Package rdkit :: Package Chem :: Module rdChemReactions :: Class ChemicalReaction

class ChemicalReaction

 object --+    
          |    
??.instance --+
              |
             ChemicalReaction

A class for storing and applying chemical reactions.

Sample Usage:
>>> rxn = rdChemReactions.ReactionFromSmarts('[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]')
>>> reacts = (Chem.MolFromSmiles('C(=O)O'),Chem.MolFromSmiles('CNC'))
>>> products = rxn.RunReactants(reacts)
>>> len(products)
1
>>> len(products[0])
1
>>> Chem.MolToSmiles(products[0])
'CN(C)C=O'

Instance Methods

[hide private]

AddAgentTemplate(...)
AddAgentTemplate( (ChemicalReaction)arg1, (Mol)arg2) -> int : adds a agent (a Molecule)

AddProductTemplate(...)
AddProductTemplate( (ChemicalReaction)arg1, (Mol)arg2) -> int : adds a product (a Molecule)

AddReactantTemplate(...)
AddReactantTemplate( (ChemicalReaction)arg1, (Mol)arg2) -> int : adds a reactant (a Molecule) to the reaction

AddRecursiveQueriesToReaction(...)
AddRecursiveQueriesToReaction( (ChemicalReaction)reaction [, (dict)queries={} [, (str)propName='molFileValue' [, (bool)getLabels=False]]]) -> object : adds recursive queries and returns reactant labels

GetAgentTemplate(...)
GetAgentTemplate( (ChemicalReaction)self, (int)which) -> Mol : returns one of our agent templates

GetAgents(...)
GetAgents( (ChemicalReaction)arg1) -> ROMolList : get the agent templates

GetNumAgentTemplates(...)
GetNumAgentTemplates( (ChemicalReaction)arg1) -> int : returns the number of agents this reaction expects

GetNumProductTemplates(...)
GetNumProductTemplates( (ChemicalReaction)arg1) -> int : returns the number of products this reaction generates

GetNumReactantTemplates(...)
GetNumReactantTemplates( (ChemicalReaction)arg1) -> int : returns the number of reactants this reaction expects

GetProductTemplate(...)
GetProductTemplate( (ChemicalReaction)self, (int)which) -> Mol : returns one of our product templates

GetProducts(...)
GetProducts( (ChemicalReaction)arg1) -> ROMolList : get the product templates

GetReactantTemplate(...)
GetReactantTemplate( (ChemicalReaction)self, (int)which) -> Mol : returns one of our reactant templates

GetReactants(...)
GetReactants( (ChemicalReaction)arg1) -> ROMolList : get the reactant templates

GetReactingAtoms(...)
GetReactingAtoms( (ChemicalReaction)self [, (bool)mappedAtomsOnly=False]) -> object : returns a sequence of sequences with the atoms that change in the reaction

Initialize(...)
Initialize( (ChemicalReaction)arg1) -> None : initializes the reaction so that it can be used

IsInitialized(...)
IsInitialized( (ChemicalReaction)arg1) -> bool : checks if the reaction is ready for use

IsMoleculeAgent(...)
IsMoleculeAgent( (ChemicalReaction)arg1, (Mol)arg2) -> bool : returns whether or not the molecule has a substructure match to one of the agents.

IsMoleculeProduct(...)
IsMoleculeProduct( (ChemicalReaction)arg1, (Mol)arg2) -> bool : returns whether or not the molecule has a substructure match to one of the products.

IsMoleculeReactant(...)
IsMoleculeReactant( (ChemicalReaction)arg1, (Mol)arg2) -> bool : returns whether or not the molecule has a substructure match to one of the reactants.

RemoveAgentTemplates(...)
RemoveAgentTemplates( (ChemicalReaction)self [, (AtomPairsParameters)targetList=None]) -> None : Removes agents from reaction.

RemoveUnmappedProductTemplates(...)
RemoveUnmappedProductTemplates( (ChemicalReaction)self [, (float)thresholdUnmappedAtoms=0.2 [, (bool)moveToAgentTemplates=True [, (AtomPairsParameters)targetList=None]]]) -> None : Removes molecules with an atom mapping ratio below thresholdUnmappedAtoms from product templates to the agent templates or to a given targetList

RemoveUnmappedReactantTemplates(...)
RemoveUnmappedReactantTemplates( (ChemicalReaction)self [, (float)thresholdUnmappedAtoms=0.2 [, (bool)moveToAgentTemplates=True [, (AtomPairsParameters)targetList=None]]]) -> None : Removes molecules with an atom mapping ratio below thresholdUnmappedAtoms from reactant templates to the agent templates or to a given targetList

RunReactant(...)
RunReactant( (ChemicalReaction)arg1, (AtomPairsParameters)arg2, (int)arg3) -> object : apply the reaction to a single reactant

RunReactants(...)
RunReactants( (ChemicalReaction)arg1, (tuple)arg2) -> object : apply the reaction to a sequence of reactant molecules and return the products as a tuple of tuples

ToBinary(...)
ToBinary( (ChemicalReaction)arg1) -> object : Returns a binary string representation of the reaction.

Validate(...)
Validate( (ChemicalReaction)self [, (bool)silent=False]) -> tuple : checks the reaction for potential problems, returns (numWarnings,numErrors)

__getinitargs__(...)
__getinitargs__( (ChemicalReaction)arg1) -> tuple :

__init__(...)
__init__( (object)arg1) -> None : Constructor, takes no arguments

__reduce__(...)

_getImplicitPropertiesFlag(...)
_getImplicitPropertiesFlag( (ChemicalReaction)self) -> bool : EXPERT USER: returns whether or not the reaction can have implicit properties

_setImplicitPropertiesFlag(...)
_setImplicitPropertiesFlag( (ChemicalReaction)self, (bool)val) -> None : EXPERT USER: indicates that the reaction can have implicit properties

Inherited from unreachable.instance: __new__

Class Variables

[hide private]

__instance_size__ = 96

__safe_for_unpickling__ = True

Method Details

[hide private]

AddAgentTemplate(...)


AddAgentTemplate( (ChemicalReaction)arg1, (Mol)arg2) -> int :
    adds a agent (a Molecule)

    C++ signature :
        unsigned int AddAgentTemplate(RDKit::ChemicalReaction {lvalue},boost::shared_ptr<RDKit::ROMol>)

AddProductTemplate(...)


AddProductTemplate( (ChemicalReaction)arg1, (Mol)arg2) -> int :
    adds a product (a Molecule)

    C++ signature :
        unsigned int AddProductTemplate(RDKit::ChemicalReaction {lvalue},boost::shared_ptr<RDKit::ROMol>)

AddReactantTemplate(...)


AddReactantTemplate( (ChemicalReaction)arg1, (Mol)arg2) -> int :
    adds a reactant (a Molecule) to the reaction

    C++ signature :
        unsigned int AddReactantTemplate(RDKit::ChemicalReaction {lvalue},boost::shared_ptr<RDKit::ROMol>)

AddRecursiveQueriesToReaction(...)


AddRecursiveQueriesToReaction( (ChemicalReaction)reaction [, (dict)queries={} [, (str)propName='molFileValue' [, (bool)getLabels=False]]]) -> object :
    adds recursive queries and returns reactant labels

    C++ signature :
        boost::python::api::object AddRecursiveQueriesToReaction(RDKit::ChemicalReaction {lvalue} [,boost::python::dict={} [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >='molFileValue' [,bool=False]]])

GetAgentTemplate(...)


GetAgentTemplate( (ChemicalReaction)self, (int)which) -> Mol :
    returns one of our agent templates

    C++ signature :
        RDKit::ROMol* GetAgentTemplate(RDKit::ChemicalReaction const*,unsigned int)

GetAgents(...)


GetAgents( (ChemicalReaction)arg1) -> ROMolList :
    get the agent templates

    C++ signature :
        std::vector<boost::shared_ptr<RDKit::ROMol>, std::allocator<boost::shared_ptr<RDKit::ROMol> > > GetAgents(RDKit::ChemicalReaction {lvalue})

GetNumAgentTemplates(...)


GetNumAgentTemplates( (ChemicalReaction)arg1) -> int :
    returns the number of agents this reaction expects

    C++ signature :
        unsigned int GetNumAgentTemplates(RDKit::ChemicalReaction {lvalue})

GetNumProductTemplates(...)


GetNumProductTemplates( (ChemicalReaction)arg1) -> int :
    returns the number of products this reaction generates

    C++ signature :
        unsigned int GetNumProductTemplates(RDKit::ChemicalReaction {lvalue})

GetNumReactantTemplates(...)


GetNumReactantTemplates( (ChemicalReaction)arg1) -> int :
    returns the number of reactants this reaction expects

    C++ signature :
        unsigned int GetNumReactantTemplates(RDKit::ChemicalReaction {lvalue})

GetProductTemplate(...)


GetProductTemplate( (ChemicalReaction)self, (int)which) -> Mol :
    returns one of our product templates

    C++ signature :
        RDKit::ROMol* GetProductTemplate(RDKit::ChemicalReaction const*,unsigned int)

GetProducts(...)


GetProducts( (ChemicalReaction)arg1) -> ROMolList :
    get the product templates

    C++ signature :
        std::vector<boost::shared_ptr<RDKit::ROMol>, std::allocator<boost::shared_ptr<RDKit::ROMol> > > GetProducts(RDKit::ChemicalReaction {lvalue})

GetReactantTemplate(...)


GetReactantTemplate( (ChemicalReaction)self, (int)which) -> Mol :
    returns one of our reactant templates

    C++ signature :
        RDKit::ROMol* GetReactantTemplate(RDKit::ChemicalReaction const*,unsigned int)

GetReactants(...)


GetReactants( (ChemicalReaction)arg1) -> ROMolList :
    get the reactant templates

    C++ signature :
        std::vector<boost::shared_ptr<RDKit::ROMol>, std::allocator<boost::shared_ptr<RDKit::ROMol> > > GetReactants(RDKit::ChemicalReaction {lvalue})

GetReactingAtoms(...)


GetReactingAtoms( (ChemicalReaction)self [, (bool)mappedAtomsOnly=False]) -> object :
    returns a sequence of sequences with the atoms that change in the reaction

    C++ signature :
        boost::python::api::object GetReactingAtoms(RDKit::ChemicalReaction [,bool=False])

Initialize(...)


Initialize( (ChemicalReaction)arg1) -> None :
    initializes the reaction so that it can be used

    C++ signature :
        void Initialize(RDKit::ChemicalReaction {lvalue})

IsInitialized(...)


IsInitialized( (ChemicalReaction)arg1) -> bool :
    checks if the reaction is ready for use

    C++ signature :
        bool IsInitialized(RDKit::ChemicalReaction {lvalue})

IsMoleculeAgent(...)


IsMoleculeAgent( (ChemicalReaction)arg1, (Mol)arg2) -> bool :
    returns whether or not the molecule has a substructure match to one of the agents.

    C++ signature :
        bool IsMoleculeAgent(RDKit::ChemicalReaction,RDKit::ROMol)

IsMoleculeProduct(...)


IsMoleculeProduct( (ChemicalReaction)arg1, (Mol)arg2) -> bool :
    returns whether or not the molecule has a substructure match to one of the products.

    C++ signature :
        bool IsMoleculeProduct(RDKit::ChemicalReaction,RDKit::ROMol)

IsMoleculeReactant(...)


IsMoleculeReactant( (ChemicalReaction)arg1, (Mol)arg2) -> bool :
    returns whether or not the molecule has a substructure match to one of the reactants.

    C++ signature :
        bool IsMoleculeReactant(RDKit::ChemicalReaction,RDKit::ROMol)

RemoveAgentTemplates(...)


RemoveAgentTemplates( (ChemicalReaction)self [, (AtomPairsParameters)targetList=None]) -> None :
    Removes agents from reaction. If targetList is provide the agents will be transfered to that list.

    C++ signature :
        void RemoveAgentTemplates(RDKit::ChemicalReaction {lvalue} [,boost::python::api::object=None])

RemoveUnmappedProductTemplates(...)


RemoveUnmappedProductTemplates( (ChemicalReaction)self [, (float)thresholdUnmappedAtoms=0.2 [, (bool)moveToAgentTemplates=True [, (AtomPairsParameters)targetList=None]]]) -> None :
    Removes molecules with an atom mapping ratio below thresholdUnmappedAtoms from product templates to the agent templates or to a given targetList

    C++ signature :
        void RemoveUnmappedProductTemplates(RDKit::ChemicalReaction* [,double=0.2 [,bool=True [,boost::python::api::object=None]]])

RemoveUnmappedReactantTemplates(...)


RemoveUnmappedReactantTemplates( (ChemicalReaction)self [, (float)thresholdUnmappedAtoms=0.2 [, (bool)moveToAgentTemplates=True [, (AtomPairsParameters)targetList=None]]]) -> None :
    Removes molecules with an atom mapping ratio below thresholdUnmappedAtoms from reactant templates to the agent templates or to a given targetList

    C++ signature :
        void RemoveUnmappedReactantTemplates(RDKit::ChemicalReaction* [,double=0.2 [,bool=True [,boost::python::api::object=None]]])

RunReactant(...)


RunReactant( (ChemicalReaction)arg1, (AtomPairsParameters)arg2, (int)arg3) -> object :
    apply the reaction to a single reactant

    C++ signature :
        _object* RunReactant(RDKit::ChemicalReaction*,boost::python::api::object,unsigned int)

RunReactants(...)


RunReactants( (ChemicalReaction)arg1, (tuple)arg2) -> object :
    apply the reaction to a sequence of reactant molecules and return the products as a tuple of tuples

    C++ signature :
        _object* RunReactants(RDKit::ChemicalReaction*,boost::python::tuple)

RunReactants( (ChemicalReaction)arg1, (list)arg2) -> object :
    apply the reaction to a sequence of reactant molecules and return the products as a tuple of tuples

    C++ signature :
        _object* RunReactants(RDKit::ChemicalReaction*,boost::python::list)

ToBinary(...)


ToBinary( (ChemicalReaction)arg1) -> object :
    Returns a binary string representation of the reaction.

    C++ signature :
        boost::python::api::object ToBinary(RDKit::ChemicalReaction)

Validate(...)


Validate( (ChemicalReaction)self [, (bool)silent=False]) -> tuple :
    checks the reaction for potential problems, returns (numWarnings,numErrors)

    C++ signature :
        boost::python::tuple Validate(RDKit::ChemicalReaction const* [,bool=False])

getinitargs(...)


__getinitargs__( (ChemicalReaction)arg1) -> tuple :

    C++ signature :
        boost::python::tuple __getinitargs__(RDKit::ChemicalReaction)

init(...)
(Constructor)


__init__( (object)arg1) -> None :
    Constructor, takes no arguments

    C++ signature :
        void __init__(_object*)

__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, (ChemicalReaction)arg2) -> None :

    C++ signature :
        void __init__(_object*,RDKit::ChemicalReaction)

Overrides: object.__init__

reduce(...)

Overrides: object.__reduce__: (inherited documentation)

_getImplicitPropertiesFlag(...)


_getImplicitPropertiesFlag( (ChemicalReaction)self) -> bool :
    EXPERT USER: returns whether or not the reaction can have implicit properties

    C++ signature :
        bool _getImplicitPropertiesFlag(RDKit::ChemicalReaction {lvalue})

_setImplicitPropertiesFlag(...)


_setImplicitPropertiesFlag( (ChemicalReaction)self, (bool)val) -> None :
    EXPERT USER: indicates that the reaction can have implicit properties

    C++ signature :
        void _setImplicitPropertiesFlag(RDKit::ChemicalReaction {lvalue},bool)

class ChemicalReaction

AddAgentTemplate(...)

AddProductTemplate(...)

AddReactantTemplate(...)

AddRecursiveQueriesToReaction(...)

GetAgentTemplate(...)

GetAgents(...)

GetNumAgentTemplates(...)

GetNumProductTemplates(...)

GetNumReactantTemplates(...)

GetProductTemplate(...)

GetProducts(...)

GetReactantTemplate(...)

GetReactants(...)

GetReactingAtoms(...)

Initialize(...)

IsInitialized(...)

IsMoleculeAgent(...)

IsMoleculeProduct(...)

IsMoleculeReactant(...)

RemoveAgentTemplates(...)

RemoveUnmappedProductTemplates(...)

RemoveUnmappedReactantTemplates(...)

RunReactant(...)

RunReactants(...)

ToBinary(...)

Validate(...)

__getinitargs__(...)

__init__(...) (Constructor)

__reduce__(...)

_getImplicitPropertiesFlag(...)

_setImplicitPropertiesFlag(...)

getinitargs(...)

init(...)
(Constructor)

reduce(...)