Trees | Indices | Help |
|
---|
|
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.
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
|
|||
Inherited from Inherited from |
|
|||
__instance_size__ = 40
|
|
|||
Inherited from |
|
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( (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*) |
GetAtomicNum( (Atom)arg1) -> int : Returns the atomic number. C++ signature : int GetAtomicNum(RDKit::Atom {lvalue}) |
GetBonds( (Atom)arg1) -> tuple : Returns a read-only sequence of the atom's bonds C++ signature : boost::python::tuple GetBonds(RDKit::Atom*) |
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( (Atom)arg1) -> ChiralType : C++ signature : RDKit::Atom::ChiralType GetChiralTag(RDKit::Atom {lvalue}) |
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( (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( (Atom)arg1) -> int : Returns the number of explicit Hs on the atom. C++ signature : int GetExplicitValence(RDKit::Atom {lvalue}) |
GetFormalCharge( (Atom)arg1) -> int : C++ signature : int GetFormalCharge(RDKit::Atom {lvalue}) |
GetHybridization( (Atom)arg1) -> HybridizationType : Returns the atom's hybridization. C++ signature : RDKit::Atom::HybridizationType GetHybridization(RDKit::Atom {lvalue}) |
GetIdx( (Atom)arg1) -> int : Returns the atom's index (ordering in the molecule) C++ signature : unsigned int GetIdx(RDKit::Atom {lvalue}) |
GetImplicitValence( (Atom)arg1) -> int : Returns the number of implicit Hs on the atom. C++ signature : int GetImplicitValence(RDKit::Atom {lvalue}) |
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( (Atom)arg1) -> bool : C++ signature : bool GetIsAromatic(RDKit::Atom {lvalue}) |
GetIsotope( (Atom)arg1) -> int : C++ signature : unsigned int GetIsotope(RDKit::Atom {lvalue}) |
GetMass( (Atom)arg1) -> float : C++ signature : double GetMass(RDKit::Atom {lvalue}) |
GetMonomerInfo( (Atom)arg1) -> AtomMonomerInfo : Returns the atom's MonomerInfo object, if there is one. C++ signature : RDKit::AtomMonomerInfo* GetMonomerInfo(RDKit::Atom*) |
GetNeighbors( (Atom)arg1) -> tuple : Returns a read-only sequence of the atom's neighbors C++ signature : boost::python::tuple GetNeighbors(RDKit::Atom*) |
GetNoImplicit( (Atom)arg1) -> bool : Returns whether or not the atom is *allowed* to have implicit Hs. C++ signature : bool GetNoImplicit(RDKit::Atom {lvalue}) |
GetNumExplicitHs( (Atom)arg1) -> int : C++ signature : unsigned int GetNumExplicitHs(RDKit::Atom {lvalue}) |
GetNumImplicitHs( (Atom)arg1) -> int : Returns the total number of implicit Hs on the atom. C++ signature : unsigned int GetNumImplicitHs(RDKit::Atom {lvalue}) |
GetNumRadicalElectrons( (Atom)arg1) -> int : C++ signature : unsigned int GetNumRadicalElectrons(RDKit::Atom {lvalue}) |
GetOwningMol( (Atom)arg1) -> Mol : Returns the Mol that owns this atom. C++ signature : RDKit::ROMol {lvalue} GetOwningMol(RDKit::Atom {lvalue}) |
GetPDBResidueInfo( (Atom)arg1) -> AtomPDBResidueInfo : Returns the atom's MonomerInfo object, if there is one. C++ signature : RDKit::AtomPDBResidueInfo* GetPDBResidueInfo(RDKit::Atom*) |
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*) |
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}) |
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) |
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*) |
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}) |
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( (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)arg1) -> int : Returns the total valence (explicit + implicit) of the atom. C++ signature : unsigned int GetTotalValence(RDKit::Atom {lvalue}) |
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( (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( (Atom)arg1) -> bool : Returns whether or not the atom has an associated query C++ signature : bool HasQuery(RDKit::Atom {lvalue}) |
InvertChirality( (Atom)arg1) -> None : C++ signature : void InvertChirality(RDKit::Atom {lvalue}) |
IsInRing( (Atom)arg1) -> bool : Returns whether or not the atom is in a ring C++ signature : bool IsInRing(RDKit::Atom const*) |
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( (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( (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}) |
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( (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( (Atom)arg1, (ChiralType)arg2) -> 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*,char const*,double) |
SetFormalCharge( (Atom)arg1, (int)arg2) -> None : C++ signature : void SetFormalCharge(RDKit::Atom {lvalue},int) |
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( (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( (Atom)arg1, (bool)arg2) -> None : C++ signature : void SetIsAromatic(RDKit::Atom {lvalue},bool) |
SetIsotope( (Atom)arg1, (int)arg2) -> None : C++ signature : void SetIsotope(RDKit::Atom {lvalue},unsigned int) |
SetMonomerInfo( (Atom)arg1, (AtomMonomerInfo)arg2) -> None : Sets the atom's MonomerInfo object. C++ signature : void SetMonomerInfo(RDKit::Atom*,RDKit::AtomMonomerInfo const*) |
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( (Atom)arg1, (int)arg2) -> None : C++ signature : void SetNumExplicitHs(RDKit::Atom {lvalue},unsigned int) |
SetNumRadicalElectrons( (Atom)arg1, (int)arg2) -> None : C++ signature : void SetNumRadicalElectrons(RDKit::Atom {lvalue},unsigned int) |
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> >) |
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( (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__( (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)
|
helper for pickle
|
Trees | Indices | Help |
|
---|
Generated by Epydoc 3.0.1 on Thu Aug 25 09:59:06 2016 | http://epydoc.sourceforge.net |