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RDKit
Open-source cheminformatics and machine learning.
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11 #ifndef _RD_FILEPARSERS_H
12 #define _RD_FILEPARSERS_H
22 #include <boost/shared_ptr.hpp>
36 const char *
message()
const {
return _msg.c_str(); };
64 bool strictParsing =
true);
70 bool strictParsing =
true);
84 bool strictParsing =
true);
99 bool strictParsing =
true);
113 bool includeStereo =
true,
115 bool kekulize =
true,
116 bool forceV3000 =
false);
130 const ROMol &mol,
const std::string &fName,
bool includeStereo =
true,
131 int confId = -1,
bool kekulize =
true,
bool forceV3000 =
false);
136 const ROMol &mol,
const std::string &fName,
int confId = -1);
160 bool sanitize =
true,
161 bool skipFirstConf =
false);
179 bool sanitize =
true,
180 bool skipFirstConf =
false);
183 const ROMol &mol,
const std::string &partialChargeProp =
"_GasteigerCharge",
184 bool writeFirstConfTwice =
false);
186 const ROMol &mol,
const std::string &fName,
187 const std::string &partialChargeProp =
"_GasteigerCharge",
188 bool writeFirstConfTwice =
false);
210 bool sanitize =
true,
213 bool cleanupSubstructures =
true);
226 std::istream *inStream,
bool sanitize =
true,
bool removeHs =
true,
230 std::istream &inStream,
bool sanitize =
true,
bool removeHs =
true,
244 const std::string &molBlock,
bool sanitize =
true,
bool removeHs =
true,
248 bool sanitize =
true,
250 unsigned int flavor = 0,
251 bool proximityBonding =
true);
254 bool sanitize =
true,
256 unsigned int flavor = 0,
257 bool proximityBonding =
true);
259 std::istream *inStream,
bool sanitize =
true,
bool removeHs =
true,
260 unsigned int flavor = 0,
bool proximityBonding =
true);
262 std::istream &inStream,
bool sanitize =
true,
bool removeHs =
true,
263 unsigned int flavor = 0,
bool proximityBonding =
true);
265 bool sanitize =
true,
267 unsigned int flavor = 0,
268 bool proximityBonding =
true);
284 unsigned int flavor = 0);
299 const std::string &fname,
301 unsigned int flavor = 0);
313 bool sanitize =
true,
318 bool sanitize =
true,
RDKIT_FILEPARSERS_EXPORT void MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0)
RDKIT_FILEPARSERS_EXPORT std::string MolToTPLText(const ROMol &mol, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)
const int MOLFILE_MAXLINE
MolFileUnhandledFeatureException(const char *msg)
construct with an error message
RDKIT_FILEPARSERS_EXPORT void MolToTPLFile(const ROMol &mol, const std::string &fName, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)
#define RDKIT_FILEPARSERS_EXPORT
RWMol is a molecule class that is intended to be edited.
RDKIT_FILEPARSERS_EXPORT RWMol * Mol2DataStreamToMol(std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=true)
RDKIT_FILEPARSERS_EXPORT std::string strip(const std::string &orig)
RDKIT_FILEPARSERS_EXPORT std::string MolToXYZBlock(const ROMol &mol, int confId=-1)
RDKIT_FILEPARSERS_EXPORT RWMol * TPLFileToMol(const std::string &fName, bool sanitize=true, bool skipFirstConf=false)
construct a multi-conf molecule from a TPL (BioCad format) file
~MolFileUnhandledFeatureException() noexcept override
pulls in the core RDKit functionality
RDKIT_FILEPARSERS_EXPORT void MolToXYZFile(const ROMol &mol, const std::string &fName, int confId=-1)
RDKIT_FILEPARSERS_EXPORT RWMol * MolBlockToMol(const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RDKIT_FILEPARSERS_EXPORT void MolToMolFile(const ROMol &mol, const std::string &fName, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false)
RDKIT_FILEPARSERS_EXPORT RWMol * MolDataStreamToMol(std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RDKIT_FILEPARSERS_EXPORT RWMol * TPLDataStreamToMol(std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false)
translate TPL data (BioCad format) into a multi-conf molecule
RDKIT_FILEPARSERS_EXPORT RWMol * Mol2FileToMol(const std::string &fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=true)
RDKIT_FILEPARSERS_EXPORT RWMol * RDKitSVGToMol(const std::string &svg, bool sanitize=true, bool removeHs=true)
const char * message() const
get the error message
std::vector< RWMOL_SPTR > RWMOL_SPTR_VECT
RDKIT_FILEPARSERS_EXPORT RWMol * PDBBlockToMol(const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RDKIT_GRAPHMOL_EXPORT ROMol * removeHs(const ROMol &mol, bool implicitOnly=false, bool updateExplicitCount=false, bool sanitize=true)
returns a copy of a molecule with hydrogens removed
MolFileUnhandledFeatureException(const std::string msg)
construct with an error message
RDKIT_FILEPARSERS_EXPORT std::string MolToMolBlock(const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false)
RDKIT_FILEPARSERS_EXPORT RWMol * PDBFileToMol(const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RDKIT_FILEPARSERS_EXPORT RWMol * Mol2BlockToMol(const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=true)
RDKIT_FILEPARSERS_EXPORT RWMol * MolFileToMol(const std::string &fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RDKIT_FILEPARSERS_EXPORT RWMol * PDBDataStreamToMol(std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RDKIT_FILEPARSERS_EXPORT std::string MolToPDBBlock(const ROMol &mol, int confId=-1, unsigned int flavor=0)