Lazy evaluation: the resonance structures are not constructed until we ask for them:

  >        >>> suppl = ResonanceMolSupplier(mol)
  >        >>> for resMol in suppl:
  >        ...    resMol.GetNumAtoms()

  > 2. Lazy evaluation 2:

  >        >>> suppl = ResonanceMolSupplier(mol)
  >        >>> resMol1 = next(suppl)
  >        >>> resMol2 = next(suppl)
  >        >>> suppl.reset()
  >        >>> resMol3 = next(suppl)
  >        # resMol3 and resMol1 are the same:
  >        >>> MolToSmiles(resMol3)==MolToSmiles(resMol1)

  > 3. Random Access:

  >        >>> suppl = ResonanceMolSupplier(mol)
  >        >>> resMol1 = suppl[0]
  >        >>> resMol2 = suppl[1]

  >    NOTE: this will generate an IndexError if the supplier doesn’t have that many molecules.

  > 4. Random Access 2: looping over all resonance structures >>> suppl = ResonanceMolSupplier(mol) >>> nResMols = len(suppl) >>> for i in range(nResMols): … suppl[i].GetNumAtoms()

  C++ signature :

    void __init__(_object*,RDKit::ROMol {lvalue} [,unsigned int=0 [,unsigned int=1000]])

  Enumerate((ResonanceMolSupplier)self) → None :

    Ask ResonanceMolSupplier to enumerate resonance structures(automatically done as soon as any attempt to access them is made).

    C++ signature :

      void Enumerate(RDKit::ResonanceMolSupplier {lvalue})

  GetAtomConjGrpIdx((ResonanceMolSupplier)self, (int)ai) → int :

    Given an atom index, it returns the index of the conjugated groupthe atom belongs to, or -1 if it is not conjugated.

    C++ signature :

      int GetAtomConjGrpIdx(RDKit::ResonanceMolSupplier {lvalue},unsigned int)

  GetBondConjGrpIdx((ResonanceMolSupplier)self, (int)bi) → int :

    Given a bond index, it returns the index of the conjugated groupthe bond belongs to, or -1 if it is not conjugated.

    C++ signature :

      int GetBondConjGrpIdx(RDKit::ResonanceMolSupplier {lvalue},unsigned int)

  GetIsEnumerated((ResonanceMolSupplier)self) → bool :

    Returns true if resonance structure enumeration has already happened.

    C++ signature :

      bool GetIsEnumerated(RDKit::ResonanceMolSupplier {lvalue})

  GetNumConjGrps((ResonanceMolSupplier)self) → int :

    Returns the number of individual conjugated groups in the molecule.

    C++ signature :

      unsigned int GetNumConjGrps(RDKit::ResonanceMolSupplier {lvalue})

  GetProgressCallback((ResonanceMolSupplier)self) → object :

    Get the ResonanceMolSupplierCallback subclass instance, or None if none was set.

    C++ signature :

      boost::python::api::object GetProgressCallback(RDKit::ResonanceMolSupplier)

  GetSubstructMatch((ResonanceMolSupplier)self, (Mol)query[, (bool)useChirality=False[, (bool)useQueryQueryMatches=False]]) → object :

    Returns the indices of the molecule’s atoms that match a substructure query, taking into account all resonance structures in ResonanceMolSupplier.

    > ARGUMENTS:

    >   - query: a Molecule

    >   - useChirality: enables the use of stereochemistry in the matching

    >   - useQueryQueryMatches: use query-query matching logic

    > RETURNS: a tuple of integers

    > NOTES:

    >   - only a single match is returned

    >   - the ordering of the indices corresponds to the atom ordering

    >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

    C++ signature :

      _object* GetSubstructMatch(RDKit::ResonanceMolSupplier {lvalue},RDKit::ROMol [,bool=False [,bool=False]])

  GetSubstructMatches((ResonanceMolSupplier)self, (Mol)query[, (bool)uniquify=False[, (bool)useChirality=False[, (bool)useQueryQueryMatches=False[, (int)maxMatches=1000[, (int)numThreads=1]]]]]) → object :

    Returns tuples of the indices of the molecule’s atoms that match a substructure query, taking into account all resonance structures in ResonanceMolSupplier.

    > ARGUMENTS:

    >   - query: a Molecule.

    >   - uniquify: (optional) determines whether or not the matches are uniquified.

    >       Defaults to 1.

    >   - useChirality: enables the use of stereochemistry in the matching

    >   - useQueryQueryMatches: use query-query matching logic

    >   - maxMatches: The maximum number of matches that will be returned.

    >       In high-symmetry cases with medium-sized molecules, it is very easy to end up with a combinatorial explosion in the number of possible matches. This argument prevents that from having unintended consequences

    >   - numThreads: The number of threads to be used (defaults to 1; 0 selects the

    >       number of concurrent threads supported by the hardware; negative values are added to the number of concurrent threads supported by the hardware).

    > RETURNS: a tuple of tuples of integers

    > NOTE:
    >   - the ordering of the indices corresponds to the atom ordering

    >       in the query. For example, the first index is for the atom in this molecule that matches the first atom in the query.

    C++ signature :

      _object* GetSubstructMatches(RDKit::ResonanceMolSupplier {lvalue},RDKit::ROMol [,bool=False [,bool=False [,bool=False [,unsigned int=1000 [,int=1]]]]])

  SetNumThreads((ResonanceMolSupplier)self, (int)numThreads) → None :

    Sets the number of threads to be used to enumerate resonance structures (defaults to 1; 0 selects the number of concurrent threads supported by the hardware; negative values are added to the number of concurrent threads supported by the hardware).

    C++ signature :

      void SetNumThreads(RDKit::ResonanceMolSupplier {lvalue},unsigned int)

  SetProgressCallback((ResonanceMolSupplier)self, (object)callback) → None :

    Pass an instance of a class derived from ResonanceMolSupplierCallback, which must implement the __call__() method.

    C++ signature :

      void SetProgressCallback(RDKit::ResonanceMolSupplier {lvalue},_object*)

  WasCanceled((ResonanceMolSupplier)self) → bool :

    Returns True if the resonance structure generation was canceled.

    C++ signature :

      bool WasCanceled(RDKit::ResonanceMolSupplier {lvalue})

  atEnd((ResonanceMolSupplier)self) → bool :

    Returns whether or not we have hit the end of the resonance structure supplier.

    C++ signature :

      bool atEnd(RDKit::ResonanceMolSupplier {lvalue})

  reset((ResonanceMolSupplier)self) → None :

    Resets our position in the resonance structure supplier to the beginning.

    C++ signature :

      void reset(RDKit::ResonanceMolSupplier {lvalue})

class rdkit.Chem.rdchem.ResonanceMolSupplierCallback((object)self) → None :

  Bases: `instance`

  Create a derived class from this abstract base class and implement the __call__() method. The __call__() method is called at each iteration of the algorithm, and provides a mechanism to monitor or stop its progress.

  To have your callback called, pass an instance of your derived class to ResonanceMolSupplier.SetProgressCallback()

  C++ signature :

    void __init__(_object*)

  GetMaxStructures((ResonanceMolSupplierCallback)self) → int :

    Get the number of conjugated groups this molecule has.

    C++ signature :

      unsigned long GetMaxStructures(RDKit::PyResonanceMolSupplierCallback {lvalue})

  GetNumConjGrps((ResonanceMolSupplierCallback)self) → int :

    Returns the number of individual conjugated groups in the molecule.

    C++ signature :

      unsigned int GetNumConjGrps(RDKit::PyResonanceMolSupplierCallback {lvalue})

  GetNumDiverseStructures((ResonanceMolSupplierCallback)self, (int)conjGrpIdx) → int :

    Get the number of non-degenrate resonance structures generated so far for the passed conjugated group index.

    C++ signature :

      unsigned long GetNumDiverseStructures(RDKit::PyResonanceMolSupplierCallback {lvalue},unsigned int)

  GetNumStructures((ResonanceMolSupplierCallback)self, (int)conjGrpIdx) → int :

    Get the number of resonance structures generated so far for the passed conjugated group index.

    C++ signature :

      unsigned long GetNumStructures(RDKit::PyResonanceMolSupplierCallback {lvalue},unsigned int)

class rdkit.Chem.rdchem.RingInfo

  Bases: `instance`

  contains information about a molecule’s rings

  Raises an exception This class cannot be instantiated from Python

  AddRing((RingInfo)self, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)atomIds, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)bondIds) → None :

    Adds a ring to the set. Be very careful with this operation.

    C++ signature :

      void AddRing(RDKit::RingInfo*,boost::python::api::object,boost::python::api::object)

  AreAtomsInSameRing((RingInfo)self, (int)idx1, (int)idx2) → bool :
    C++ signature :

      bool AreAtomsInSameRing(RDKit::RingInfo {lvalue},unsigned int,unsigned int)

  AreAtomsInSameRingOfSize((RingInfo)self, (int)idx1, (int)idx2, (int)size) → bool :
    C++ signature :

      bool AreAtomsInSameRingOfSize(RDKit::RingInfo {lvalue},unsigned int,unsigned int,unsigned int)

  AreBondsInSameRing((RingInfo)self, (int)idx1, (int)idx2) → bool :
    C++ signature :

      bool AreBondsInSameRing(RDKit::RingInfo {lvalue},unsigned int,unsigned int)

  AreBondsInSameRingOfSize((RingInfo)self, (int)idx1, (int)idx2, (int)size) → bool :
    C++ signature :

      bool AreBondsInSameRingOfSize(RDKit::RingInfo {lvalue},unsigned int,unsigned int,unsigned int)

  AreRingFamiliesInitialized((RingInfo)self) → bool :
    C++ signature :

      bool AreRingFamiliesInitialized(RDKit::RingInfo {lvalue})

  AreRingsFused((RingInfo)self, (int)ring1Idx, (int)ring2Idx) → bool :
    C++ signature :

      bool AreRingsFused(RDKit::RingInfo {lvalue},unsigned int,unsigned int)

  AtomMembers((RingInfo)self, (int)idx) → object :
    C++ signature :

      boost::python::api::object AtomMembers(RDKit::RingInfo const*,unsigned int)

  AtomRingFamilies((RingInfo)self) → object :
    C++ signature :

      boost::python::api::object AtomRingFamilies(RDKit::RingInfo const*)

  AtomRingSizes((RingInfo)self, (int)idx) → object :
    C++ signature :

      boost::python::api::object AtomRingSizes(RDKit::RingInfo const*,unsigned int)

  AtomRings((RingInfo)self) → object :
    C++ signature :

      boost::python::api::object AtomRings(RDKit::RingInfo const*)

  BondMembers((RingInfo)self, (int)idx) → object :
    C++ signature :

      boost::python::api::object BondMembers(RDKit::RingInfo const*,unsigned int)

  BondRingFamilies((RingInfo)self) → object :
    C++ signature :

      boost::python::api::object BondRingFamilies(RDKit::RingInfo const*)

  BondRingSizes((RingInfo)self, (int)idx) → object :
    C++ signature :

      boost::python::api::object BondRingSizes(RDKit::RingInfo const*,unsigned int)

  BondRings((RingInfo)self) → object :
    C++ signature :

      boost::python::api::object BondRings(RDKit::RingInfo const*)

  IsAtomInRingOfSize((RingInfo)self, (int)idx, (int)size) → bool :
    C++ signature :

      bool IsAtomInRingOfSize(RDKit::RingInfo {lvalue},unsigned int,unsigned int)

  IsBondInRingOfSize((RingInfo)self, (int)idx, (int)size) → bool :
    C++ signature :

      bool IsBondInRingOfSize(RDKit::RingInfo {lvalue},unsigned int,unsigned int)

  IsRingFused((RingInfo)self, (int)ringIdx) → bool :
    C++ signature :

      bool IsRingFused(RDKit::RingInfo {lvalue},unsigned int)

  MinAtomRingSize((RingInfo)self, (int)idx) → int :
    C++ signature :

      unsigned int MinAtomRingSize(RDKit::RingInfo {lvalue},unsigned int)

  MinBondRingSize((RingInfo)self, (int)idx) → int :
    C++ signature :

      unsigned int MinBondRingSize(RDKit::RingInfo {lvalue},unsigned int)

  NumAtomRings((RingInfo)self, (int)idx) → int :
    C++ signature :

      unsigned int NumAtomRings(RDKit::RingInfo {lvalue},unsigned int)

  NumBondRings((RingInfo)self, (int)idx) → int :
    C++ signature :

      unsigned int NumBondRings(RDKit::RingInfo {lvalue},unsigned int)

  NumFusedBonds((RingInfo)self, (int)ringIdx) → int :
    C++ signature :

      unsigned int NumFusedBonds(RDKit::RingInfo {lvalue},unsigned int)

  NumRelevantCycles((RingInfo)self) → int :
    C++ signature :

      unsigned int NumRelevantCycles(RDKit::RingInfo {lvalue})

  NumRingFamilies((RingInfo)self) → int :
    C++ signature :

      unsigned int NumRingFamilies(RDKit::RingInfo {lvalue})

  NumRings((RingInfo)self) → int :
    C++ signature :

      unsigned int NumRings(RDKit::RingInfo {lvalue})

rdkit.Chem.rdchem.SetAtomAlias((Atom)atom, (str)rlabel) → None :

  Sets the atom’s MDL alias text. Setting to an empty string clears the alias.

  C++ signature :

    void SetAtomAlias(RDKit::Atom*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

rdkit.Chem.rdchem.SetAtomRLabel((Atom)atom, (int)rlabel) → None :

  Sets the atom’s MDL RLabel (this is an integer from 0 to 99). Setting to 0 clears the rlabel.

  C++ signature :

    void SetAtomRLabel(RDKit::Atom*,int)

rdkit.Chem.rdchem.SetAtomValue((Atom)atom, (str)rlabel) → None :

  Sets the atom’s MDL alias text. Setting to an empty string clears the alias.

  C++ signature :

    void SetAtomValue(RDKit::Atom*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

rdkit.Chem.rdchem.SetDefaultPickleProperties((int)arg1) → None :

  Set the current global mol pickler options.

  C++ signature :

    void SetDefaultPickleProperties(unsigned int)

rdkit.Chem.rdchem.SetSupplementalSmilesLabel((Atom)atom, (str)label) → None :

  Sets a supplemental label on an atom that is written to the smiles string.

      >>> m = Chem.MolFromSmiles("C")
      >>> Chem.SetSupplementalSmilesLabel(m.GetAtomWithIdx(0), '<xxx>')
      >>> Chem.MolToSmiles(m)
      'C<xxx>'

  C++ signature :

    void SetSupplementalSmilesLabel(RDKit::Atom*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

class rdkit.Chem.rdchem.StereoDescriptor

  Bases: `enum`

  Bond_Cis = rdkit.Chem.rdchem.StereoDescriptor.Bond_Cis
  Bond_Trans = rdkit.Chem.rdchem.StereoDescriptor.Bond_Trans
  NoValue = rdkit.Chem.rdchem.StereoDescriptor.NoValue
  Tet_CCW = rdkit.Chem.rdchem.StereoDescriptor.Tet_CCW
  Tet_CW = rdkit.Chem.rdchem.StereoDescriptor.Tet_CW
  names = {'Bond_Cis': rdkit.Chem.rdchem.StereoDescriptor.Bond_Cis, 'Bond_Trans': rdkit.Chem.rdchem.StereoDescriptor.Bond_Trans, 'NoValue': rdkit.Chem.rdchem.StereoDescriptor.NoValue, 'Tet_CCW': rdkit.Chem.rdchem.StereoDescriptor.Tet_CCW, 'Tet_CW': rdkit.Chem.rdchem.StereoDescriptor.Tet_CW}
  values = {0: rdkit.Chem.rdchem.StereoDescriptor.NoValue, 1: rdkit.Chem.rdchem.StereoDescriptor.Tet_CW, 2: rdkit.Chem.rdchem.StereoDescriptor.Tet_CCW, 3: rdkit.Chem.rdchem.StereoDescriptor.Bond_Cis, 4: rdkit.Chem.rdchem.StereoDescriptor.Bond_Trans}

class rdkit.Chem.rdchem.StereoGroup

  Bases: `instance`

  A collection of atoms with a defined stereochemical relationship.

  Used to help represent a sample with unknown stereochemistry, or that is a mix of diastereomers.

  Raises an exception This class cannot be instantiated from Python

  GetAtoms((StereoGroup)self) → object :

    access the atoms in the StereoGroup.

    C++ signature :

      boost::python::api::object GetAtoms(RDKit::StereoGroup {lvalue})

  GetBonds((StereoGroup)self) → object :

    access the bonds in the StereoGroup.

    C++ signature :

      boost::python::api::object GetBonds(RDKit::StereoGroup {lvalue})

  GetGroupType((StereoGroup)self) → StereoGroupType :

    Returns the StereoGroupType.

    C++ signature :

      RDKit::StereoGroupType GetGroupType(RDKit::StereoGroup {lvalue})

  GetReadId((StereoGroup)self) → int :

    return the StereoGroup’s original ID. Note that the ID only makes sense for AND/OR groups.

    C++ signature :

      unsigned int GetReadId(RDKit::StereoGroup {lvalue})

  GetWriteId((StereoGroup)self) → int :

    return the StereoGroup’s ID that will be exported. Note that the ID only makes sense for AND/OR groups.

    C++ signature :

      unsigned int GetWriteId(RDKit::StereoGroup {lvalue})

  SetWriteId((StereoGroup)self, (int)id) → None :

    return the StereoGroup’s ID that will be exported. Note that the ID only makes sense for AND/OR groups.

    C++ signature :

      void SetWriteId(RDKit::StereoGroup {lvalue},unsigned int)

class rdkit.Chem.rdchem.StereoGroupType

  Bases: `enum`

  STEREO_ABSOLUTE = rdkit.Chem.rdchem.StereoGroupType.STEREO_ABSOLUTE
  STEREO_AND = rdkit.Chem.rdchem.StereoGroupType.STEREO_AND
  STEREO_OR = rdkit.Chem.rdchem.StereoGroupType.STEREO_OR
  names = {'STEREO_ABSOLUTE': rdkit.Chem.rdchem.StereoGroupType.STEREO_ABSOLUTE, 'STEREO_AND': rdkit.Chem.rdchem.StereoGroupType.STEREO_AND, 'STEREO_OR': rdkit.Chem.rdchem.StereoGroupType.STEREO_OR}
  values = {0: rdkit.Chem.rdchem.StereoGroupType.STEREO_ABSOLUTE, 1: rdkit.Chem.rdchem.StereoGroupType.STEREO_OR, 2: rdkit.Chem.rdchem.StereoGroupType.STEREO_AND}

class rdkit.Chem.rdchem.StereoGroup_vect((object)arg1) → None :

  Bases: `instance`

  C++ signature :

    void __init__(_object*)

  append((StereoGroup_vect)arg1, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)arg2) → None :
    C++ signature :

      void append(std::vector<RDKit::StereoGroup, std::allocator<RDKit::StereoGroup> > {lvalue},boost::python::api::object)

  extend((StereoGroup_vect)arg1, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)arg2) → None :
    C++ signature :

      void extend(std::vector<RDKit::StereoGroup, std::allocator<RDKit::StereoGroup> > {lvalue},boost::python::api::object)

class rdkit.Chem.rdchem.StereoInfo((object)arg1) → None :

  Bases: `instance`

  Class describing stereochemistry

  C++ signature :

    void __init__(_object*)

  NOATOM = 4294967295
  property centeredOn

    index of the item the stereo concerns

  property controllingAtoms

    indices of the atoms controlling the stereo

  property descriptor

    stereo descriptor

  property permutation

    permutation index (used for non-tetrahedral chirality)

  property specified

    whether or not it is specified

  property type

    the type of stereo

class rdkit.Chem.rdchem.StereoSpecified

  Bases: `enum`

  Specified = rdkit.Chem.rdchem.StereoSpecified.Specified
  Unknown = rdkit.Chem.rdchem.StereoSpecified.Unknown
  Unspecified = rdkit.Chem.rdchem.StereoSpecified.Unspecified
  names = {'Specified': rdkit.Chem.rdchem.StereoSpecified.Specified, 'Unknown': rdkit.Chem.rdchem.StereoSpecified.Unknown, 'Unspecified': rdkit.Chem.rdchem.StereoSpecified.Unspecified}
  values = {0: rdkit.Chem.rdchem.StereoSpecified.Unspecified, 1: rdkit.Chem.rdchem.StereoSpecified.Specified, 2: rdkit.Chem.rdchem.StereoSpecified.Unknown}

class rdkit.Chem.rdchem.StereoType

  Bases: `enum`

  Atom_Octahedral = rdkit.Chem.rdchem.StereoType.Atom_Octahedral
  Atom_SquarePlanar = rdkit.Chem.rdchem.StereoType.Atom_SquarePlanar
  Atom_Tetrahedral = rdkit.Chem.rdchem.StereoType.Atom_Tetrahedral
  Atom_TrigonalBipyramidal = rdkit.Chem.rdchem.StereoType.Atom_TrigonalBipyramidal
  Bond_Atropisomer = rdkit.Chem.rdchem.StereoType.Bond_Atropisomer
  Bond_Cumulene_Even = rdkit.Chem.rdchem.StereoType.Bond_Cumulene_Even
  Bond_Double = rdkit.Chem.rdchem.StereoType.Bond_Double
  Unspecified = rdkit.Chem.rdchem.StereoType.Unspecified
  names = {'Atom_Octahedral': rdkit.Chem.rdchem.StereoType.Atom_Octahedral, 'Atom_SquarePlanar': rdkit.Chem.rdchem.StereoType.Atom_SquarePlanar, 'Atom_Tetrahedral': rdkit.Chem.rdchem.StereoType.Atom_Tetrahedral, 'Atom_TrigonalBipyramidal': rdkit.Chem.rdchem.StereoType.Atom_TrigonalBipyramidal, 'Bond_Atropisomer': rdkit.Chem.rdchem.StereoType.Bond_Atropisomer, 'Bond_Cumulene_Even': rdkit.Chem.rdchem.StereoType.Bond_Cumulene_Even, 'Bond_Double': rdkit.Chem.rdchem.StereoType.Bond_Double, 'Unspecified': rdkit.Chem.rdchem.StereoType.Unspecified}
  values = {0: rdkit.Chem.rdchem.StereoType.Unspecified, 1: rdkit.Chem.rdchem.StereoType.Atom_Tetrahedral, 2: rdkit.Chem.rdchem.StereoType.Atom_SquarePlanar, 3: rdkit.Chem.rdchem.StereoType.Atom_TrigonalBipyramidal, 4: rdkit.Chem.rdchem.StereoType.Atom_Octahedral, 5: rdkit.Chem.rdchem.StereoType.Bond_Double, 6: rdkit.Chem.rdchem.StereoType.Bond_Cumulene_Even, 7: rdkit.Chem.rdchem.StereoType.Bond_Atropisomer}

class rdkit.Chem.rdchem.SubstanceGroup

  Bases: `instance`

  A collection of atoms and bonds with associated properties

  Raises an exception This class cannot be instantiated from Python

  AddAtomWithBookmark((SubstanceGroup)self, (int)mark) → None :
    C++ signature :

      void AddAtomWithBookmark(RDKit::SubstanceGroup {lvalue},int)

  AddAtomWithIdx((SubstanceGroup)self, (int)idx) → None :
    C++ signature :

      void AddAtomWithIdx(RDKit::SubstanceGroup {lvalue},unsigned int)

  AddAttachPoint((SubstanceGroup)self, (int)aIdx, (int)lvIdx, (str)idStr) → None :
    C++ signature :

      void AddAttachPoint(RDKit::SubstanceGroup {lvalue},unsigned int,int,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  AddBondWithBookmark((SubstanceGroup)self, (int)mark) → None :
    C++ signature :

      void AddBondWithBookmark(RDKit::SubstanceGroup {lvalue},int)

  AddBondWithIdx((SubstanceGroup)self, (int)idx) → None :
    C++ signature :

      void AddBondWithIdx(RDKit::SubstanceGroup {lvalue},unsigned int)

  AddBracket((SubstanceGroup)self, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)pts) → None :
    C++ signature :

      void AddBracket(RDKit::SubstanceGroup {lvalue},boost::python::api::object)

  AddCState((SubstanceGroup)self, (int)bondIdx, (rdkit.Geometry.rdGeometry.Point3D)vector) → None :
    C++ signature :

      void AddCState(RDKit::SubstanceGroup {lvalue},unsigned int,RDGeom::Point3D)

  AddParentAtomWithBookmark((SubstanceGroup)self, (int)mark) → None :
    C++ signature :

      void AddParentAtomWithBookmark(RDKit::SubstanceGroup {lvalue},int)

  AddParentAtomWithIdx((SubstanceGroup)self, (int)idx) → None :
    C++ signature :

      void AddParentAtomWithIdx(RDKit::SubstanceGroup {lvalue},unsigned int)

  ClearAttachPoints((SubstanceGroup)self) → None :
    C++ signature :

      void ClearAttachPoints(RDKit::SubstanceGroup {lvalue})

  ClearBrackets((SubstanceGroup)self) → None :
    C++ signature :

      void ClearBrackets(RDKit::SubstanceGroup {lvalue})

  ClearCStates((SubstanceGroup)self) → None :
    C++ signature :

      void ClearCStates(RDKit::SubstanceGroup {lvalue})

  ClearProp((SubstanceGroup)self, (str)key) → None :

    Removes a particular property (does nothing if not set).

    C++ signature :

      void ClearProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetAtoms((SubstanceGroup)self) → rdkit.rdBase._vectj :

    returns a list of the indices of the atoms in this SubstanceGroup

    C++ signature :

      std::vector<unsigned int, std::allocator<unsigned int> > GetAtoms(RDKit::SubstanceGroup {lvalue})

  GetAttachPoints((SubstanceGroup)self) → tuple :
    C++ signature :

      boost::python::tuple GetAttachPoints(RDKit::SubstanceGroup)

  GetBonds((SubstanceGroup)self) → rdkit.rdBase._vectj :

    returns a list of the indices of the bonds in this SubstanceGroup

    C++ signature :

      std::vector<unsigned int, std::allocator<unsigned int> > GetBonds(RDKit::SubstanceGroup {lvalue})

  GetBoolProp((SubstanceGroup)self, (str)key) → bool :

    returns the value of a particular property

    C++ signature :

      bool GetBoolProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetBrackets((SubstanceGroup)self) → tuple :
    C++ signature :

      boost::python::tuple GetBrackets(RDKit::SubstanceGroup)

  GetCStates((SubstanceGroup)self) → tuple :
    C++ signature :

      boost::python::tuple GetCStates(RDKit::SubstanceGroup)

  GetDoubleProp((SubstanceGroup)self, (str)key) → float :

    returns the value of a particular property

    C++ signature :

      double GetDoubleProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetIndexInMol((SubstanceGroup)self) → int :

    returns the index of this SubstanceGroup in the owning molecule’s list.

    C++ signature :

      unsigned int GetIndexInMol(RDKit::SubstanceGroup {lvalue})

  GetIntProp((SubstanceGroup)self, (str)key) → int :

    returns the value of a particular property

    C++ signature :

      int GetIntProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetOwningMol((SubstanceGroup)self) → Mol :

    returns the molecule owning this SubstanceGroup

    C++ signature :

      RDKit::ROMol {lvalue} GetOwningMol(RDKit::SubstanceGroup {lvalue})

  GetParentAtoms((SubstanceGroup)self) → rdkit.rdBase._vectj :

    returns a list of the indices of the parent atoms in this SubstanceGroup

    C++ signature :

      std::vector<unsigned int, std::allocator<unsigned int> > GetParentAtoms(RDKit::SubstanceGroup {lvalue})

  GetProp((SubstanceGroup)self, (str)key[, (bool)autoConvert=False]) → object :

    Returns the value of the property.

    > ARGUMENTS:

    >   - key: the name of the property to return (a string).

    >   - autoConvert: if True attempt to convert the property into a python object

    > RETURNS: a string

    > NOTE:

    >   - If the property has not been set, a KeyError exception will be raised.

    C++ signature :

      _object* GetProp(RDKit::SubstanceGroup const*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > [,bool=False])

  GetPropNames((SubstanceGroup)self[, (bool)includePrivate=False[, (bool)includeComputed=False]]) → rdkit.rdBase._vectNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE :

    Returns a list of the properties set on the SubstanceGroup.

    C++ signature :

      std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > GetPropNames(RDKit::SubstanceGroup {lvalue} [,bool=False [,bool=False]])

  GetPropsAsDict((SubstanceGroup)self[, (bool)includePrivate=True[, (bool)includeComputed=True[, (bool)autoConvertStrings=True]]]) → dict :
    Returns a dictionary of the properties set on the SubstanceGroup.

      n.b. some properties cannot be converted to python types.

    C++ signature :

      boost::python::dict GetPropsAsDict(RDKit::SubstanceGroup [,bool=True [,bool=True [,bool=True]]])

  GetStringVectProp((SubstanceGroup)self, (str)key) → rdkit.rdBase._vectNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE :

    returns the value of a particular property

    C++ signature :

      std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > GetStringVectProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetUnsignedProp((SubstanceGroup)self, (str)key) → int :

    returns the value of a particular property

    C++ signature :

      unsigned int GetUnsignedProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  GetUnsignedVectProp((SubstanceGroup)self, (str)key) → rdkit.rdBase._vectj :

    returns the value of a particular property

    C++ signature :

      std::vector<unsigned int, std::allocator<unsigned int> > GetUnsignedVectProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  HasProp((SubstanceGroup)self, (str)key) → bool :

    returns whether or not a particular property exists

    C++ signature :

      bool HasProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

  SetAtoms((SubstanceGroup)self, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)iterable) → None :

    Set the list of the indices of the atoms in this SubstanceGroup. Note that this does not update properties, CStates or Attachment Points.

    C++ signature :

      void SetAtoms(RDKit::SubstanceGroup {lvalue},boost::python::api::object)

  SetBonds((SubstanceGroup)self, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)iterable) → None :

    Set the list of the indices of the bonds in this SubstanceGroup. Note that this does not update properties, CStates or Attachment Points.

    C++ signature :

      void SetBonds(RDKit::SubstanceGroup {lvalue},boost::python::api::object)

  SetBoolProp((SubstanceGroup)self, (str)key, (bool)val[, (bool)computed=False]) → None :

    sets the value of a particular property

    C++ signature :

      void SetBoolProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,bool [,bool=False])

  SetDoubleProp((SubstanceGroup)self, (str)key, (float)val[, (bool)computed=False]) → None :

    sets the value of a particular property

    C++ signature :

      void SetDoubleProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,double [,bool=False])

  SetIntProp((SubstanceGroup)self, (str)key, (int)val[, (bool)computed=False]) → None :

    sets the value of a particular property

    C++ signature :

      void SetIntProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,int [,bool=False])

  SetParentAtoms((SubstanceGroup)self, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)iterable) → None :

    Set the list of the indices of the parent atoms in this SubstanceGroup. Note that this does not update properties, CStates or Attachment Points.

    C++ signature :

      void SetParentAtoms(RDKit::SubstanceGroup {lvalue},boost::python::api::object)

  SetProp((SubstanceGroup)self, (str)key, (str)val[, (bool)computed=False]) → None :

    sets the value of a particular property

    C++ signature :

      void SetProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > [,bool=False])

  SetUnsignedProp((SubstanceGroup)self, (str)key, (int)val[, (bool)computed=False]) → None :

    sets the value of a particular property

    C++ signature :

      void SetUnsignedProp(RDKit::SubstanceGroup {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,unsigned int [,bool=False])

class rdkit.Chem.rdchem.SubstanceGroupAttach((object)self) → None :

  Bases: `instance`

  AttachPoint for a SubstanceGroup

  C++ signature :

    void __init__(_object*)

  property aIdx

    attachment index

  property id

    attachment id

  property lvIdx

    leaving atom or index (0 for implied)

class rdkit.Chem.rdchem.SubstanceGroupCState((object)self) → None :

  Bases: `instance`

  CSTATE for a SubstanceGroup

  C++ signature :

    void __init__(_object*)

  property bondIdx

    None( (rdkit.Chem.rdchem.SubstanceGroupCState)arg1) -> int:

    C++ signature :

      unsigned int {lvalue} None(RDKit::SubstanceGroup::CState {lvalue})

  property vector

    None( (rdkit.Chem.rdchem.SubstanceGroupCState)arg1) -> object:

    C++ signature :

      RDGeom::Point3D {lvalue} None(RDKit::SubstanceGroup::CState {lvalue})

class rdkit.Chem.rdchem.SubstanceGroup_VECT((object)arg1) → None :

  Bases: `instance`

  C++ signature :

    void __init__(_object*)

  append((SubstanceGroup_VECT)arg1, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)arg2) → None :
    C++ signature :

      void append(std::vector<RDKit::SubstanceGroup, std::allocator<RDKit::SubstanceGroup> > {lvalue},boost::python::api::object)

  extend((SubstanceGroup_VECT)arg1, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)arg2) → None :
    C++ signature :

      void extend(std::vector<RDKit::SubstanceGroup, std::allocator<RDKit::SubstanceGroup> > {lvalue},boost::python::api::object)

class rdkit.Chem.rdchem.SubstructMatchParameters((object)arg1) → None :

  Bases: `instance`

  Parameters controlling substructure matching

  C++ signature :

    void __init__(_object*)

  property aromaticMatchesConjugated

    aromatic and conjugated bonds match each other

  property aromaticMatchesSingleOrDouble

    aromatic and single or double bonds match each other

  property atomProperties

    atom properties that must be equivalent in order to match.

  property bondProperties

    bond properties that must be equivalent in order to match.

  property extraAtomCheckOverridesDefaultCheck

    if set, only the extraAtomCheck will be used to determine whether or not atoms match

  property extraBondCheckOverridesDefaultCheck

    if set, only the extraBondCheck will be used to determine whether or not bonds match

  property maxMatches

    maximum number of matches to return

  property maxRecursiveMatches

    maximum number of recursive matches to find

  property numThreads

    number of threads to use when multi-threading is possible.0 selects the number of concurrent threads supported by thehardware. negative values are added to the number of concurrentthreads supported by the hardware.

  property recursionPossible

    Allow recursive queries

  setExtraAtomCheckFunc((SubstructMatchParameters)self, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)func) → None :
    allows you to provide a function that will be called

      > for each atom pair that matches during substructure searching, after all other comparisons have passed. The function should return true or false indicating whether or not that atom-match should be accepted.

      C++ signature :

        void setExtraAtomCheckFunc(RDKit::SubstructMatchParameters {lvalue},boost::python::api::object)

    setExtraAtomCheckFunc( (SubstructMatchParameters)self, (AtomCoordsMatcher)atomCoordsMatcher) -> None :
      allows you to provide an AtomCoordsMatcher that will be called

        for each atom pair that matches during substructure searching, after all other comparisons have passed.

      C++ signature :

        void setExtraAtomCheckFunc(RDKit::SubstructMatchParameters {lvalue},RDKit::AtomCoordsMatchFunctor)

  setExtraBondCheckFunc((SubstructMatchParameters)self, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)func) → None :
    allows you to provide a function that will be called

      for each bond pair that matches during substructure searching, after all other comparisons have passed. The function should return true or false indicating whether or not that bond-match should be accepted.

    C++ signature :

      void setExtraBondCheckFunc(RDKit::SubstructMatchParameters {lvalue},boost::python::api::object)

  setExtraFinalCheck((SubstructMatchParameters)self, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)func) → None :
    allows you to provide a function that will be called

      > with the molecule

      and a vector of atom IDs containing a potential match. The function should return true or false indicating whether or not that match should be accepted.

    C++ signature :

      void setExtraFinalCheck(RDKit::SubstructMatchParameters {lvalue},boost::python::api::object)

  property specifiedStereoQueryMatchesUnspecified

    If set, query atoms and bonds with specified stereochemistry will match atoms and bonds with unspecified stereochemistry.

  property uniquify

    uniquify (by atom index) match results

  property useChirality

    Use chirality in determining whether or not atoms/bonds match

  property useEnhancedStereo

    take enhanced stereochemistry into account while doing the match. This only has an effect if useChirality is also True.

  property useGenericMatchers

    use generic groups (=homology groups) as a post-filtering step (if any are present in the molecule)

  property useQueryQueryMatches

    Consider query-query matches, not just simple matches

class rdkit.Chem.rdchem.ValenceType

  Bases: `enum`

  EXPLICIT = rdkit.Chem.rdchem.ValenceType.EXPLICIT
  IMPLICIT = rdkit.Chem.rdchem.ValenceType.IMPLICIT
  names = {'EXPLICIT': rdkit.Chem.rdchem.ValenceType.EXPLICIT, 'IMPLICIT': rdkit.Chem.rdchem.ValenceType.IMPLICIT}
  values = {0: rdkit.Chem.rdchem.ValenceType.IMPLICIT, 1: rdkit.Chem.rdchem.ValenceType.EXPLICIT}

rdkit.Chem.rdchem.tossit() → None :
  C++ signature :

    void tossit()