11 #ifndef _RD_FILEPARSERS_H 12 #define _RD_FILEPARSERS_H 22 #include <boost/shared_ptr.hpp> 49 bool strictParsing =
true);
55 bool strictParsing =
true);
69 bool strictParsing =
true);
84 bool strictParsing =
true);
98 bool includeStereo =
true,
100 bool kekulize =
true,
101 bool forceV3000 =
false);
115 const ROMol &mol,
const std::string &fName,
bool includeStereo =
true,
116 int confId = -1,
bool kekulize =
true,
bool forceV3000 =
false);
140 bool sanitize =
true,
141 bool skipFirstConf =
false);
159 bool sanitize =
true,
160 bool skipFirstConf =
false);
163 const ROMol &mol,
const std::string &partialChargeProp =
"_GasteigerCharge",
164 bool writeFirstConfTwice =
false);
166 const ROMol &mol,
const std::string &fName,
167 const std::string &partialChargeProp =
"_GasteigerCharge",
168 bool writeFirstConfTwice =
false);
190 bool sanitize =
true,
193 bool cleanupSubstructures =
true);
206 std::istream *inStream,
bool sanitize =
true,
bool removeHs =
true,
210 std::istream &inStream,
bool sanitize =
true,
bool removeHs =
true,
224 const std::string &molBlock,
bool sanitize =
true,
bool removeHs =
true,
228 bool sanitize =
true,
230 unsigned int flavor = 0,
231 bool proximityBonding =
true);
234 bool sanitize =
true,
236 unsigned int flavor = 0,
237 bool proximityBonding =
true);
239 std::istream *inStream,
bool sanitize =
true,
bool removeHs =
true,
240 unsigned int flavor = 0,
bool proximityBonding =
true);
242 std::istream &inStream,
bool sanitize =
true,
bool removeHs =
true,
243 unsigned int flavor = 0,
bool proximityBonding =
true);
245 bool sanitize =
true,
247 unsigned int flavor = 0,
248 bool proximityBonding =
true);
264 unsigned int flavor = 0);
279 const std::string &fname,
281 unsigned int flavor = 0);
293 bool sanitize =
true,
298 bool sanitize =
true,
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
#define RDKIT_FILEPARSERS_EXPORT
std::vector< RWMOL_SPTR > RWMOL_SPTR_VECT
RDKIT_FILEPARSERS_EXPORT RWMol * MolBlockToMol(const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
const int MOLFILE_MAXLINE
RWMol is a molecule class that is intended to be edited.
RDKIT_FILEPARSERS_EXPORT RWMol * PDBDataStreamToMol(std::istream *inStream, 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
RDKIT_FILEPARSERS_EXPORT void MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0)
RDKIT_FILEPARSERS_EXPORT std::string MolToPDBBlock(const ROMol &mol, int confId=-1, unsigned int flavor=0)
RDKIT_FILEPARSERS_EXPORT RWMol * RDKitSVGToMol(const std::string &svg, bool sanitize=true, bool removeHs=true)
RDKIT_FILEPARSERS_EXPORT RWMol * Mol2DataStreamToMol(std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=true)
pulls in the core RDKit functionality
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 * 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 * MolFileToMol(const std::string &fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
RDKIT_FILEPARSERS_EXPORT std::string MolToTPLText(const ROMol &mol, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)
RDKIT_FILEPARSERS_EXPORT void MolToTPLFile(const ROMol &mol, const std::string &fName, const std::string &partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)
RDKIT_FILEPARSERS_EXPORT RWMol * PDBBlockToMol(const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
RDKIT_FILEPARSERS_EXPORT RWMol * MolDataStreamToMol(std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
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 * Mol2BlockToMol(const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=CORINA, bool cleanupSubstructures=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 std::string strip(const std::string &orig)
RDKIT_FILEPARSERS_EXPORT std::string MolToMolBlock(const ROMol &mol, bool includeStereo=true, int confId=-1, bool kekulize=true, bool forceV3000=false)