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RDKit
Open-source cheminformatics and machine learning.
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This is a class for storing and applying general chemical reactions. More...
#include <Reaction.h>
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ChemicalReaction () | |
ChemicalReaction (const ChemicalReaction &other) | |
ChemicalReaction (const std::string &binStr) | |
construct a reaction from a pickle string More... | |
unsigned int | addReactantTemplate (ROMOL_SPTR mol) |
Adds a new reactant template. More... | |
unsigned int | addAgentTemplate (ROMOL_SPTR mol) |
Adds a new agent template. More... | |
unsigned int | addProductTemplate (ROMOL_SPTR mol) |
Adds a new product template. More... | |
void | removeUnmappedReactantTemplates (double thresholdUnmappedAtoms=0.2, bool moveToAgentTemplates=true, MOL_SPTR_VECT *targetVector=NULL) |
Removes the reactant templates from a reaction if atom mapping ratio is. More... | |
void | removeUnmappedProductTemplates (double thresholdUnmappedAtoms=0.2, bool moveToAgentTemplates=true, MOL_SPTR_VECT *targetVector=NULL) |
Removes the product templates from a reaction if its atom mapping ratio is. More... | |
void | removeAgentTemplates (MOL_SPTR_VECT *targetVector=NULL) |
std::vector< MOL_SPTR_VECT > | runReactants (const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const |
Runs the reaction on a set of reactants. More... | |
std::vector< MOL_SPTR_VECT > | runReactant (ROMOL_SPTR reactant, unsigned int reactantTemplateIdx) const |
Runs a single reactant against a single reactant template. More... | |
const MOL_SPTR_VECT & | getReactants () const |
const MOL_SPTR_VECT & | getAgents () const |
const MOL_SPTR_VECT & | getProducts () const |
MOL_SPTR_VECT::const_iterator | beginReactantTemplates () const |
MOL_SPTR_VECT::const_iterator | endReactantTemplates () const |
MOL_SPTR_VECT::const_iterator | beginProductTemplates () const |
MOL_SPTR_VECT::const_iterator | endProductTemplates () const |
MOL_SPTR_VECT::const_iterator | beginAgentTemplates () const |
MOL_SPTR_VECT::const_iterator | endAgentTemplates () const |
MOL_SPTR_VECT::iterator | beginReactantTemplates () |
MOL_SPTR_VECT::iterator | endReactantTemplates () |
MOL_SPTR_VECT::iterator | beginProductTemplates () |
MOL_SPTR_VECT::iterator | endProductTemplates () |
MOL_SPTR_VECT::iterator | beginAgentTemplates () |
MOL_SPTR_VECT::iterator | endAgentTemplates () |
unsigned int | getNumReactantTemplates () const |
unsigned int | getNumProductTemplates () const |
unsigned int | getNumAgentTemplates () const |
void | initReactantMatchers () |
initializes our internal reactant-matching datastructures. More... | |
bool | isInitialized () const |
bool | validate (unsigned int &numWarnings, unsigned int &numErrors, bool silent=false) const |
validates the reactants and products to make sure the reaction seems More... | |
bool | getImplicitPropertiesFlag () const |
void | setImplicitPropertiesFlag (bool val) |
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RDProps () | |
RDProps (const RDProps &rhs) | |
RDProps & | operator= (const RDProps &rhs) |
void | clear () |
const Dict & | getDict () const |
gets the underlying Dictionary More... | |
Dict & | getDict () |
STR_VECT | getPropList (bool includePrivate=true, bool includeComputed=true) const |
returns a list with the names of our properties More... | |
template<typename T > | |
void | setProp (const std::string &key, T val, bool computed=false) const |
sets a property value More... | |
template<typename T > | |
void | getProp (const std::string &key, T &res) const |
allows retrieval of a particular property value More... | |
template<typename T > | |
T | getProp (const std::string &key) const |
template<typename T > | |
bool | getPropIfPresent (const std::string &key, T &res) const |
bool | hasProp (const std::string &key) const |
void | clearProp (const std::string &key) const |
clears the value of a property More... | |
void | clearComputedProps () const |
clears all of our computed properties More... | |
void | updateProps (const RDProps &source, bool preserveExisting=false) |
update the properties from another More... | |
Friends | |
class | ReactionPickler |
Additional Inherited Members | |
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Dict | dp_props |
This is a class for storing and applying general chemical reactions.
basic usage will be something like:
ChemicalReaction rxn; rxn.addReactantTemplate(r1); rxn.addReactantTemplate(r2); rxn.addProductTemplate(p1); rxn.initReactantMatchers(); MOL_SPTR_VECT prods; for(MOL_SPTR_VECT::const_iterator r1It=reactantSet1.begin(); r1It!=reactantSet1.end();++r1It;){ for(MOL_SPTR_VECT::const_iterator r2It=reactantSet2.begin(); r2It!=reactantSet2.end();++r2It;){ MOL_SPTR_VECT rVect(2); rVect[0] = *r1It; rVect[1] = *r2It; std::vector<MOL_SPTR_VECT> lprods; lprods = rxn.runReactants(rVect); for(std::vector<MOL_SPTR_VECT>::const_iterator lpIt=lprods.begin(); lpIt!=lprods.end();++lpIt){ // we know this is a single-product reaction: prods.push_back((*lpIt)[0]); } } }
NOTES:
std::string smi="[O:1]>>[N:1]"; ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi); rxn->initReactantMatchers(); MOL_SPTR_VECT reacts; reacts.clear(); smi = "OCO"; ROMol *mol = SmilesToMol(smi); reacts.push_back(ROMOL_SPTR(mol)); std::vector<MOL_SPTR_VECT> prods; prods = rxn->runReactants(reacts); // here prods has two entries, because there are two Os in the // reactant. reacts[0]->getAtomWithIdx(0)->setProp(common_properties::_protected,1); prods = rxn->runReactants(reacts); // here prods only has one entry, the reaction at atom 0 // has been blocked by the _protected property
Definition at line 118 of file Reaction.h.
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Definition at line 122 of file Reaction.h.
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Definition at line 124 of file Reaction.h.
References beginAgentTemplates(), beginProductTemplates(), beginReactantTemplates(), RDKit::RDProps::dp_props, endAgentTemplates(), endProductTemplates(), and endReactantTemplates().
RDKit::ChemicalReaction::ChemicalReaction | ( | const std::string & | binStr | ) |
construct a reaction from a pickle string
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Adds a new product template.
Definition at line 173 of file Reaction.h.
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Adds a new reactant template.
Definition at line 152 of file Reaction.h.
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Definition at line 253 of file Reaction.h.
Referenced by ChemicalReaction().
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Definition at line 274 of file Reaction.h.
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Definition at line 246 of file Reaction.h.
Referenced by ChemicalReaction().
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Definition at line 267 of file Reaction.h.
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Definition at line 239 of file Reaction.h.
Referenced by ChemicalReaction().
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Definition at line 260 of file Reaction.h.
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Definition at line 256 of file Reaction.h.
Referenced by ChemicalReaction().
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Definition at line 277 of file Reaction.h.
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Definition at line 249 of file Reaction.h.
Referenced by ChemicalReaction().
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Definition at line 270 of file Reaction.h.
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Definition at line 242 of file Reaction.h.
Referenced by ChemicalReaction().
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Definition at line 263 of file Reaction.h.
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Definition at line 236 of file Reaction.h.
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returns whether or not the reaction uses implicit properties on the product atoms
This toggles whether or not unspecified atomic properties in the products are considered to be implicit and should be copied from the actual reactants. This is necessary due to a semantic difference between the "reaction SMARTS" approach and the MDL RXN approach: In "reaction SMARTS", this reaction: [C:1]-[Br:2].[O-:3]>>[C:1]-[O:3].[Br-:2] applied to [CH4+]Br should yield [CH4+]O Something similar drawn in an rxn file, and applied to [CH4+]Br should yield [CH3]O. In rxn there is no charge on the product C because nothing is specified in the rxn file; in "SMARTS" the charge from the actual reactants is not removed because no charge is specified in the reaction.
Definition at line 339 of file Reaction.h.
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Definition at line 286 of file Reaction.h.
Referenced by RDKit::EnumerateLibraryBase::initFromString().
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Definition at line 283 of file Reaction.h.
Referenced by RDKit::EnumerateLibraryBase::initFromString().
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Definition at line 280 of file Reaction.h.
Referenced by RDKit::EnumerateLibraryBase::initFromString().
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Definition at line 237 of file Reaction.h.
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Definition at line 233 of file Reaction.h.
void RDKit::ChemicalReaction::initReactantMatchers | ( | ) |
initializes our internal reactant-matching datastructures.
This must be called after adding reactants and before calling runReactants.
Referenced by RDKit::EnumerateLibraryBase::EnumerateLibraryBase().
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Definition at line 297 of file Reaction.h.
void RDKit::ChemicalReaction::removeAgentTemplates | ( | MOL_SPTR_VECT * | targetVector = NULL | ) |
Removes the agent templates from a reaction if a pointer to a molecule vector is provided the agents are stored therein.
void RDKit::ChemicalReaction::removeUnmappedProductTemplates | ( | double | thresholdUnmappedAtoms = 0.2 , |
bool | moveToAgentTemplates = true , |
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MOL_SPTR_VECT * | targetVector = NULL |
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Removes the product templates from a reaction if its atom mapping ratio is.
By default the removed products templates were attached to the agent templates. An alternative will be to provide a pointer to a molecule vector where these products should be saved.
void RDKit::ChemicalReaction::removeUnmappedReactantTemplates | ( | double | thresholdUnmappedAtoms = 0.2 , |
bool | moveToAgentTemplates = true , |
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MOL_SPTR_VECT * | targetVector = NULL |
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Removes the reactant templates from a reaction if atom mapping ratio is.
By default the removed reactant templates were attached to the agent templates. An alternative will be to provide a pointer to a molecule vector where these reactants should be saved.
std::vector<MOL_SPTR_VECT> RDKit::ChemicalReaction::runReactant | ( | ROMOL_SPTR | reactant, |
unsigned int | reactantTemplateIdx | ||
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Runs a single reactant against a single reactant template.
reactant | The single reactant to use |
reactantTemplateIdx | the reactant template to target in the reaction |
std::vector<MOL_SPTR_VECT> RDKit::ChemicalReaction::runReactants | ( | const MOL_SPTR_VECT | reactants, |
unsigned int | numProducts = 1000 |
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Runs the reaction on a set of reactants.
reactants | the reactants to be used. The length of this must be equal to this->getNumReactantTemplates() |
maxProducts | if non zero, the maximum number of products to generate before stopping. If hit a warning will be generated. |
We return a vector of vectors of products because each individual template may map multiple times onto its reactant. This leads to multiple possible result sets.
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sets the implicit properties flag. See the documentation for getImplicitProertiesFlag() for a discussion of what this means.
Definition at line 342 of file Reaction.h.
References RDKit::addRecursiveQueriesToReaction(), RDKit::getReactingAtoms(), RDKit::isMoleculeAgentOfReaction(), RDKit::isMoleculeProductOfReaction(), RDKit::isMoleculeReactantOfReaction(), and RDKIT_CHEMREACTIONS_EXPORT.
bool RDKit::ChemicalReaction::validate | ( | unsigned int & | numWarnings, |
unsigned int & | numErrors, | ||
bool | silent = false |
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validates the reactants and products to make sure the reaction seems
numWarnings | used to return the number of validation warnings |
numErrors | used to return the number of validation errors |
silent | If this bool is true, no messages will be logged during the validation. By default, validation problems are reported to the warning and error logs depending on their severity. |
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Definition at line 119 of file Reaction.h.