36 #ifndef RD_REACTION_H_17Aug2006
37 #define RD_REACTION_H_17Aug2006
45 class ReactionPickler;
49 :
public std::exception {
56 const char *
what() const noexcept
override {
return _msg.c_str(); }
127 df_needsInit = other.df_needsInit;
128 df_implicitProperties = other.df_implicitProperties;
129 m_reactantTemplates.clear();
130 m_reactantTemplates.reserve(other.m_reactantTemplates.size());
131 for (
ROMOL_SPTR reactant_template : other.m_reactantTemplates) {
132 m_reactantTemplates.emplace_back(
new RWMol(*reactant_template));
134 m_productTemplates.clear();
135 m_productTemplates.reserve(other.m_productTemplates.size());
136 for (
ROMOL_SPTR product_template : other.m_productTemplates) {
137 m_productTemplates.emplace_back(
new RWMol(*product_template));
139 m_agentTemplates.clear();
140 m_agentTemplates.reserve(other.m_agentTemplates.size());
141 for (
ROMOL_SPTR agent_template : other.m_agentTemplates) {
142 m_agentTemplates.emplace_back(
new RWMol(*agent_template));
154 if (
this != &other) {
166 this->df_needsInit =
true;
167 this->m_reactantTemplates.push_back(mol);
168 return rdcast<unsigned int>(this->m_reactantTemplates.size());
177 this->m_agentTemplates.push_back(mol);
178 return rdcast<unsigned int>(this->m_agentTemplates.size());
187 this->m_productTemplates.push_back(mol);
188 return rdcast<unsigned int>(this->m_productTemplates.size());
199 bool moveToAgentTemplates =
true,
210 bool moveToAgentTemplates =
true,
233 const MOL_SPTR_VECT reactants,
unsigned int numProducts = 1000)
const;
242 ROMOL_SPTR reactant,
unsigned int reactantTemplateIdx)
const;
256 return this->m_reactantTemplates;
262 return this->m_reactantTemplates.begin();
265 return this->m_reactantTemplates.end();
269 return this->m_productTemplates.begin();
272 return this->m_productTemplates.end();
276 return this->m_agentTemplates.begin();
279 return this->m_agentTemplates.end();
283 return this->m_reactantTemplates.begin();
286 return this->m_reactantTemplates.end();
290 return this->m_productTemplates.begin();
293 return this->m_productTemplates.end();
297 return this->m_agentTemplates.begin();
300 return this->m_agentTemplates.end();
303 return rdcast<unsigned int>(this->m_reactantTemplates.size());
306 return rdcast<unsigned int>(this->m_productTemplates.size());
309 return rdcast<unsigned int>(this->m_agentTemplates.size());
339 bool validate(
unsigned int &numWarnings,
unsigned int &numErrors,
340 bool silent =
false)
const;
368 bool df_needsInit{
true};
369 bool df_implicitProperties{
false};
370 MOL_SPTR_VECT m_reactantTemplates, m_productTemplates, m_agentTemplates;
379 std::vector<unsigned int> &which,
bool stopAtFirstMatch =
false);
393 std::vector<unsigned int> &which,
bool stopAtFirstMatch =
false);
464 const std::string &propName,
465 std::vector<std::vector<std::pair<unsigned int, std::string>>>
466 *reactantLabels =
nullptr);
501 bool canonOrient =
false,
unsigned int nFlipsPerSample = 0,
502 unsigned int nSamples = 0,
int sampleSeed = 0,
503 bool permuteDeg4Nodes =
false);
pulls in the core RDKit functionality
used to indicate an error in the chemical reaction engine
ChemicalReactionException(const char *msg)
construct with an error message
ChemicalReactionException(const std::string msg)
construct with an error message
const char * what() const noexcept override
get the error message
~ChemicalReactionException() noexcept override=default
This is a class for storing and applying general chemical reactions.
unsigned int addProductTemplate(ROMOL_SPTR mol)
Adds a new product template.
unsigned int addAgentTemplate(ROMOL_SPTR mol)
Adds a new agent template.
unsigned int addReactantTemplate(ROMOL_SPTR mol)
Adds a new reactant template.
unsigned int getNumAgentTemplates() const
bool getImplicitPropertiesFlag() const
std::vector< MOL_SPTR_VECT > runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const
Runs the reaction on a set of reactants.
unsigned int getNumReactantTemplates() const
ChemicalReaction(const std::string &binStr)
construct a reaction from a pickle string
MOL_SPTR_VECT::iterator beginProductTemplates()
void removeUnmappedReactantTemplates(double thresholdUnmappedAtoms=0.2, bool moveToAgentTemplates=true, MOL_SPTR_VECT *targetVector=nullptr)
const MOL_SPTR_VECT & getProducts() const
std::vector< MOL_SPTR_VECT > runReactant(ROMOL_SPTR reactant, unsigned int reactantTemplateIdx) const
Runs a single reactant against a single reactant template.
MOL_SPTR_VECT::const_iterator beginProductTemplates() const
void initReactantMatchers(bool silent=false)
initializes our internal reactant-matching datastructures.
MOL_SPTR_VECT::const_iterator endReactantTemplates() const
void setImplicitPropertiesFlag(bool val)
MOL_SPTR_VECT::iterator endProductTemplates()
bool runReactant(RWMol &reactant) const
Runs a single reactant in place (the reactant is modified)
unsigned int getNumProductTemplates() const
const MOL_SPTR_VECT & getAgents() const
const MOL_SPTR_VECT & getReactants() const
MOL_SPTR_VECT::const_iterator endProductTemplates() const
bool isInitialized() const
ChemicalReaction & operator=(const ChemicalReaction &other)
ChemicalReaction(const ChemicalReaction &other)
MOL_SPTR_VECT::const_iterator beginAgentTemplates() const
void removeAgentTemplates(MOL_SPTR_VECT *targetVector=nullptr)
MOL_SPTR_VECT::const_iterator beginReactantTemplates() const
MOL_SPTR_VECT::iterator beginReactantTemplates()
MOL_SPTR_VECT::iterator endAgentTemplates()
MOL_SPTR_VECT::iterator beginAgentTemplates()
MOL_SPTR_VECT::iterator endReactantTemplates()
void removeUnmappedProductTemplates(double thresholdUnmappedAtoms=0.2, bool moveToAgentTemplates=true, MOL_SPTR_VECT *targetVector=nullptr)
MOL_SPTR_VECT::const_iterator endAgentTemplates() const
bool validate(unsigned int &numWarnings, unsigned int &numErrors, bool silent=false) const
RDProps & operator=(const RDProps &rhs)
RWMol is a molecule class that is intended to be edited.
handles pickling (serializing) reactions
#define RDKIT_CHEMREACTIONS_EXPORT
RDKIT_CHEMREACTIONS_EXPORT void compute2DCoordsForReaction(RDKit::ChemicalReaction &rxn, double spacing=2.0, bool updateProps=true, bool canonOrient=false, unsigned int nFlipsPerSample=0, unsigned int nSamples=0, int sampleSeed=0, bool permuteDeg4Nodes=false)
Generate 2D coordinates (a depiction) for a reaction.
std::vector< INT_VECT > VECT_INT_VECT
RDKIT_CHEMREACTIONS_EXPORT bool isMoleculeAgentOfReaction(const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which)
RDKIT_CHEMREACTIONS_EXPORT bool isMoleculeReactantOfReaction(const ChemicalReaction &rxn, const ROMol &mol, std::vector< unsigned int > &which, bool stopAtFirstMatch=false)
RDKIT_CHEMREACTIONS_EXPORT VECT_INT_VECT getReactingAtoms(const ChemicalReaction &rxn, bool mappedAtomsOnly=false)
RDKIT_CHEMREACTIONS_EXPORT bool isMoleculeProductOfReaction(const ChemicalReaction &rxn, const ROMol &mol, std::vector< unsigned int > &which, bool stopAtFirstMatch=false)
boost::shared_ptr< ROMol > ROMOL_SPTR
RDKIT_CHEMREACTIONS_EXPORT void addRecursiveQueriesToReaction(ChemicalReaction &rxn, const std::map< std::string, ROMOL_SPTR > &queries, const std::string &propName, std::vector< std::vector< std::pair< unsigned int, std::string >>> *reactantLabels=nullptr)
add the recursive queries to the reactants of a reaction
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT