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MolSGroupParsing.h
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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 &currentDataField);
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
FileParseException.h
BOOST_LOG
#define BOOST_LOG(__arg__)
Definition RDLog.h:110
rdWarningLog
RDKIT_RDGENERAL_EXPORT RDLogger rdWarningLog
SubstanceGroup.h
Defines the SubstanceGroup class.
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition RWMol.h:32
RDKit::SubstanceGroup
The class for representing SubstanceGroups.
Definition SubstanceGroup.h:55
export.h
RDKIT_FILEPARSERS_EXPORT
#define RDKIT_FILEPARSERS_EXPORT
Definition export.h:177
RDKit::SGroupParsing
Definition MolSGroupParsing.h:19
RDKit::SGroupParsing::ParseSGroupV2000SSTLine
void ParseSGroupV2000SSTLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int &line, bool strictParsing=true)
RDKit::SGroupParsing::ParseSGroupIntField
unsigned int ParseSGroupIntField(const std::string &text, unsigned int line, unsigned int &pos, bool isFieldCounter=false)
RDKit::SGroupParsing::IDX_TO_SGROUP_MAP
std::map< int, SubstanceGroup > IDX_TO_SGROUP_MAP
Definition MolSGroupParsing.h:20
RDKit::SGroupParsing::ParseSGroupV2000STYLine
void ParseSGroupV2000STYLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::ParseSGroupV2000SCDSEDLine
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 &currentDataField)
RDKit::SGroupParsing::ParseSGroupV2000SPLLine
void ParseSGroupV2000SPLLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::ParseSGroupV2000SAPLine
void ParseSGroupV2000SAPLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::FindSgIdx
SubstanceGroup * FindSgIdx(IDX_TO_SGROUP_MAP &sGroupMap, int sgIdx, unsigned int line)
RDKit::SGroupParsing::ParseV3000CStateLabel
void ParseV3000CStateLabel(RWMol *mol, SubstanceGroup &sgroup, std::stringstream &stream, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::ParseSGroupV2000SCNLine
void ParseSGroupV2000SCNLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::ParseSGroupV2000SLBLine
void ParseSGroupV2000SLBLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::ParseV3000SAPLabel
void ParseV3000SAPLabel(RWMol *mol, SubstanceGroup &sgroup, std::stringstream &stream, bool strictParsing=true)
RDKit::SGroupParsing::ParseSGroupV2000SDSLine
void ParseSGroupV2000SDSLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::ParseV3000SGroupsBlock
std::string ParseV3000SGroupsBlock(std::istream *inStream, unsigned int &line, unsigned int nSgroups, RWMol *mol, bool strictParsing)
RDKit::SGroupParsing::ParseSGroupV2000SCLLine
void ParseSGroupV2000SCLLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::ParseSGroupV2000SDILine
void ParseSGroupV2000SDILine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::ParseSGroupV2000SBTLine
void ParseSGroupV2000SBTLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::SGroupWarnOrThrow
void SGroupWarnOrThrow(bool strictParsing, const std::string &msg)
Definition MolSGroupParsing.h:45
RDKit::SGroupParsing::ParseV3000StringPropLabel
std::string ParseV3000StringPropLabel(std::stringstream &stream)
RDKit::SGroupParsing::ParseV3000Array
RDKIT_FILEPARSERS_EXPORT std::vector< T > ParseV3000Array(std::stringstream &stream, int maxV=-1, bool strictParsing=false)
RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine
void ParseSGroupV2000VectorDataLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::ParseSGroupV2000SDTLine
void ParseSGroupV2000SDTLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::ParseSGroupV2000SDDLine
void ParseSGroupV2000SDDLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::IDX_TO_STR_VECT_MAP
std::map< int, STR_VECT > IDX_TO_STR_VECT_MAP
Definition MolSGroupParsing.h:21
RDKit::SGroupParsing::ParseSGroupV2000SBVLine
void ParseSGroupV2000SBVLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::ParseSGroupV2000SNCLine
void ParseSGroupV2000SNCLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true)
RDKit::SGroupParsing::ParseSGroupDoubleField
double ParseSGroupDoubleField(const std::string &text, unsigned int line, unsigned int &pos)
RDKit::SGroupParsing::ParseSGroupV2000SMTLine
void ParseSGroupV2000SMTLine(IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int &line, bool strictParsing=true)
RDKit
Std stuff.
Definition Abbreviations.h:19