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SLNAttribs.h
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//
// Copyright (c) 2008, 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.
//
// Created by Greg Landrum, September 2006
//
#include <RDGeneral/export.h>
#ifndef __RD_SLNATTRIBS_H__
#define __RD_SLNATTRIBS_H__
#include <string>
#include <vector>
#include <boost/smart_ptr.hpp>
namespace RDKit {
class Atom;
class Bond;
namespace SLNParse {
typedef enum {
AttribLowPriAnd = 0,
AttribOr,
AttribAnd,
AttribNot
} AttribCombineOp;
class RDKIT_SLNPARSE_EXPORT AttribType {
public:
AttribType() : first(""), second(""), op("") {}
std::string first;
std::string second;
std::string op;
bool negated{false};
void *structQuery{nullptr};
};
typedef std::vector<std::pair<AttribCombineOp, boost::shared_ptr<AttribType>>>
AttribListType;
//! parses the attributes provided for an atom and sets
/// the appropriate RD properties/queries.
/// NOTES:
/// 1) Some SLN query values cannot be properly set until the molecule is
/// fully/
/// initialized. These are handled by parseFinalAtomAttribs()
//
void parseAtomAttribs(Atom *atom, AttribListType attribs, bool doingQuery);
void parseFinalAtomAttribs(Atom *atom, bool doingQuery);
//! parses the attributes provided for a bond and sets
/// the appropriate RD properties/queries.
/// NOTES:
/// 1) Some SLN query values cannot be properly set until the molecule is
/// fully/
/// initialized. These are handled by parseFinalBondAttribs()
void parseBondAttribs(Bond *bond, AttribListType attribs, bool doingQuery);
void parseFinalBondAttribs(Bond *bond, bool doingQuery);
//! parses the attributes provided for a ctab and sets
/// the appropriate RD properties/queries.
void parseMolAttribs(ROMol *mol, AttribListType attribs);
void adjustAtomChiralities(RWMol *mol);
} // namespace SLNParse
} // namespace RDKit
#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:319
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:513
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