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>
T	RDKit::FileParserUtils::stripSpacesAndCast (std::string_view input, bool acceptSpaces=false)
template<typename T>
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, bool expectMacroAtoms=false)
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 Atom *	RDKit::FileParserUtils::replaceAtomWithQueryAtom (RWMol *mol, Atom *atom)
	Deprecated, please use QueryOps::replaceAtomWithQueryAtom instead.
template<typename T, typename U>
void	RDKit::FileParserUtils::applyMolListProp (ROMol &mol, const std::string &pn, const std::string &prefix, const std::string &missingValueMarker, size_t nItems, U getter)
	applies a particular property to the atoms as an atom property list
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, typename U>
void	RDKit::FileParserUtils::applyMolListProps (ROMol &mol, const std::string &prefix, size_t nItems, U getter, const std::string missingValueMarker="n/a")
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, typename U>
std::string	RDKit::FileParserUtils::getPropertyList (U getter, const std::string &propName, std::string missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
template<typename T>
std::string	RDKit::FileParserUtils::getAtomPropertyList (ROMol &mol, const std::string &atomPropName, std::string missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
template<typename T, typename U>
void	RDKit::FileParserUtils::createPropertyList (ROMol &mol, U getter, const std::string &prefix, const std::string &typeMarker, const std::string &propName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	RDKit::FileParserUtils::createAtomIntPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	RDKit::FileParserUtils::createAtomDoublePropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	RDKit::FileParserUtils::createAtomBoolPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	RDKit::FileParserUtils::createAtomStringPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	RDKit::FileParserUtils::createBondIntPropertyList (ROMol &mol, const std::string &bondPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	RDKit::FileParserUtils::createBondDoublePropertyList (ROMol &mol, const std::string &bondPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	RDKit::FileParserUtils::createBondBoolPropertyList (ROMol &mol, const std::string &bondPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
void	RDKit::FileParserUtils::createBondStringPropertyList (ROMol &mol, const std::string &bondPropName, const std::string &missingValueMarker="", unsigned int lineSize=DEFAULT_LINESIZE)
RDKIT_FILEPARSERS_EXPORT void	RDKit::FileParserUtils::moveAdditionalPropertiesToSGroups (RWMol &mol)

Variables
static constexpr std::string_view	RDKit::FileParserUtils::atomPropPrefixView = "atom."
static constexpr size_t	RDKit::FileParserUtils::atomPropPrefixLength = atomPropPrefixView.length()
static const std::string	RDKit::FileParserUtils::atomPropPrefix = std::string(atomPropPrefixView)
static constexpr std::string_view	RDKit::FileParserUtils::bondPropPrefixView = "bond."
static constexpr size_t	RDKit::FileParserUtils::bondPropPrefixLength = bondPropPrefixView.length()
static const std::string	RDKit::FileParserUtils::bondPropPrefix = std::string(bondPropPrefixView)
static constexpr unsigned int	RDKit::FileParserUtils::DEFAULT_LINESIZE = 190