RDKit: SLNAttribs.h Source File

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SLNAttribs.h
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1 //
2 // Copyright (c) 2008, 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
18 // written 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 // Created by Greg Landrum, September 2006
33 //
34 #ifndef __RD_SLNATTRIBS_H__
35 #define __RD_SLNATTRIBS_H__
36
37 #include <string>
38 #include <vector>
39 #include <boost/smart_ptr.hpp>
40
41 namespace RDKit {
42 class Atom;
43 class Bond;
44
45 namespace SLNParse {
46 typedef enum {
47 AttribLowPriAnd = 0,
48 AttribOr,
49 AttribAnd,
50 AttribNot
51 } AttribCombineOp;
52
53 class AttribType {
54 public:
55 AttribType()
56 : first(""), second(""), op(""), negated(false), structQuery(0){};
57 std::string first;
58 std::string second;
59 std::string op;
60 bool negated;
61 void *structQuery;
62 };
63
64 typedef std::vector<std::pair<AttribCombineOp, boost::shared_ptr<AttribType> > >
65 AttribListType;
66
67 //! parses the attributes provided for an atom and sets
68 // the appropriate RD properties/queries.
69 // NOTES:
70 // 1) Some SLN query values cannot be properly set until the molecule is
71 // fully/
72 // initialized. These are handled by parseFinalAtomAttribs()
73 //
74 void parseAtomAttribs(Atom *atom, AttribListType attribs, bool doingQuery);
75 void parseFinalAtomAttribs(Atom *atom, bool doingQuery);
76
77 //! parses the attributes provided for a bond and sets
78 // the appropriate RD properties/queries.
79 // NOTES:
80 // 1) Some SLN query values cannot be properly set until the molecule is
81 // fully/
82 // initialized. These are handled by parseFinalBondAttribs()
83 void parseBondAttribs(Bond *bond, AttribListType attribs, bool doingQuery);
84 void parseFinalBondAttribs(Bond *bond, bool doingQuery);
85
86 //! parses the attributes provided for a ctab and sets
87 // the appropriate RD properties/queries.
88 void parseMolAttribs(ROMol *mol, AttribListType attribs);
89
90 void adjustAtomChiralities(RWMol *mol);
91 }
92 }
93 #endif
RDKit::SLNParse::AttribType::first
std::string first
Definition: SLNAttribs.h:56
RDKit::SLNParse::AttribCombineOp
AttribCombineOp
Definition: SLNAttribs.h:46
RDKit::SLNParse::AttribLowPriAnd
Definition: SLNAttribs.h:47
RDKit::SLNParse::AttribNot
Definition: SLNAttribs.h:50
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:30
RDKit::SLNParse::parseAtomAttribs
void parseAtomAttribs(Atom *atom, AttribListType attribs, bool doingQuery)
parses the attributes provided for an atom and sets
RDKit::SLNParse::AttribType::AttribType
AttribType()
Definition: SLNAttribs.h:55
RDKit::SLNParse::AttribType::negated
bool negated
Definition: SLNAttribs.h:60
RDKit::SLNParse::parseBondAttribs
void parseBondAttribs(Bond *bond, AttribListType attribs, bool doingQuery)
parses the attributes provided for a bond and sets
RDKit::SLNParse::parseMolAttribs
void parseMolAttribs(ROMol *mol, AttribListType attribs)
parses the attributes provided for a ctab and sets
RDKit::SLNParse::AttribType::op
std::string op
Definition: SLNAttribs.h:59
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:103
RDKit::SLNParse::AttribType
Definition: SLNAttribs.h:53
RDKit::SLNParse::adjustAtomChiralities
void adjustAtomChiralities(RWMol *mol)
RDKit::SLNParse::AttribType::second
std::string second
Definition: SLNAttribs.h:58
RDKit::SLNParse::parseFinalBondAttribs
void parseFinalBondAttribs(Bond *bond, bool doingQuery)
RDKit
Std stuff.
Definition: Atom.h:29
RDKit::Bond
class for representing a bond
Definition: Bond.h:47
RDKit::SLNParse::AttribType::structQuery
void * structQuery
Definition: SLNAttribs.h:61
RDKit::SLNParse::AttribOr
Definition: SLNAttribs.h:48
RDKit::Atom
The class for representing atoms.
Definition: Atom.h:68
RDKit::SLNParse::AttribAnd
Definition: SLNAttribs.h:49
RDKit::SLNParse::AttribListType
std::vector< std::pair< AttribCombineOp, boost::shared_ptr< AttribType > > > AttribListType
Definition: SLNAttribs.h:65
RDKit::SLNParse::parseFinalAtomAttribs
void parseFinalAtomAttribs(Atom *atom, bool doingQuery)