RDKit: FileParsers.h File Reference

| RDKit Open-source cheminformatics and machine learning.

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Classes | Namespaces | Enumerations | Functions
FileParsers.h File Reference
`#include <RDGeneral/export.h>`
`#include <RDGeneral/types.h>`
`#include <GraphMol/RDKitBase.h>`
`#include <GraphMol/FileParsers/FileWriters.h>`
`#include "CDXMLParser.h"`
`#include <string>`
`#include <string_view>`
`#include <vector>`
`#include <exception>`
`#include <boost/shared_ptr.hpp>`

Go to the source code of this file.

## Classes
class | RDKit::v2::FileParsers::MolFileUnhandledFeatureException
struct | RDKit::v2::FileParsers::MolFileParserParams
struct | RDKit::v2::FileParsers::MolFromSCSRParams
struct | RDKit::v2::FileParsers::TPLParserParams
struct | RDKit::v2::FileParsers::Mol2ParserParams
struct | RDKit::v2::FileParsers::PDBParserParams
class | RDKit::v1::MolFileUnhandledFeatureException
struct | RDKit::v1::PDBParserParams

## Namespaces
namespace | RDKit
| Std stuff.
namespace | RDKit::v2
namespace | RDKit::v2::FileParsers
namespace | RDKit::v1

## Enumerations
enum class | RDKit::v2::FileParsers::SCSRTemplateNames { RDKit::v2::FileParsers::AsEntered , RDKit::v2::FileParsers::UseFirstName , RDKit::v2::FileParsers::UseSecondName }
enum class | RDKit::v2::FileParsers::SCSRBaseHbondOptions { RDKit::v2::FileParsers::Ignore , RDKit::v2::FileParsers::UseSapAll , RDKit::v2::FileParsers::UseSapOne , RDKit::v2::FileParsers::Auto }
enum | RDKit::v2::FileParsers::Mol2Type { RDKit::v2::FileParsers::CORINA = 0 }
enum | RDKit::v1::Mol2Type

## Functions
RDKIT_FILEPARSERS_EXPORT std::string | RDKit::strip (const std::string &orig)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromMolDataStream (std::istream &inStream, unsigned int &line, const MolFileParserParams &params=MolFileParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromMolBlock (const std::string &molBlock, const MolFileParserParams &params=MolFileParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromMolFile (const std::string &fName, const MolFileParserParams &params=MolFileParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RDKit::RWMol > | RDKit::v2::FileParsers::MolFromSCSRDataStream (std::istream &inStream, unsigned int &line, const MolFileParserParams &molFileParserParams=MolFileParserParams(), const MolFromSCSRParams &molFromSCSRParams=MolFromSCSRParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RDKit::RWMol > | RDKit::v2::FileParsers::MolFromSCSRBlock (const std::string &molBlock, const MolFileParserParams &molFileParserParams=MolFileParserParams(), const MolFromSCSRParams &molFromSCSRParams=MolFromSCSRParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RDKit::RWMol > | RDKit::v2::FileParsers::MolFromSCSRFile (const std::string &fName, const MolFileParserParams &molFileParserParams=MolFileParserParams(), const MolFromSCSRParams &molFromSCSRParams=MolFromSCSRParams())
RWMol * | RDKit::v1::MolDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RWMol * | RDKit::v1::MolDataStreamToMol (std::istream &inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RWMol * | RDKit::v1::MolBlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RWMol * | RDKit::v1::MolFileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromTPLDataStream (std::istream &inStream, unsigned int &line, const TPLParserParams &params=TPLParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromTPLFile (const std::string &fName, const TPLParserParams &params=TPLParserParams())
RWMol * | RDKit::v1::TPLDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false)
| translate TPL data (BioCad format) into a multi-conf molecule
RWMol * | RDKit::v1::TPLFileToMol (const std::string &fName, bool sanitize=true, bool skipFirstConf=false)
| construct a multi-conf molecule from a TPL (BioCad format) file
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromMol2DataStream (std::istream &inStream, const Mol2ParserParams &params=Mol2ParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromMol2Block (const std::string &molBlock, const Mol2ParserParams &params=Mol2ParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromMol2File (const std::string &fName, const Mol2ParserParams &params=Mol2ParserParams())
RWMol * | RDKit::v1::Mol2FileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
RWMol * | RDKit::v1::Mol2DataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
RWMol * | RDKit::v1::Mol2DataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
RWMol * | RDKit::v1::Mol2BlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromXYZDataStream (std::istream &inStream)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromXYZBlock (const std::string &xyzBlock)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromXYZFile (const std::string &fName)
RWMol * | RDKit::v1::XYZDataStreamToMol (std::istream &inStream)
RWMol * | RDKit::v1::XYZBlockToMol (const std::string &xyzBlock)
RWMol * | RDKit::v1::XYZFileToMol (const std::string &fName)
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromPDBDataStream (std::istream &inStream, const PDBParserParams &params=PDBParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromPDBFile (const std::string &fname, const PDBParserParams &params=PDBParserParams())
RDKIT_FILEPARSERS_EXPORT std::unique_ptr< RWMol > | RDKit::v2::FileParsers::MolFromPDBBlock (const std::string &str, const PDBParserParams &params=PDBParserParams())
RWMol * | RDKit::v1::PDBBlockToMol (const std::string &str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RWMol * | RDKit::v1::PDBBlockToMol (const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RWMol * | RDKit::v1::PDBFileToMol (const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RWMol * | RDKit::v1::PDBDataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RWMol * | RDKit::v1::PDBDataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RDKIT_FILEPARSERS_EXPORT RWMol * | RDKit::RDKitSVGToMol (const std::string &svg, bool sanitize=true, bool removeHs=true)
RDKIT_FILEPARSERS_EXPORT RWMol * | RDKit::RDKitSVGToMol (std::istream *instream, bool sanitize=true, bool removeHs=true)
std::unique_ptr< RDKit::RWMol > | RDKit::operator""_ctab (const char *text, size_t len)
std::unique_ptr< RDKit::RWMol > | RDKit::operator""_mol2 (const char *text, size_t len)
std::unique_ptr< RDKit::RWMol > | RDKit::operator""_pdb (const char *text, size_t len)