rdkit.Chem.rdChemReactions

Package rdkit :: Package Chem :: Module rdChemReactions |
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# Module rdChemReactions

    Module containing classes and functions for working with chemical reactions.

Classes | [hide private]
| ChemicalReaction A class for storing and applying chemical reactions.
| FingerprintType
| ROMolList
| ReactionFingerprintParams A class for storing parameters to manipulate the calculation of fingerprints of chemical reactions.

Functions | [hide private]
Compute2DCoordsForReaction(...) Compute2DCoordsForReaction( (ChemicalReaction)reaction [, (float)spacing=2.0 [, (bool)updateProps=True [, (bool)canonOrient=True [, (int)nFlipsPerSample=0 [, (int)nSample=0 [, (int)sampleSeed=0 [, (bool)permuteDeg4Nodes=False [, (float)bondLength=-1.0]]]]]]]]) -> None : Compute 2D coordinates for a reaction. |
CreateDifferenceFingerprintForReaction(...) CreateDifferenceFingerprintForReaction( (ChemicalReaction)reaction [, (ReactionFingerprintParams)ReactionFingerPrintParams=<rdkit.Chem.rdChemReactions.ReactionFingerprintParams object at 0x7f6ae1fe5380>]) -> UIntSparseIntVect : construct a difference fingerprint for a ChemicalReaction by subtracting the reactant fingerprint from the product fingerprint |
CreateStructuralFingerprintForReaction(...) CreateStructuralFingerprintForReaction( (ChemicalReaction)reaction [, (ReactionFingerprintParams)ReactionFingerPrintParams=<rdkit.Chem.rdChemReactions.ReactionFingerprintParams object at 0x7f6ae1fe5408>]) -> ExplicitBitVect : construct a structural fingerprint for a ChemicalReaction by concatenating the reactant fingerprint and the product fingerprint |
HasAgentTemplateSubstructMatch(...) HasAgentTemplateSubstructMatch( (ChemicalReaction)reaction, (ChemicalReaction)queryReaction) -> bool : tests if the agents of a queryReaction are the same as those of a reaction |
HasProductTemplateSubstructMatch(...) HasProductTemplateSubstructMatch( (ChemicalReaction)reaction, (ChemicalReaction)queryReaction) -> bool : tests if the products of a queryReaction are substructures of the products of a reaction |
HasReactantTemplateSubstructMatch(...) HasReactantTemplateSubstructMatch( (ChemicalReaction)reaction, (ChemicalReaction)queryReaction) -> bool : tests if the reactants of a queryReaction are substructures of the reactants of a reaction |
HasReactionAtomMapping(...) HasReactionAtomMapping( (ChemicalReaction)arg1) -> bool : tests if a reaction obtains any atom mapping |
HasReactionSubstructMatch(...) HasReactionSubstructMatch( (ChemicalReaction)reaction, (ChemicalReaction)queryReaction [, (bool)includeAgents=False]) -> bool : tests if the queryReaction is a substructure of a reaction |
IsReactionTemplateMoleculeAgent(...) IsReactionTemplateMoleculeAgent( (Mol)molecule, (float)agentThreshold) -> bool : tests if a molecule can be classified as an agent depending on the ratio of mapped atoms and a give threshold |
ReactionFromMolecule(...) ReactionFromMolecule( (Mol)arg1) -> ChemicalReaction : construct a ChemicalReaction from an molecule if the RXN role property of the molecule is set |
ReactionFromRxnBlock(...) ReactionFromRxnBlock( (str)arg1) -> ChemicalReaction : construct a ChemicalReaction from an string in MDL rxn format |
ReactionFromRxnFile(...) ReactionFromRxnFile( (str)arg1) -> ChemicalReaction : construct a ChemicalReaction from an MDL rxn file |
ReactionFromSmarts(...) ReactionFromSmarts( (str)SMARTS [, (dict)replacements={} [, (bool)useSmiles=False]]) -> ChemicalReaction : construct a ChemicalReaction from a reaction SMARTS string. |
ReactionToMolecule(...) ReactionToMolecule( (ChemicalReaction)reaction) -> Mol : construct a molecule for a ChemicalReaction with RXN role property set |
ReactionToRxnBlock(...) ReactionToRxnBlock( (ChemicalReaction)reaction [, (bool)separateAgents=False]) -> str : construct a string in MDL rxn format for a ChemicalReaction |
ReactionToSmarts(...) ReactionToSmarts( (ChemicalReaction)reaction) -> str : construct a reaction SMARTS string for a ChemicalReaction |
ReactionToSmiles(...) ReactionToSmiles( (ChemicalReaction)reaction [, (bool)canonical=True]) -> str : construct a reaction SMILES string for a ChemicalReaction |
ReduceProductToSideChains(...) ReduceProductToSideChains( (Mol)product [, (bool)addDummyAtoms=True]) -> Mol : reduce the product of a reaction to the side chains added by the reaction. |
RemoveMappingNumbersFromReactions(...) RemoveMappingNumbersFromReactions( (ChemicalReaction)reaction) -> None : Removes the mapping numbers from the molecules of a reaction |
UpdateProductsStereochemistry(...) UpdateProductsStereochemistry( (ChemicalReaction)reaction) -> None : Caution: This is an expert-user function which will change a property (molInversionFlag) of your products. |

Variables | [hide private]
| __package__ = `None` hash(x)

Function Details | [hide private]

### Compute2DCoordsForReaction(...) |
    Compute2DCoordsForReaction( (ChemicalReaction)reaction [, (float)spacing=2.0 [, (bool)updateProps=True [, (bool)canonOrient=True [, (int)nFlipsPerSample=0 [, (int)nSample=0 [, (int)sampleSeed=0 [, (bool)permuteDeg4Nodes=False [, (float)bondLength=-1.0]]]]]]]]) -> None :
        Compute 2D coordinates for a reaction.
          ARGUMENTS:

             reaction - the reaction of interest
             spacing - the amount of space left between components of the reaction
             canonOrient - orient the reactants and products in a canonical way
             updateProps - if set, properties such as conjugation and
                hybridization will be calculated for the reactant and product
                templates before generating coordinates. This should result in
                better depictions, but can lead to errors in some cases.
             nFlipsPerSample - number of rotatable bonds that are
                        flipped at random at a time.
             nSample - Number of random samplings of rotatable bonds.
             sampleSeed - seed for the random sampling process.
             permuteDeg4Nodes - allow permutation of bonds at a degree 4
                         node during the sampling process
             bondLength - change the default bond length for depiction

        C++ signature :
            void Compute2DCoordsForReaction(RDKit::ChemicalReaction {lvalue} [,double=2.0 [,bool=True [,bool=True [,unsigned int=0 [,unsigned int=0 [,int=0 [,bool=False [,double=-1.0]]]]]]]])

### CreateDifferenceFingerprintForReaction(...) |
    CreateDifferenceFingerprintForReaction( (ChemicalReaction)reaction [, (ReactionFingerprintParams)ReactionFingerPrintParams=<rdkit.Chem.rdChemReactions.ReactionFingerprintParams object at 0x7f6ae1fe5380>]) -> UIntSparseIntVect :
        construct a difference fingerprint for a ChemicalReaction by subtracting the reactant fingerprint from the product fingerprint

        C++ signature :
            RDKit::SparseIntVect<unsigned int>* CreateDifferenceFingerprintForReaction(RDKit::ChemicalReaction [,RDKit::ReactionFingerprintParams=<rdkit.Chem.rdChemReactions.ReactionFingerprintParams object at 0x7f6ae1fe5380>])

### CreateStructuralFingerprintForReaction(...) |
    CreateStructuralFingerprintForReaction( (ChemicalReaction)reaction [, (ReactionFingerprintParams)ReactionFingerPrintParams=<rdkit.Chem.rdChemReactions.ReactionFingerprintParams object at 0x7f6ae1fe5408>]) -> ExplicitBitVect :
        construct a structural fingerprint for a ChemicalReaction by concatenating the reactant fingerprint and the product fingerprint

        C++ signature :
            ExplicitBitVect* CreateStructuralFingerprintForReaction(RDKit::ChemicalReaction [,RDKit::ReactionFingerprintParams=<rdkit.Chem.rdChemReactions.ReactionFingerprintParams object at 0x7f6ae1fe5408>])

### HasAgentTemplateSubstructMatch(...) |
    HasAgentTemplateSubstructMatch( (ChemicalReaction)reaction, (ChemicalReaction)queryReaction) -> bool :
        tests if the agents of a queryReaction are the same as those of a reaction

        C++ signature :
            bool HasAgentTemplateSubstructMatch(RDKit::ChemicalReaction,RDKit::ChemicalReaction)

### HasProductTemplateSubstructMatch(...) |
    HasProductTemplateSubstructMatch( (ChemicalReaction)reaction, (ChemicalReaction)queryReaction) -> bool :
        tests if the products of a queryReaction are substructures of the products of a reaction

        C++ signature :
            bool HasProductTemplateSubstructMatch(RDKit::ChemicalReaction,RDKit::ChemicalReaction)

### HasReactantTemplateSubstructMatch(...) |
    HasReactantTemplateSubstructMatch( (ChemicalReaction)reaction, (ChemicalReaction)queryReaction) -> bool :
        tests if the reactants of a queryReaction are substructures of the reactants of a reaction

        C++ signature :
            bool HasReactantTemplateSubstructMatch(RDKit::ChemicalReaction,RDKit::ChemicalReaction)

### HasReactionAtomMapping(...) |
    HasReactionAtomMapping( (ChemicalReaction)arg1) -> bool :
        tests if a reaction obtains any atom mapping

        C++ signature :
            bool HasReactionAtomMapping(RDKit::ChemicalReaction)

### HasReactionSubstructMatch(...) |
    HasReactionSubstructMatch( (ChemicalReaction)reaction, (ChemicalReaction)queryReaction [, (bool)includeAgents=False]) -> bool :
        tests if the queryReaction is a substructure of a reaction

        C++ signature :
            bool HasReactionSubstructMatch(RDKit::ChemicalReaction,RDKit::ChemicalReaction [,bool=False])

### IsReactionTemplateMoleculeAgent(...) |
    IsReactionTemplateMoleculeAgent( (Mol)molecule, (float)agentThreshold) -> bool :
        tests if a molecule can be classified as an agent depending on the ratio of mapped atoms and a give threshold

        C++ signature :
            bool IsReactionTemplateMoleculeAgent(RDKit::ROMol,double)

### ReactionFromMolecule(...) |
    ReactionFromMolecule( (Mol)arg1) -> ChemicalReaction :
        construct a ChemicalReaction from an molecule if the RXN role property of the molecule is set

        C++ signature :
            RDKit::ChemicalReaction* ReactionFromMolecule(RDKit::ROMol)

### ReactionFromRxnBlock(...) |
    ReactionFromRxnBlock( (str)arg1) -> ChemicalReaction :
        construct a ChemicalReaction from an string in MDL rxn format

        C++ signature :
            RDKit::ChemicalReaction* ReactionFromRxnBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

### ReactionFromRxnFile(...) |
    ReactionFromRxnFile( (str)arg1) -> ChemicalReaction :
        construct a ChemicalReaction from an MDL rxn file

        C++ signature :
            RDKit::ChemicalReaction* ReactionFromRxnFile(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

### ReactionFromSmarts(...) |
    ReactionFromSmarts( (str)SMARTS [, (dict)replacements={} [, (bool)useSmiles=False]]) -> ChemicalReaction :
        construct a ChemicalReaction from a reaction SMARTS string.
        see the documentation for rdkit.Chem.MolFromSmiles for an explanation
        of the replacements argument.

        C++ signature :
            RDKit::ChemicalReaction* ReactionFromSmarts(char const* [,boost::python::dict={} [,bool=False]])

### ReactionToMolecule(...) |
    ReactionToMolecule( (ChemicalReaction)reaction) -> Mol :
        construct a molecule for a ChemicalReaction with RXN role property set

        C++ signature :
            RDKit::ROMol* ReactionToMolecule(RDKit::ChemicalReaction)

### ReactionToRxnBlock(...) |
    ReactionToRxnBlock( (ChemicalReaction)reaction [, (bool)separateAgents=False]) -> str :
        construct a string in MDL rxn format for a ChemicalReaction

        C++ signature :
            std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > ReactionToRxnBlock(RDKit::ChemicalReaction [,bool=False])

### ReactionToSmarts(...) |
    ReactionToSmarts( (ChemicalReaction)reaction) -> str :
        construct a reaction SMARTS string for a ChemicalReaction

        C++ signature :
            std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > ReactionToSmarts(RDKit::ChemicalReaction)

### ReactionToSmiles(...) |
    ReactionToSmiles( (ChemicalReaction)reaction [, (bool)canonical=True]) -> str :
        construct a reaction SMILES string for a ChemicalReaction

        C++ signature :
            std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > ReactionToSmiles(RDKit::ChemicalReaction [,bool=True])

### ReduceProductToSideChains(...) |
    ReduceProductToSideChains( (Mol)product [, (bool)addDummyAtoms=True]) -> Mol :
        reduce the product of a reaction to the side chains added by the reaction.              The output is a molecule with attached wildcards indicating where the product was attached.              The dummy atom has the same reaction-map number as the product atom (if available).

        C++ signature :
            RDKit::ROMol* ReduceProductToSideChains(boost::shared_ptr<RDKit::ROMol> [,bool=True])

### RemoveMappingNumbersFromReactions(...) |
    RemoveMappingNumbersFromReactions( (ChemicalReaction)reaction) -> None :
        Removes the mapping numbers from the molecules of a reaction

        C++ signature :
            void RemoveMappingNumbersFromReactions(RDKit::ChemicalReaction)

### UpdateProductsStereochemistry(...) |
    UpdateProductsStereochemistry( (ChemicalReaction)reaction) -> None :
        Caution: This is an expert-user function which will change a property (molInversionFlag) of your products.          This function is called by default using the RXN or SMARTS parser for reactions and should really only be called if reactions have been constructed some other way.          The function updates the stereochemistry of the product by considering 4 different cases: inversion, retention, removal, and introduction

        C++ signature :
            void UpdateProductsStereochemistry(RDKit::ChemicalReaction*)