10 #ifndef _RD_FILEPARSERS_H 11 #define _RD_FILEPARSERS_H 21 #include <boost/shared_ptr.hpp> 25 std::string
strip(
const std::string &orig);
45 bool sanitize=
true,
bool removeHs=
true,
46 bool strictParsing=
true);
49 bool sanitize=
true,
bool removeHs=
true,
50 bool strictParsing=
true);
62 bool removeHs=
true,
bool strictParsing=
true);
75 bool removeHs=
true,
bool strictParsing=
true);
87 int confId=-1,
bool kekulize=
true,
bool forceV3000=
false);
99 int confId=-1,
bool kekulize=
true,
bool forceV3000=
false);
123 bool skipFirstConf=
false);
140 bool skipFirstConf=
false);
143 std::string partialChargeProp=
"_GasteigerCharge",
144 bool writeFirstConfTwice=
false);
146 std::string partialChargeProp=
"_GasteigerCharge",
147 bool writeFirstConfTwice=
false);
195 bool removeHs=
true,
unsigned int flavor=0);
198 bool removeHs=
true,
unsigned int flavor=0);
200 bool removeHs=
true,
unsigned int flavor=0);
202 bool removeHs=
true,
unsigned int flavor=0);
204 bool removeHs=
true,
unsigned int flavor=0);
232 void MolToPDBFile(
const ROMol &mol,
const std::string &fname,
int confId=-1,
unsigned int flavor=0);
std::vector< RWMOL_SPTR > RWMOL_SPTR_VECT
RWMol * PDBDataStreamToMol(std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0)
RWMol * PDBBlockToMol(const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0)
ROMol * removeHs(const ROMol &mol, bool implicitOnly=false, bool updateExplicitCount=false, bool sanitize=true)
returns a copy of a molecule with hydrogens removed
RWMol * Mol2DataStreamToMol(std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA)
void MolToMolFile(const ROMol &mol, std::string fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false)
const int MOLFILE_MAXLINE
RWMol is a molecule class that is intended to be edited.
RWMol * MolDataStreamToMol(std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RWMol * TPLFileToMol(std::string fName, bool sanitize=true, bool skipFirstConf=false)
construct a multi-conf molecule from a TPL (BioCad format) file
std::string MolToMolBlock(const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false)
pulls in the core RDKit functionality
ROMol is a molecule class that is intended to have a fixed topology.
RWMol * Mol2FileToMol(std::string fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA)
void MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0)
std::string strip(const std::string &orig)
RWMol * Mol2BlockToMol(const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA)
std::string MolToPDBBlock(const ROMol &mol, int confId=-1, unsigned int flavor=0)
Includes a bunch of functionality for handling Atom and Bond queries.
RWMol * TPLDataStreamToMol(std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false)
translate TPL data (BioCad format) into a multi-conf molecule
RWMol * PDBFileToMol(const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0)
RWMol * MolBlockToMol(const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RWMol * MolFileToMol(std::string fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
std::string MolToTPLText(const ROMol &mol, std::string partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)
void MolToTPLFile(const ROMol &mol, std::string fName, std::string partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)