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//
// Copyright (C) 2002-2018 Greg Landrum and T5 Informatics GmbH
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#pragma once
#include <GraphMol/SubstanceGroup.h>
#include <RDGeneral/FileParseException.h>
#include <sstream>
namespace RDKit {
namespace SGroupParsing {
typedef std::map<int, SubstanceGroup> IDX_TO_SGROUP_MAP;
typedef std::map<int, STR_VECT> IDX_TO_STR_VECT_MAP;
/* ------------------ V2000 Utils ------------------ */
unsigned int ParseSGroupIntField(const std::string &text, unsigned int line,
unsigned int &pos,
bool isFieldCounter = false);
unsigned int ParseSGroupIntField(bool &ok, bool strictParsing,
const std::string &text, unsigned int line,
unsigned int &pos,
bool isFieldCounter = false);
double ParseSGroupDoubleField(const std::string &text, unsigned int line,
unsigned int &pos);
double ParseSGroupDoubleField(bool &ok, bool strictParsing,
const std::string &text, unsigned int line,
unsigned int &pos);
SubstanceGroup *FindSgIdx(IDX_TO_SGROUP_MAP &sGroupMap, int sgIdx,
unsigned int line);
template <class Exc = FileParseException>
void SGroupWarnOrThrow(bool strictParsing, const std::string &msg) {
if (strictParsing) {
throw Exc(msg);
} else {
BOOST_LOG(rdWarningLog) << msg << std::endl;
}
}
void ParseSGroupV2000STYLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000VectorDataLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SDILine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SSTLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SMTLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SLBLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SCNLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SDSLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SBVLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SDTLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SDDLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SCDSEDLine(IDX_TO_SGROUP_MAP &sGroupMap,
IDX_TO_STR_VECT_MAP &dataFieldsMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing, unsigned int &counter,
unsigned int &lastDataSGroup,
std::ostringstream ¤tDataField);
void ParseSGroupV2000SPLLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SNCLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
//! if the SAP line is malformed and has no lvIdx and no id,
//! lvIdx is set to mol->getNumAtoms() and id is set to " "
//! the user is responsible for replacing lvIdx with the correct
//! index: if d_bonds.size() == 1, and one of the bond atom indices
//! is aIdx, the other can be safely assigned to lvIdx
void ParseSGroupV2000SAPLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SCLLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
void ParseSGroupV2000SBTLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol,
const std::string &text, unsigned int line,
bool strictParsing = true);
/* ------------------ V3000 Utils ------------------ */
template <class T>
RDKIT_FILEPARSERS_EXPORT std::vector<T> ParseV3000Array(
std::stringstream &stream, int maxV = -1, bool strictParsing = false);
#if defined(_MSC_VER) && defined(RDKIT_DYN_LINK)
template RDKIT_FILEPARSERS_EXPORT std::vector<int> ParseV3000Array(
std::stringstream &, int, bool);
template RDKIT_FILEPARSERS_EXPORT std::vector<unsigned int> ParseV3000Array(
std::stringstream &, int, bool);
#endif
template <class T>
std::vector<T> ParseV3000Array(const std::string &s, int maxV = -1,
bool strictParsing = false) {
std::stringstream stream(s);
return ParseV3000Array<T>(stream, maxV, strictParsing);
}
void ParseV3000CStateLabel(RWMol *mol, SubstanceGroup &sgroup,
std::stringstream &stream, unsigned int line,
bool strictParsing = true);
void ParseV3000SAPLabel(RWMol *mol, SubstanceGroup &sgroup,
std::stringstream &stream, bool strictParsing = true);
std::string ParseV3000StringPropLabel(std::stringstream &stream);
// returns the last line read in the SGroups block
std::string ParseV3000SGroupsBlock(std::istream *inStream, unsigned int line,
unsigned int nSgroups, RWMol *mol,
bool strictParsing);
} // namespace SGroupParsing
} // namespace RDKit
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