RDCode: Reaction.h Source File

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# Reaction.h

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    00001 //
    00002 //  Copyright (c) 2007, Novartis Institutes for BioMedical Research Inc.
    00003 //  All rights reserved.
    00004 //
    00005 // Redistribution and use in source and binary forms, with or without
    00006 // modification, are permitted provided that the following conditions are
    00007 // met:
    00008 //
    00009 //     * Redistributions of source code must retain the above copyright
    00010 //       notice, this list of conditions and the following disclaimer.
    00011 //     * Redistributions in binary form must reproduce the above
    00012 //       copyright notice, this list of conditions and the following
    00013 //       disclaimer in the documentation and/or other materials provided
    00014 //       with the distribution.
    00015 //     * Neither the name of Novartis Institutes for BioMedical Research Inc.
    00016 //       nor the names of its contributors may be used to endorse or promote
    00017 //       products derived from this software without specific prior written permission.
    00018 //
    00019 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
    00020 // "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
    00021 // LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
    00022 // A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
    00023 // OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
    00024 // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
    00025 // LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
    00026 // DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
    00027 // THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    00028 // (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
    00029 // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
    00030 //
    00031
    00032 #ifndef __RD_REACTION_H_17Aug2006__
    00033 #define __RD_REACTION_H_17Aug2006__
    00034
    00035 #include <GraphMol/RDKitBase.h>
    00036 #include <GraphMol/Substruct/SubstructMatch.h>
    00037 #include <vector>
    00038
    00039 namespace RDKit{
    00040
    00041   //! used to indicate an error in the chemical reaction engine
    00042   class ChemicalReactionException : public std::exception {
    00043   public:
    00044     //! construct with an error message
    00045     explicit ChemicalReactionException(const char *msg) : _msg(msg) {};
    00046     //! construct with an error message
    00047     explicit ChemicalReactionException(const std::string msg) : _msg(msg) {};
    00048     //! get the error message
    00049     const char *message () const { return _msg.c_str(); };
    00050     ~ChemicalReactionException () throw () {};
    00051   private:
    00052     std::string _msg;
    00053   };
    00054
    00055   //! This is a class for storing and applying general chemical reactions.
    00056   /*!
    00057      basic usage will be something like:
    00058
    00059      \verbatim
    00060      ChemicalReaction rxn;
    00061      rxn.addReactantTemplate(r1);
    00062      rxn.addReactantTemplate(r2);
    00063      rxn.addProductTemplate(p1);
    00064      rxn.initReactantMatchers();
    00065
    00066      MOL_SPTR_VECT prods;
    00067      for(MOL_SPTR_VECT::const_iterator r1It=reactantSet1.begin();
    00068          r1It!=reactantSet1.end();++r1It;){
    00069        for(MOL_SPTR_VECT::const_iterator r2It=reactantSet2.begin();
    00070            r2It!=reactantSet2.end();++r2It;){
    00071          MOL_SPTR_VECT rVect(2);
    00072          rVect[0] = *r1It;
    00073          rVect[1] = *r2It;
    00074
    00075          std::vector<MOL_SPTR_VECT> lprods;
    00076          lprods = rxn.runReactants(rVect);
    00077          for(std::vector<MOL_SPTR_VECT>::const_iterator lpIt=lprods.begin();
    00078             lpIt!=lprods.end();++lpIt){
    00079             // we know this is a single-product reaction:
    00080             prods.push_back((*lpIt)[0]);
    00081          }
    00082        }
    00083      }
    00084      \endverbatim
    00085
    00086   */
    00087   class ChemicalReaction {
    00088   public:
    00089     ChemicalReaction() : df_needsInit(true), df_implicitProperties(false) {};
    00090     ChemicalReaction(const ChemicalReaction &other){
    00091         df_needsInit=true;
    00092         df_implicitProperties=other.df_implicitProperties;
    00093         m_reactantTemplates=other.m_reactantTemplates;
    00094         m_productTemplates=other.m_productTemplates;
    00095     }
    00096     //! Adds a new reactant template
    00097     /*!
    00098       \return the number of reactants
    00099
    00100     */
    00101     unsigned int addReactantTemplate(ROMOL_SPTR mol){
    00102       this->df_needsInit = true;
    00103       this->m_reactantTemplates.push_back(mol);
    00104       return this->m_reactantTemplates.size();
    00105     }
    00106
    00107     //! Adds a new product template
    00108     /*!
    00109       \return the number of products
    00110
    00111     */
    00112     unsigned int addProductTemplate(ROMOL_SPTR mol){
    00113       this->m_productTemplates.push_back(mol);
    00114       return this->m_productTemplates.size();
    00115     }
    00116
    00117
    00118     //! Runs the reaction on a set of reactants
    00119     /*!
    00120
    00121       \param reactants: the reactants to be used. The length of this must be equal to
    00122                         this->getNumReactantTemplates()
    00123
    00124       \return a vector of vectors of products. Each subvector will be this->getNumProductTemplates()
    00125               long.
    00126
    00127       We return a vector of vectors of products because each individual template may map multiple times
    00128       onto its reactant. This leads to multiple possible result sets.
    00129     */
    00130     std::vector<MOL_SPTR_VECT> runReactants(const MOL_SPTR_VECT reactants) const;
    00131
    00132     MOL_SPTR_VECT::const_iterator beginReactantTemplates() const {
    00133         return this->m_reactantTemplates.begin();
    00134     }
    00135     MOL_SPTR_VECT::const_iterator endReactantTemplates() const {
    00136         return this->m_reactantTemplates.end();
    00137     }
    00138
    00139     MOL_SPTR_VECT::const_iterator beginProductTemplates() const {
    00140         return this->m_productTemplates.begin();
    00141     }
    00142     MOL_SPTR_VECT::const_iterator endProductTemplates() const {
    00143         return this->m_productTemplates.end();
    00144     }
    00145     unsigned int getNumReactantTemplates() const { return this->m_reactantTemplates.size(); };
    00146     unsigned int getNumProductTemplates() const { return this->m_productTemplates.size(); };
    00147
    00148     //! initializes our internal reactant-matching datastructures.
    00149     /*!
    00150         This must be called after adding reactants and before calling
    00151         runReactants.
    00152     */
    00153     void initReactantMatchers();
    00154
    00155     //! validates the reactants and products to make sure the reaction seems "reasonable"
    00156     /*!
    00157         \return   true if the reaction validates without errors (warnings do not stop validation)
    00158
    00159         \param numWarnings: used to return the number of validation warnings
    00160         \param numErrors:   used to return the number of validation errors
    00161
    00162         \param silent: If this bool is true, no messages will be logged during the validation.
    00163                        By default, validation problems are reported to the warning and error
    00164                        logs depending on their severity.
    00165
    00166     */
    00167     bool validate(unsigned int &numWarnings,unsigned int &numErrors,bool silent=false) const;
    00168
    00169
    00170     //! returns whether or not the reaction uses implicit
    00171     //! properties on the product atoms
    00172     /*!
    00173
    00174       This toggles whether or not unspecified atomic properties in the
    00175       products are considered to be implicit and should be copied from
    00176       the actual reactants. This is necessary due to a semantic difference
    00177       between the "reaction SMARTS" approach and the MDL RXN
    00178       approach:
    00179         In "reaction SMARTS", this reaction:
    00180           [C:1]-[Br:2].[O-:3]>>[C:1]-[O:3].[Br-:2]
    00181         applied to [CH4+]Br should yield [CH4+]O
    00182         Something similar drawn in an rxn file, and applied to
    00183         [CH4+]Br should yield [CH3]O.
    00184         In rxn there is no charge on the product C because nothing is
    00185         specified in the rxn file; in "SMARTS" the charge from the
    00186         actual reactants is not *removed* because no charge is
    00187         specified in the reaction.
    00188
    00189     */
    00190     bool getImplicitPropertiesFlag() const { return df_implicitProperties; };
    00191     //! sets the implicit properties flag. See the documentation for
    00192     //! getImplicitProertiesFlag() for a discussion of what this means.
    00193     void setImplicitPropertiesFlag(bool val) { df_implicitProperties=val; };
    00194
    00195   private:
    00196     bool df_needsInit;
    00197     bool df_implicitProperties;
    00198     MOL_SPTR_VECT m_reactantTemplates,m_productTemplates;
    00199     ChemicalReaction &operator=(const ChemicalReaction &); // disable assignment
    00200     MOL_SPTR_VECT generateOneProductSet(const MOL_SPTR_VECT &reactants,const std::vector<MatchVectType> &reactantsMatch) const;
    00201   };
    00202
    00203 } // end of RDKit namespace
    00204
    00205 #endif