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object --+
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??.instance --+
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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.
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Inherited from |
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__instance_size__ = 64
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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*)
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DescribeQuery( (Atom)arg1) -> 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*)
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GetAtomicNum( (Atom)arg1) -> int :
Returns the atomic number.
C++ signature :
int GetAtomicNum(RDKit::Atom {lvalue})
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GetBonds( (Atom)arg1) -> tuple :
Returns a read-only sequence of the atom's bonds
C++ signature :
boost::python::tuple GetBonds(RDKit::Atom*)
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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*)
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GetChiralTag( (Atom)arg1) -> ChiralType :
C++ signature :
RDKit::Atom::ChiralType GetChiralTag(RDKit::Atom {lvalue})
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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})
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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*)
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GetExplicitValence( (Atom)arg1) -> int :
Returns the number of explicit Hs on the atom.
C++ signature :
int GetExplicitValence(RDKit::Atom {lvalue})
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GetFormalCharge( (Atom)arg1) -> int :
C++ signature :
int GetFormalCharge(RDKit::Atom {lvalue})
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GetHybridization( (Atom)arg1) -> HybridizationType :
Returns the atom's hybridization.
C++ signature :
RDKit::Atom::HybridizationType GetHybridization(RDKit::Atom {lvalue})
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GetIdx( (Atom)arg1) -> int :
Returns the atom's index (ordering in the molecule)
C++ signature :
unsigned int GetIdx(RDKit::Atom {lvalue})
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GetImplicitValence( (Atom)arg1) -> int :
Returns the number of implicit Hs on the atom.
C++ signature :
int GetImplicitValence(RDKit::Atom {lvalue})
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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*)
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GetIsAromatic( (Atom)arg1) -> bool :
C++ signature :
bool GetIsAromatic(RDKit::Atom {lvalue})
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GetIsotope( (Atom)arg1) -> int :
C++ signature :
unsigned int GetIsotope(RDKit::Atom {lvalue})
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GetMass( (Atom)arg1) -> float :
C++ signature :
double GetMass(RDKit::Atom {lvalue})
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GetMonomerInfo( (Atom)arg1) -> AtomMonomerInfo :
Returns the atom's MonomerInfo object, if there is one.
C++ signature :
RDKit::AtomMonomerInfo* GetMonomerInfo(RDKit::Atom*)
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GetNeighbors( (Atom)arg1) -> tuple :
Returns a read-only sequence of the atom's neighbors
C++ signature :
boost::python::tuple GetNeighbors(RDKit::Atom*)
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GetNoImplicit( (Atom)arg1) -> bool :
Returns whether or not the atom is *allowed* to have implicit Hs.
C++ signature :
bool GetNoImplicit(RDKit::Atom {lvalue})
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GetNumExplicitHs( (Atom)arg1) -> int :
C++ signature :
unsigned int GetNumExplicitHs(RDKit::Atom {lvalue})
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GetNumImplicitHs( (Atom)arg1) -> int :
Returns the total number of implicit Hs on the atom.
C++ signature :
unsigned int GetNumImplicitHs(RDKit::Atom {lvalue})
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GetNumRadicalElectrons( (Atom)arg1) -> int :
C++ signature :
unsigned int GetNumRadicalElectrons(RDKit::Atom {lvalue})
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GetOwningMol( (Atom)arg1) -> Mol :
Returns the Mol that owns this atom.
C++ signature :
RDKit::ROMol {lvalue} GetOwningMol(RDKit::Atom {lvalue})
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GetPDBResidueInfo( (Atom)arg1) -> AtomPDBResidueInfo :
Returns the atom's MonomerInfo object, if there is one.
C++ signature :
RDKit::AtomPDBResidueInfo* GetPDBResidueInfo(RDKit::Atom*)
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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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetProp(RDKit::Atom*,char const*)
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GetPropNames( (Atom)self) -> _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})
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GetPropsAsDict( (Atom)self) -> 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)
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GetSmarts( (Atom)arg1) -> 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*)
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GetSymbol( (Atom)arg1) -> 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})
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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})
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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])
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GetTotalValence( (Atom)arg1) -> int :
Returns the total valence (explicit + implicit) of the atom.
C++ signature :
unsigned int GetTotalValence(RDKit::Atom {lvalue})
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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*)
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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*)
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HasQuery( (Atom)arg1) -> bool :
Returns whether or not the atom has an associated query
C++ signature :
bool HasQuery(RDKit::Atom {lvalue})
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InvertChirality( (Atom)arg1) -> None :
C++ signature :
void InvertChirality(RDKit::Atom {lvalue})
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IsInRing( (Atom)arg1) -> bool :
Returns whether or not the atom is in a ring
C++ signature :
bool IsInRing(RDKit::Atom const*)
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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)
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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*)
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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})
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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)
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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)
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SetChiralTag( (Atom)arg1, (ChiralType)arg2) -> None :
C++ signature :
void SetChiralTag(RDKit::Atom {lvalue},RDKit::Atom::ChiralType)
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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)
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SetFormalCharge( (Atom)arg1, (int)arg2) -> None :
C++ signature :
void SetFormalCharge(RDKit::Atom {lvalue},int)
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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)
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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)
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SetIsAromatic( (Atom)arg1, (bool)arg2) -> None :
C++ signature :
void SetIsAromatic(RDKit::Atom {lvalue},bool)
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SetIsotope( (Atom)arg1, (int)arg2) -> None :
C++ signature :
void SetIsotope(RDKit::Atom {lvalue},unsigned int)
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SetMonomerInfo( (Atom)arg1, (AtomMonomerInfo)arg2) -> None :
Sets the atom's MonomerInfo object.
C++ signature :
void SetMonomerInfo(RDKit::Atom*,RDKit::AtomMonomerInfo const*)
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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)
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SetNumExplicitHs( (Atom)arg1, (int)arg2) -> None :
C++ signature :
void SetNumExplicitHs(RDKit::Atom {lvalue},unsigned int)
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SetNumRadicalElectrons( (Atom)arg1, (int)arg2) -> None :
C++ signature :
void SetNumRadicalElectrons(RDKit::Atom {lvalue},unsigned int)
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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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
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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)
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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])
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__init__( (object)arg1, (str)arg2) -> None :
C++ signature :
void __init__(_object*,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
__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)
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