RDKit: SLNAttribs.h Source File

| RDKit Open-source cheminformatics and machine learning.

Loading...
Searching...
No Matches
SLNAttribs.h
Go to the documentation of this file.
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#include <RDGeneral/export.h>
35#ifndef __RD_SLNATTRIBS_H__
36#define __RD_SLNATTRIBS_H__
37
38#include <string>
39#include <vector>
40#include <boost/smart_ptr.hpp>
41
42namespace RDKit {
43class Atom;
44class Bond;
45
46 namespace SLNParse {
47 typedef enum {
48 AttribLowPriAnd = 0,
49 AttribOr,
50 AttribAnd,
51 AttribNot
52} AttribCombineOp;
53
54 class RDKIT_SLNPARSE_EXPORT AttribType {
55 public:
56 AttribType() : first(""), second(""), op("") {}
57 std::string first;
58 std::string second;
59 std::string op;
60 bool negated{false};
61 void *structQuery{nullptr};
62};
63
64typedef 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} // namespace SLNParse
92} // namespace RDKit
93#endif
RDKit::Atom
The class for representing atoms.
Definition Atom.h:74
RDKit::Bond
class for representing a bond
Definition Bond.h:46
RDKit::ROMol
Definition ROMol.h:199
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition RWMol.h:32
RDKit::SLNParse::AttribType::negated
bool negated
Definition SLNAttribs.h:60
RDKit::SLNParse::AttribType::op
std::string op
Definition SLNAttribs.h:59
RDKit::SLNParse::AttribType::second
std::string second
Definition SLNAttribs.h:58
RDKit::SLNParse::AttribType::structQuery
void * structQuery
Definition SLNAttribs.h:61
RDKit::SLNParse::AttribType::AttribType
AttribType()
Definition SLNAttribs.h:56
RDKit::SLNParse::AttribType::first
std::string first
Definition SLNAttribs.h:57
export.h
RDKIT_SLNPARSE_EXPORT
#define RDKIT_SLNPARSE_EXPORT
Definition export.h:505
RDKit::SLNParse
Definition SLNAttribs.h:46
RDKit::SLNParse::AttribListType
std::vector< std::pair< AttribCombineOp, boost::shared_ptr< AttribType > > > AttribListType
Definition SLNAttribs.h:65
RDKit::SLNParse::adjustAtomChiralities
void adjustAtomChiralities(RWMol *mol)
RDKit::SLNParse::AttribCombineOp
AttribCombineOp
Definition SLNAttribs.h:47
RDKit::SLNParse::AttribAnd
@ AttribAnd
Definition SLNAttribs.h:50
RDKit::SLNParse::AttribNot
@ AttribNot
Definition SLNAttribs.h:51
RDKit::SLNParse::AttribLowPriAnd
@ AttribLowPriAnd
Definition SLNAttribs.h:48
RDKit::SLNParse::AttribOr
@ AttribOr
Definition SLNAttribs.h:49
RDKit::SLNParse::parseFinalBondAttribs
void parseFinalBondAttribs(Bond *bond, bool doingQuery)
RDKit::SLNParse::parseAtomAttribs
void parseAtomAttribs(Atom *atom, AttribListType attribs, bool doingQuery)
RDKit::SLNParse::parseMolAttribs
void parseMolAttribs(ROMol *mol, AttribListType attribs)
RDKit::SLNParse::parseBondAttribs
void parseBondAttribs(Bond *bond, AttribListType attribs, bool doingQuery)
RDKit::SLNParse::parseFinalAtomAttribs
void parseFinalAtomAttribs(Atom *atom, bool doingQuery)
RDKit
Std stuff.
Definition Abbreviations.h:19