RDKit
Open-source cheminformatics and machine learning.
FileParsers.h File Reference
#include <RDGeneral/types.h>
#include <GraphMol/RDKitBase.h>
#include <string>
#include <iostream>
#include <vector>
#include <exception>
#include <boost/shared_ptr.hpp>

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Namespaces

 RDKit
 Std stuff.
 

Typedefs

typedef std::vector< RWMOL_SPTR > RDKit::RWMOL_SPTR_VECT
 

Enumerations

enum  RDKit::Mol2Type { RDKit::CORINA = 0 }
 

Functions

std::string RDKit::strip (const std::string &orig)
 
RWMol * RDKit::MolDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
 
RWMol * RDKit::MolDataStreamToMol (std::istream &inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
 
RWMol * RDKit::MolBlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
 
RWMol * RDKit::MolFileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
 
std::string RDKit::MolToMolBlock (const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false)
 
void RDKit::MolToMolFile (const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false)
 
RWMol * RDKit::TPLDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false)
 translate TPL data (BioCad format) into a multi-conf molecule More...
 
RWMol * RDKit::TPLFileToMol (const std::string &fName, bool sanitize=true, bool skipFirstConf=false)
 construct a multi-conf molecule from a TPL (BioCad format) file More...
 
std::string RDKit::MolToTPLText (const ROMol &mol, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)
 
void RDKit::MolToTPLFile (const ROMol &mol, const std::string &fName, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)
 
RWMol * RDKit::Mol2FileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA)
 
RWMol * RDKit::Mol2DataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA)
 
RWMol * RDKit::Mol2DataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA)
 
RWMol * RDKit::Mol2BlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA)
 
RWMol * RDKit::PDBBlockToMol (const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0)
 
RWMol * RDKit::PDBBlockToMol (const std::string &str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0)
 
RWMol * RDKit::PDBDataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0)
 
RWMol * RDKit::PDBDataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0)
 
RWMol * RDKit::PDBFileToMol (const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0)
 
std::string RDKit::MolToPDBBlock (const ROMol &mol, int confId=-1, unsigned int flavor=0)
 
void RDKit::MolToPDBFile (const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0)
 

Variables

const int RDKit::MOLFILE_MAXLINE = 256