RDKit
Open-source cheminformatics and machine learning.
ReactionParser.h
Go to the documentation of this file.
1 //
2 // Copyright (c) 2007-2014, Novartis Institutes for BioMedical Research Inc.
3 // All rights reserved.
4 //
5 // Redistribution and use in source and binary forms, with or without
6 // modification, are permitted provided that the following conditions are
7 // met:
8 //
9 // * Redistributions of source code must retain the above copyright
10 // notice, this list of conditions and the following disclaimer.
11 // * Redistributions in binary form must reproduce the above
12 // copyright notice, this list of conditions and the following
13 // disclaimer in the documentation and/or other materials provided
14 // with the distribution.
15 // * Neither the name of Novartis Institutes for BioMedical Research Inc.
16 // nor the names of its contributors may be used to endorse or promote
17 // products derived from this software without specific prior written
18 // permission.
19 //
20 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
21 // "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
22 // LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
23 // A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
24 // OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
25 // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
26 // LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
27 // DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
28 // THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
29 // (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
30 // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
31 //
32 
33 #ifndef __RD_REACTIONPARSER_H_21Aug2006__
34 #define __RD_REACTIONPARSER_H_21Aug2006__
35 
36 #include <string>
37 #include <iostream>
38 
39 namespace RDKit {
40 class ChemicalReaction;
41 
42 //! used to indicate an error in parsing reaction data
43 class ChemicalReactionParserException : public std::exception {
44  public:
45  //! construct with an error message
46  explicit ChemicalReactionParserException(const char *msg) : _msg(msg){};
47  //! construct with an error message
48  explicit ChemicalReactionParserException(const std::string &msg)
49  : _msg(msg){};
50  //! get the error message
51  const char *message() const { return _msg.c_str(); };
53 
54  private:
55  std::string _msg;
56 };
57 
58 //! Parse a text block in MDL rxn format into a ChemicalReaction
59 ChemicalReaction *RxnBlockToChemicalReaction(const std::string &rxnBlock);
60 //! Parse a file in MDL rxn format into a ChemicalReaction
61 ChemicalReaction *RxnFileToChemicalReaction(const std::string &fileName);
62 //! Parse a text stream in MDL rxn format into a ChemicalReaction
63 ChemicalReaction *RxnDataStreamToChemicalReaction(std::istream &rxnStream,
64  unsigned int &line);
65 
66 //! Parse a string containing "Reaction SMARTS" into a ChemicalReaction
67 /*!
68  Our definition of Reaction SMARTS is something that looks a lot like
69  reaction SMILES, except that SMARTS queries are allowed on the reactant
70  side and that atom-map numbers are required (at least for now)
71 
72  \param text the SMARTS to convert
73  \param replacements a string->string map of replacement strings.
74  \see SmilesToMol for more information about replacements
75  \param useSmiles if set, the SMILES parser will be used instead of the
76  SMARTS
77  parserfor the individual components
78  */
80  const std::string &text,
81  std::map<std::string, std::string> *replacements = 0,
82  bool useSmiles = false);
83 
84 //! Parse a ROMol into a ChemicalReaction, RXN role must be set before
85 /*!
86  Alternative to build a reaction from a molecule (fragments) which have RXN
87  roles
88  set as atom properties: common_properties::molRxnRole (1=reactant, 2=product,
89  3=agent)
90 
91  \param mol ROMol with RXN roles set
92  */
94 
95 //! returns the reaction SMARTS for a reaction
96 std::string ChemicalReactionToRxnSmarts(const ChemicalReaction &rxn);
97 
98 //! returns the reaction SMILES for a reaction
99 std::string ChemicalReactionToRxnSmiles(const ChemicalReaction &rxn,
100  bool canonical = true);
101 
102 //! returns an RXN block for a reaction
103 /*!
104  \param rxn chemical reaction
105  \param separateAgents flag to decide if agents were put in a seperate block,
106  otherwise they were included in the reactants block
107  (default)
108  */
109 std::string ChemicalReactionToRxnBlock(const ChemicalReaction &rxn,
110  bool separateAgents = false);
111 
112 //! returns a ROMol with RXN roles used to describe the reaction
114 
115 }; // end of RDKit namespace
116 
117 #endif
ChemicalReactionParserException(const char *msg)
construct with an error message
used to indicate an error in parsing reaction data
ChemicalReaction * RxnMolToChemicalReaction(const ROMol &mol)
Parse a ROMol into a ChemicalReaction, RXN role must be set before.
const char * message() const
get the error message
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:116
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:103
ROMol * ChemicalReactionToRxnMol(const ChemicalReaction &rxn)
returns a ROMol with RXN roles used to describe the reaction
ChemicalReactionParserException(const std::string &msg)
construct with an error message
ChemicalReaction * RxnBlockToChemicalReaction(const std::string &rxnBlock)
Parse a text block in MDL rxn format into a ChemicalReaction.
ChemicalReaction * RxnFileToChemicalReaction(const std::string &fileName)
Parse a file in MDL rxn format into a ChemicalReaction.
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:29
std::string ChemicalReactionToRxnSmarts(const ChemicalReaction &rxn)
returns the reaction SMARTS for a reaction
ChemicalReaction * RxnDataStreamToChemicalReaction(std::istream &rxnStream, unsigned int &line)
Parse a text stream in MDL rxn format into a ChemicalReaction.
ChemicalReaction * RxnSmartsToChemicalReaction(const std::string &text, std::map< std::string, std::string > *replacements=0, bool useSmiles=false)
Parse a string containing "Reaction SMARTS" into a ChemicalReaction.
std::string ChemicalReactionToRxnSmiles(const ChemicalReaction &rxn, bool canonical=true)
returns the reaction SMILES for a reaction
std::string ChemicalReactionToRxnBlock(const ChemicalReaction &rxn, bool separateAgents=false)
returns an RXN block for a reaction