RDKit
Open-source cheminformatics and machine learning.
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FileParserUtils.h File Reference
#include <RDGeneral/export.h>
#include <string>
#include <iostream>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/lexical_cast.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/format.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include "FileParsers.h"
#include <string_view>

Go to the source code of this file.

Namespaces

namespace  RDKit
 Std stuff.
 
namespace  RDKit::FileParserUtils
 

Functions

RDKIT_FILEPARSERS_EXPORT std::string_view RDKit::FileParserUtils::strip (std::string_view orig, std::string stripChars=" \t\r\n")
 
template<typename T >
RDKit::FileParserUtils::stripSpacesAndCast (std::string_view input, bool acceptSpaces=false)
 
template<typename T >
RDKit::FileParserUtils::stripSpacesAndCast (const std::string &input, bool acceptSpaces=false)
 
RDKIT_FILEPARSERS_EXPORT int RDKit::FileParserUtils::toInt (const std::string &input, bool acceptSpaces=true)
 
RDKIT_FILEPARSERS_EXPORT unsigned int RDKit::FileParserUtils::toUnsigned (const std::string &input, bool acceptSpaces=true)
 
RDKIT_FILEPARSERS_EXPORT double RDKit::FileParserUtils::toDouble (const std::string &input, bool acceptSpaces=true)
 
RDKIT_FILEPARSERS_EXPORT int RDKit::FileParserUtils::toInt (const std::string_view input, bool acceptSpaces=true)
 
RDKIT_FILEPARSERS_EXPORT unsigned int RDKit::FileParserUtils::toUnsigned (std::string_view input, bool acceptSpaces=true)
 
RDKIT_FILEPARSERS_EXPORT double RDKit::FileParserUtils::toDouble (const std::string_view input, bool acceptSpaces=true)
 
RDKIT_FILEPARSERS_EXPORT std::string RDKit::FileParserUtils::getV3000CTAB (const ROMol &tmol, const boost::dynamic_bitset<> &wasAromatic, int confId=-1, unsigned int precision=6)
 
std::string RDKit::FileParserUtils::getV3000CTAB (const ROMol &tmol, int confId=-1, unsigned int precision=6)
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
 
RDKIT_FILEPARSERS_EXPORT std::string RDKit::FileParserUtils::getV3000Line (std::istream *inStream, unsigned int &line)
 
RDKIT_FILEPARSERS_EXPORT bool RDKit::FileParserUtils::ParseV3000CTAB (std::istream *inStream, unsigned int &line, RWMol *mol, Conformer *&conf, bool &chiralityPossible, unsigned int &nAtoms, unsigned int &nBonds, bool strictParsing=true, bool expectMEND=true)
 
RDKIT_FILEPARSERS_EXPORT bool RDKit::FileParserUtils::ParseV2000CTAB (std::istream *inStream, unsigned int &line, RWMol *mol, Conformer *&conf, bool &chiralityPossible, unsigned int &nAtoms, unsigned int &nBonds, bool strictParsing=true)
 
RDKIT_FILEPARSERS_EXPORT void RDKit::FileParserUtils::finishMolProcessing (RWMol *res, bool chiralityPossible, const v2::FileParsers::MolFileParserParams &ps)
 
void RDKit::FileParserUtils::finishMolProcessing (RWMol *res, bool chiralityPossible, bool sanitize, bool removeHs)
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
 
RDKIT_FILEPARSERS_EXPORT AtomRDKit::FileParserUtils::replaceAtomWithQueryAtom (RWMol *mol, Atom *atom)
 Deprecated, please use QueryOps::replaceAtomWithQueryAtom instead.
 
template<typename T >
void RDKit::FileParserUtils::applyMolListPropToAtoms (ROMol &mol, const std::string &pn, const std::string &prefix, const std::string &missingValueMarker="n/a")
 applies a particular property to the atoms as an atom property list
 
template<typename T >
void RDKit::FileParserUtils::applyMolListPropsToAtoms (ROMol &mol, const std::string &prefix, const std::string missingValueMarker="n/a")
 
void RDKit::FileParserUtils::processMolPropertyList (ROMol &mol, const std::string pn, const std::string &missingValueMarker="n/a")
 
void RDKit::FileParserUtils::processMolPropertyLists (ROMol &mol, const std::string &missingValueMarker="n/a")
 
template<typename T >
std::string RDKit::FileParserUtils::getAtomPropertyList (ROMol &mol, const std::string &atomPropName, std::string missingValueMarker="", unsigned int lineSize=190)
 
void RDKit::FileParserUtils::createAtomIntPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=190)
 
void RDKit::FileParserUtils::createAtomDoublePropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=190)
 
void RDKit::FileParserUtils::createAtomBoolPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=190)
 
void RDKit::FileParserUtils::createAtomStringPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=190)
 
RDKIT_FILEPARSERS_EXPORT void RDKit::FileParserUtils::moveAdditionalPropertiesToSGroups (RWMol &mol)
 

Variables

static const std::string RDKit::FileParserUtils::atomPropPrefix = "atom."