1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
|
// $Id: DaylightParser.cpp 1730 2011-05-22 10:45:14Z glandrum $
//
// Copyright (c) 2007, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <boost/algorithm/string.hpp>
#include <vector>
#include <string>
namespace RDKit {
namespace DaylightParserUtils {
void updateProductsStereochem(ChemicalReaction *rxn){
// EFF: this isn't the speediest code the world has ever seen,
// but we hopefully aren't going to be calling this a lot.
for(MOL_SPTR_VECT::const_iterator prodIt=rxn->beginProductTemplates();
prodIt!=rxn->endProductTemplates();++prodIt){
for(ROMol::AtomIterator prodAtomIt=(*prodIt)->beginAtoms();
prodAtomIt!=(*prodIt)->endAtoms();++prodAtomIt){
if((*prodAtomIt)->getChiralTag()!=Atom::CHI_UNSPECIFIED &&
(*prodAtomIt)->getChiralTag()!=Atom::CHI_OTHER &&
(*prodAtomIt)->hasProp("molAtomMapNumber")) {
int mapNum;
(*prodAtomIt)->getProp("molAtomMapNumber",mapNum);
for(MOL_SPTR_VECT::const_iterator reactIt=rxn->beginReactantTemplates();
reactIt!=rxn->endReactantTemplates();++reactIt){
for(ROMol::AtomIterator reactAtomIt=(*reactIt)->beginAtoms();
reactAtomIt!=(*reactIt)->endAtoms();++reactAtomIt){
if((*reactAtomIt)->getChiralTag()!=Atom::CHI_UNSPECIFIED &&
(*reactAtomIt)->getChiralTag()!=Atom::CHI_OTHER &&
(*reactAtomIt)->hasProp("molAtomMapNumber")) {
int reactMapNum;
(*reactAtomIt)->getProp("molAtomMapNumber",reactMapNum);
if(reactMapNum==mapNum){
// finally, in the bowels of the nesting, we get to some actual
// work:
if((*reactAtomIt)->getChiralTag()==(*prodAtomIt)->getChiralTag()){
(*prodAtomIt)->setProp("molInversionFlag",2);
//BOOST_LOG(rdInfoLog) << "preserve at " << (*prodAtomIt)->getIdx() << std::endl;
} else {
// FIX: this is technically fragile: it should be checking
// if the atoms both have tetrahedral chirality. However,
// at the moment that's the only chirality available, so there's
// no need to go monkeying around.
(*prodAtomIt)->setProp("molInversionFlag",1);
//BOOST_LOG(rdInfoLog) << "invert at " << (*prodAtomIt)->getIdx() << std::endl;
}
}
}
}
}
}
}
}
}
} // end of namespace DaylightParserUtils
ChemicalReaction * RxnSmartsToChemicalReaction(const std::string &text,
std::map<std::string,std::string> *replacements) {
int pos=text.find(">>");
if(pos==std::string::npos){
throw ChemicalReactionParserException("a reaction requires at least one reactant and one product");
}
if(text.rfind(">>")!=pos){
throw ChemicalReactionParserException("multi-step reactions not supported");
}
std::string reactText=text.substr(0,pos);
std::vector<std::string> reactSmarts;
boost::split(reactSmarts,reactText,boost::is_any_of("."));
std::string productText=text.substr(pos+2);
ChemicalReaction *rxn=new ChemicalReaction();
for(std::vector<std::string>::const_iterator txtIt=reactSmarts.begin();
txtIt!=reactSmarts.end();++txtIt){
ROMol *mol=SmartsToMol(*txtIt,0,false,replacements);
if(!mol){
std::string errMsg="Problems constructing reactant from SMARTS: ";
errMsg += *txtIt;
throw ChemicalReactionParserException(errMsg);
}
rxn->addReactantTemplate(ROMOL_SPTR(mol));
}
//std::cerr << " ---------------------------------------------------------" << std::endl;
ROMol *prodMol=SmartsToMol(productText,0,false,replacements);
if(!prodMol){
std::string errMsg="Problems constructing product from SMARTS: ";
errMsg += productText;
throw ChemicalReactionParserException(errMsg);
}
std::vector<ROMOL_SPTR> prods=MolOps::getMolFrags(*prodMol,false);
delete prodMol;
for(std::vector<ROMOL_SPTR>::iterator pIt=prods.begin();
pIt!=prods.end();++pIt){
rxn->addProductTemplate(*pIt);
}
//std::cerr << " ---------------------------------------------------------" << std::endl;
DaylightParserUtils::updateProductsStereochem(rxn);
// "SMARTS"-based reactions have implicit properties
rxn->setImplicitPropertiesFlag(true);
return rxn;
}
}
|
