Package rdkit :: Package Chem :: Module rdchem :: Class Atom
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Class Atom

 object --+    
          |    
??.instance --+
              |
             Atom
Known Subclasses:

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.
 
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 :
 
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) -> _vectSs : Returns a list 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.
 
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 :
 
SetIsotope(...)
SetIsotope( (Atom)arg1, (int)arg2) -> None :
 
SetMass(...)
SetMass( (Atom)arg1, (float)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
 
__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__ = 112
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*)

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, but is dependent
        on whether or not Hs are explicit in the graph.
    

    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})

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 const*,char const*)

GetPropNames(...)

 

GetPropNames( (Atom)self) -> _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})

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})

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)

SetIsotope(...)

 

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

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

SetMass(...)

 

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

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

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)

__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)