rdkit.Chem.rdchem.Atom

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

# Class Atom

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

    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]
GetAtomicNum(...) GetAtomicNum( (Atom)arg1) -> int : Returns the atomic number. |
GetBonds(...) GetBonds( (Atom)arg1) -> tuple : Returns a read-only sequence of the atom's bonds |
GetChiralTag(...) GetChiralTag( (Atom)arg1) -> ChiralType : |
GetDegree(...) GetDegree( (Atom)arg1) -> int : Returns the degree of the atom in the molecule. |
GetExplicitValence(...) GetExplicitValence( (Atom)arg1) -> int : Returns the number of explicit Hs on 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. |
GetIsAromatic(...) GetIsAromatic( (Atom)arg1) -> bool : |
GetMass(...) GetMass( (Atom)arg1) -> float : |
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. |
GetProp(...) GetProp( (Atom)arg1, (str)arg2) -> str : Returns the value of the property. |
GetSmarts(...) GetSmarts( (Atom)arg1) -> str : returns the SMARTS (or SMILES) string for an Atom |
GetSymbol(...) GetSymbol( (Atom)arg1) -> str : Returns the atomic number (a string) |
GetTotalNumHs(...) GetTotalNumHs( (Atom)self [, (bool)includeNeighbors=False]) -> int : Returns the total number of Hs (explicit and implicit) on the atom. |
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. |
SetAtomicNum(...) SetAtomicNum( (Atom)arg1, (int)arg2) -> None : Sets the atomic number, takes an integer value as an argument |
SetChiralTag(...) SetChiralTag( (Atom)arg1, (ChiralType)arg2) -> None : |
SetFormalCharge(...) SetFormalCharge( (Atom)arg1, (int)arg2) -> None : |
SetHybridization(...) SetHybridization( (Atom)arg1, (HybridizationType)arg2) -> None : Sets the hybridization of the atom. |
SetIsAromatic(...) SetIsAromatic( (Atom)arg1, (bool)arg2) -> None : |
SetMass(...) SetMass( (Atom)arg1, (float)arg2) -> None : |
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 |
__init__(...) __init__( (object)arg1, (str)arg2) -> None : |
__reduce__(...) helper for pickle |
Inherited from `unreachable.instance`: `__new__` Inherited from `object`: `__delattr__`, `__getattribute__`, `__hash__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__str__`

Class Variables | [hide private]
| __instance_size__ = `72`

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

Method Details | [hide private]

### 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*)

### 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.

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

### GetExplicitValence(...) |
    GetExplicitValence( (Atom)arg1) -> int :
        Returns the number of explicit Hs on 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})

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

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

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

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

### 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})

### 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 const*,char const*)

### 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 number (a string)

        C++ signature :
            std::string GetSymbol(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])

### 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*)

### 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)

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

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

### 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)

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

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

### SetMass(...) |
    SetMass( (Atom)arg1, (float)arg2) -> None :

        C++ signature :
            void SetMass(RDKit::Atom {lvalue},double)

### 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)

### __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)