rdkit.Chem.rdchem.Atom

Package rdkit :: Package Chem :: Module rdchem :: Class Atom |
[hide private]
[frames] | no frames]

# Class Atom

     object --+
              |
    ??.instance --+
                  |
                 Atom

Known Subclasses:
  - QueryAtom

    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.

Instance Methods | [hide private]
ClearProp(...) ClearProp( (Atom)arg1, (str)arg2) -> None : Removes a particular property from an Atom (does nothing if not already set). |
DescribeQuery(...) DescribeQuery( (Atom)arg1) -> str : returns a text description of the query. |
GetAtomMapNum(...) GetAtomMapNum( (Atom)arg1) -> int : Gets the atoms map number, returns 0 if not set |
GetAtomicNum(...) GetAtomicNum( (Atom)arg1) -> int : Returns the atomic number. |
GetBonds(...) GetBonds( (Atom)arg1) -> tuple : Returns a read-only sequence of the atom's bonds |
GetBoolProp(...) GetBoolProp( (Atom)arg1, (str)arg2) -> bool : Returns the value of the property. |
GetChiralTag(...) GetChiralTag( (Atom)arg1) -> ChiralType : |
GetDegree(...) GetDegree( (Atom)arg1) -> int : Returns the degree of the atom in the molecule. |
GetDoubleProp(...) GetDoubleProp( (Atom)arg1, (str)arg2) -> float : Returns the value of the property. |
GetExplicitValence(...) GetExplicitValence( (Atom)arg1) -> int : Returns the explicit valence of the atom. |
GetFormalCharge(...) GetFormalCharge( (Atom)arg1) -> int : |
GetHybridization(...) GetHybridization( (Atom)arg1) -> HybridizationType : Returns the atom's hybridization. |
GetIdx(...) GetIdx( (Atom)arg1) -> int : Returns the atom's index (ordering in the molecule) |
GetImplicitValence(...) GetImplicitValence( (Atom)arg1) -> int : Returns the number of implicit Hs on the atom. |
GetIntProp(...) GetIntProp( (Atom)arg1, (str)arg2) -> int : Returns the value of the property. |
GetIsAromatic(...) GetIsAromatic( (Atom)arg1) -> bool : |
GetIsotope(...) GetIsotope( (Atom)arg1) -> int : |
GetMass(...) GetMass( (Atom)arg1) -> float : |
GetMonomerInfo(...) GetMonomerInfo( (Atom)arg1) -> AtomMonomerInfo : Returns the atom's MonomerInfo object, if there is one. |
GetNeighbors(...) GetNeighbors( (Atom)arg1) -> tuple : Returns a read-only sequence of the atom's neighbors |
GetNoImplicit(...) GetNoImplicit( (Atom)arg1) -> bool : Returns whether or not the atom is *allowed* to have implicit Hs. |
GetNumExplicitHs(...) GetNumExplicitHs( (Atom)arg1) -> int : |
GetNumImplicitHs(...) GetNumImplicitHs( (Atom)arg1) -> int : Returns the total number of implicit Hs on the atom. |
GetNumRadicalElectrons(...) GetNumRadicalElectrons( (Atom)arg1) -> int : |
GetOwningMol(...) GetOwningMol( (Atom)arg1) -> Mol : Returns the Mol that owns this atom. |
GetPDBResidueInfo(...) GetPDBResidueInfo( (Atom)arg1) -> AtomPDBResidueInfo : Returns the atom's MonomerInfo object, if there is one. |
GetProp(...) GetProp( (Atom)arg1, (str)arg2) -> str : Returns the value of the property. |
GetPropNames(...) GetPropNames( (Atom)self [, (bool)includePrivate=False [, (bool)includeComputed=False]]) -> _vectSs : Returns a list of the properties set on the Atom. |
GetPropsAsDict(...) GetPropsAsDict( (Atom)self [, (bool)includePrivate=True [, (bool)includeComputed=True]]) -> dict : Returns a dictionary of the properties set on the Atom. |
GetSmarts(...) GetSmarts( (Atom)arg1) -> str : returns the SMARTS (or SMILES) string for an Atom |
GetSymbol(...) GetSymbol( (Atom)arg1) -> str : Returns the atomic symbol (a string) |
GetTotalDegree(...) GetTotalDegree( (Atom)arg1) -> int : Returns the degree of the atom in the molecule including Hs. |
GetTotalNumHs(...) GetTotalNumHs( (Atom)self [, (bool)includeNeighbors=False]) -> int : Returns the total number of Hs (explicit and implicit) on the atom. |
GetTotalValence(...) GetTotalValence( (Atom)arg1) -> int : Returns the total valence (explicit + implicit) of the atom. |
GetUnsignedProp(...) GetUnsignedProp( (Atom)arg1, (str)arg2) -> int : Returns the value of the property. |
HasProp(...) HasProp( (Atom)arg1, (str)arg2) -> int : Queries a Atom to see if a particular property has been assigned. |
HasQuery(...) HasQuery( (Atom)arg1) -> bool : Returns whether or not the atom has an associated query |
InvertChirality(...) InvertChirality( (Atom)arg1) -> None : |
IsInRing(...) IsInRing( (Atom)arg1) -> bool : Returns whether or not the atom is in a ring |
IsInRingSize(...) IsInRingSize( (Atom)arg1, (int)arg2) -> bool : Returns whether or not the atom is in a ring of a particular size. |
Match(...) Match( (Atom)arg1, (Atom)arg2) -> bool : Returns whether or not this atom matches another Atom. |
NeedsUpdatePropertyCache(...) NeedsUpdatePropertyCache( (Atom)self) -> bool : Returns true or false depending on whether implicit and explicit valence of the molecule have already been calculated. |
SetAtomMapNum(...) SetAtomMapNum( (Atom)self, (int)mapno [, (bool)strict=False]) -> None : Sets the atoms map number, a value of 0 clears the atom map |
SetAtomicNum(...) SetAtomicNum( (Atom)arg1, (int)arg2) -> None : Sets the atomic number, takes an integer value as an argument |
SetBoolProp(...) SetBoolProp( (Atom)self, (str)key, (bool)val) -> None : Sets an atomic property |
SetChiralTag(...) SetChiralTag( (Atom)arg1, (ChiralType)arg2) -> None : |
SetDoubleProp(...) SetDoubleProp( (Atom)self, (str)key, (float)val) -> None : Sets an atomic property |
SetFormalCharge(...) SetFormalCharge( (Atom)arg1, (int)arg2) -> None : |
SetHybridization(...) SetHybridization( (Atom)arg1, (HybridizationType)arg2) -> None : Sets the hybridization of the atom. |
SetIntProp(...) SetIntProp( (Atom)self, (str)key, (int)val) -> None : Sets an atomic property |
SetIsAromatic(...) SetIsAromatic( (Atom)arg1, (bool)arg2) -> None : |
SetIsotope(...) SetIsotope( (Atom)arg1, (int)arg2) -> None : |
SetMonomerInfo(...) SetMonomerInfo( (Atom)arg1, (AtomMonomerInfo)arg2) -> None : Sets the atom's MonomerInfo object. |
SetNoImplicit(...) SetNoImplicit( (Atom)arg1, (bool)arg2) -> None : Sets a marker on the atom that *disallows* implicit Hs. |
SetNumExplicitHs(...) SetNumExplicitHs( (Atom)arg1, (int)arg2) -> None : |
SetNumRadicalElectrons(...) SetNumRadicalElectrons( (Atom)arg1, (int)arg2) -> None : |
SetProp(...) SetProp( (Atom)self, (str)key, (str)val) -> None : Sets an atomic property |
SetUnsignedProp(...) SetUnsignedProp( (Atom)self, (str)key, (int)val) -> None : Sets an atomic property |
UpdatePropertyCache(...) UpdatePropertyCache( (Atom)self [, (bool)strict=True]) -> None : Regenerates computed properties like implicit valence and ring information. |
__init__(...) __init__( (object)arg1, (str)arg2) -> None : |
__reduce__(...) helper for pickle |
Inherited from `unreachable.instance`: `__new__` Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Class Variables | [hide private]
| __instance_size__ = `88`

Properties | [hide private]
Inherited from `object`: `__class__`

Method Details | [hide private]

### ClearProp(...) |
    ClearProp( (Atom)arg1, (str)arg2) -> 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*,char const*)

### DescribeQuery(...) |
    DescribeQuery( (Atom)arg1) -> str :
        returns a text description of the query. Primarily intended for debugging purposes.

        C++ signature :
            std::string DescribeQuery(RDKit::Atom const*)

### GetAtomMapNum(...) |
    GetAtomMapNum( (Atom)arg1) -> int :
        Gets the atoms map number, returns 0 if not set

        C++ signature :
            int GetAtomMapNum(RDKit::Atom {lvalue})

### GetAtomicNum(...) |
    GetAtomicNum( (Atom)arg1) -> int :
        Returns the atomic number.

        C++ signature :
            int GetAtomicNum(RDKit::Atom {lvalue})

### GetBonds(...) |
    GetBonds( (Atom)arg1) -> tuple :
        Returns a read-only sequence of the atom's bonds

        C++ signature :
            boost::python::tuple GetBonds(RDKit::Atom*)

### GetBoolProp(...) |
    GetBoolProp( (Atom)arg1, (str)arg2) -> bool :
        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 :
            bool GetBoolProp(RDKit::Atom*,char const*)

### GetChiralTag(...) |
    GetChiralTag( (Atom)arg1) -> ChiralType :

        C++ signature :
            RDKit::Atom::ChiralType GetChiralTag(RDKit::Atom {lvalue})

### GetDegree(...) |
    GetDegree( (Atom)arg1) -> 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(...) |
    GetDoubleProp( (Atom)arg1, (str)arg2) -> float :
        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 :
            double GetDoubleProp(RDKit::Atom*,char const*)

### GetExplicitValence(...) |
    GetExplicitValence( (Atom)arg1) -> int :
        Returns the explicit valence of the atom.

        C++ signature :
            int GetExplicitValence(RDKit::Atom {lvalue})

### GetFormalCharge(...) |
    GetFormalCharge( (Atom)arg1) -> int :

        C++ signature :
            int GetFormalCharge(RDKit::Atom {lvalue})

### GetHybridization(...) |
    GetHybridization( (Atom)arg1) -> HybridizationType :
        Returns the atom's hybridization.

        C++ signature :
            RDKit::Atom::HybridizationType GetHybridization(RDKit::Atom {lvalue})

### GetIdx(...) |
    GetIdx( (Atom)arg1) -> int :
        Returns the atom's index (ordering in the molecule)

        C++ signature :
            unsigned int GetIdx(RDKit::Atom {lvalue})

### GetImplicitValence(...) |
    GetImplicitValence( (Atom)arg1) -> int :
        Returns the number of implicit Hs on the atom.

        C++ signature :
            int GetImplicitValence(RDKit::Atom {lvalue})

### GetIntProp(...) |
    GetIntProp( (Atom)arg1, (str)arg2) -> int :
        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 :
            int GetIntProp(RDKit::Atom*,char const*)

### GetIsAromatic(...) |
    GetIsAromatic( (Atom)arg1) -> bool :

        C++ signature :
            bool GetIsAromatic(RDKit::Atom {lvalue})

### GetIsotope(...) |
    GetIsotope( (Atom)arg1) -> int :

        C++ signature :
            unsigned int GetIsotope(RDKit::Atom {lvalue})

### GetMass(...) |
    GetMass( (Atom)arg1) -> float :

        C++ signature :
            double GetMass(RDKit::Atom {lvalue})

### GetMonomerInfo(...) |
    GetMonomerInfo( (Atom)arg1) -> AtomMonomerInfo :
        Returns the atom's MonomerInfo object, if there is one.

        C++ signature :
            RDKit::AtomMonomerInfo* GetMonomerInfo(RDKit::Atom*)

### GetNeighbors(...) |
    GetNeighbors( (Atom)arg1) -> tuple :
        Returns a read-only sequence of the atom's neighbors

        C++ signature :
            boost::python::tuple GetNeighbors(RDKit::Atom*)

### GetNoImplicit(...) |
    GetNoImplicit( (Atom)arg1) -> bool :
        Returns whether or not the atom is *allowed* to have implicit Hs.

        C++ signature :
            bool GetNoImplicit(RDKit::Atom {lvalue})

### GetNumExplicitHs(...) |
    GetNumExplicitHs( (Atom)arg1) -> int :

        C++ signature :
            unsigned int GetNumExplicitHs(RDKit::Atom {lvalue})

### GetNumImplicitHs(...) |
    GetNumImplicitHs( (Atom)arg1) -> int :
        Returns the total number of implicit Hs on the atom.

        C++ signature :
            unsigned int GetNumImplicitHs(RDKit::Atom {lvalue})

### GetNumRadicalElectrons(...) |
    GetNumRadicalElectrons( (Atom)arg1) -> int :

        C++ signature :
            unsigned int GetNumRadicalElectrons(RDKit::Atom {lvalue})

### GetOwningMol(...) |
    GetOwningMol( (Atom)arg1) -> Mol :
        Returns the Mol that owns this atom.

        C++ signature :
            RDKit::ROMol {lvalue} GetOwningMol(RDKit::Atom {lvalue})

### GetPDBResidueInfo(...) |
    GetPDBResidueInfo( (Atom)arg1) -> AtomPDBResidueInfo :
        Returns the atom's MonomerInfo object, if there is one.

        C++ signature :
            RDKit::AtomPDBResidueInfo* GetPDBResidueInfo(RDKit::Atom*)

### GetProp(...) |
    GetProp( (Atom)arg1, (str)arg2) -> str :
        Returns the value of the property.

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

          RETURNS: a string

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

        C++ signature :
            std::string GetProp(RDKit::Atom*,char const*)

### GetPropNames(...) |
    GetPropNames( (Atom)self [, (bool)includePrivate=False [, (bool)includeComputed=False]]) -> _vectSs :
        Returns a list of the properties set on the Atom.

        C++ signature :
            std::vector<std::string, std::allocator<std::string> > GetPropNames(RDKit::Atom {lvalue} [,bool=False [,bool=False]])

### GetPropsAsDict(...) |
    GetPropsAsDict( (Atom)self [, (bool)includePrivate=True [, (bool)includeComputed=True]]) -> dict :
        Returns a dictionary of the properties set on the Atom.
         n.b. some properties cannot be converted to python types.

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

### GetSmarts(...) |
    GetSmarts( (Atom)arg1) -> str :
        returns the SMARTS (or SMILES) string for an Atom

        C++ signature :
            std::string GetSmarts(RDKit::Atom const*)

### GetSymbol(...) |
    GetSymbol( (Atom)arg1) -> str :
        Returns the atomic symbol (a string)

        C++ signature :
            std::string GetSymbol(RDKit::Atom {lvalue})

### GetTotalDegree(...) |
    GetTotalDegree( (Atom)arg1) -> 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(...) |
    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(...) |
    GetTotalValence( (Atom)arg1) -> int :
        Returns the total valence (explicit + implicit) of the atom.

        C++ signature :
            unsigned int GetTotalValence(RDKit::Atom {lvalue})

### GetUnsignedProp(...) |
    GetUnsignedProp( (Atom)arg1, (str)arg2) -> int :
        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 :
            unsigned int GetUnsignedProp(RDKit::Atom*,char const*)

### HasProp(...) |
    HasProp( (Atom)arg1, (str)arg2) -> 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*,char const*)

### HasQuery(...) |
    HasQuery( (Atom)arg1) -> bool :
        Returns whether or not the atom has an associated query

        C++ signature :
            bool HasQuery(RDKit::Atom {lvalue})

### InvertChirality(...) |
    InvertChirality( (Atom)arg1) -> None :

        C++ signature :
            void InvertChirality(RDKit::Atom {lvalue})

### IsInRing(...) |
    IsInRing( (Atom)arg1) -> bool :
        Returns whether or not the atom is in a ring

        C++ signature :
            bool IsInRing(RDKit::Atom const*)

### IsInRingSize(...) |
    IsInRingSize( (Atom)arg1, (int)arg2) -> 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(...) |
    Match( (Atom)arg1, (Atom)arg2) -> 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*)

### NeedsUpdatePropertyCache(...) |
    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(...) |
    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(...) |
    SetAtomicNum( (Atom)arg1, (int)arg2) -> None :
        Sets the atomic number, takes an integer value as an argument

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

### SetBoolProp(...) |
    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*,char const*,bool)

### SetChiralTag(...) |
    SetChiralTag( (Atom)arg1, (ChiralType)arg2) -> None :

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

### SetDoubleProp(...) |
    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*,char const*,double)

### SetFormalCharge(...) |
    SetFormalCharge( (Atom)arg1, (int)arg2) -> None :

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

### SetHybridization(...) |
    SetHybridization( (Atom)arg1, (HybridizationType)arg2) -> None :
        Sets the hybridization of the atom.
          The argument should be a HybridizationType

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

### SetIntProp(...) |
    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*,char const*,int)

### SetIsAromatic(...) |
    SetIsAromatic( (Atom)arg1, (bool)arg2) -> None :

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

### SetIsotope(...) |
    SetIsotope( (Atom)arg1, (int)arg2) -> None :

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

### SetMonomerInfo(...) |
    SetMonomerInfo( (Atom)arg1, (AtomMonomerInfo)arg2) -> None :
        Sets the atom's MonomerInfo object.

        C++ signature :
            void SetMonomerInfo(RDKit::Atom*,RDKit::AtomMonomerInfo const*)

### SetNoImplicit(...) |
    SetNoImplicit( (Atom)arg1, (bool)arg2) -> 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(...) |
    SetNumExplicitHs( (Atom)arg1, (int)arg2) -> None :

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

### SetNumRadicalElectrons(...) |
    SetNumRadicalElectrons( (Atom)arg1, (int)arg2) -> None :

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

### SetProp(...) |
    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*,char const*,std::string)

### SetUnsignedProp(...) |
    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*,char const*,unsigned int)

### UpdatePropertyCache(...) |
    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])

### __init__(...) (Constructor) |
    __init__( (object)arg1, (str)arg2) -> None :

        C++ signature :
            void __init__(_object*,std::string)

    __init__( (object)arg1, (int)arg2) -> None :
        Constructor, takes either an int (atomic number) or a string (atomic symbol).

        C++ signature :
            void __init__(_object*,unsigned int)
Overrides: object.__init__

### __reduce__(...) |
    helper for pickle
Overrides: object.__reduce__ (inherited documentation)