10 #ifndef _RD_CHEMTRANSFORMS_H__ 11 #define _RD_CHEMTRANSFORMS_H__ 13 #include <boost/smart_ptr.hpp> 36 bool onlyFrags=
false);
73 const ROMol &replacement,
74 bool replaceAll=
false,
75 unsigned int replacementConnectionPoint=0);
115 bool replaceDummies=
true,
bool labelByIndex=
false,
116 bool requireDummyMatch=
false);
166 std::vector<std::pair<unsigned int, std::string> > *reactantLabels=NULL);
183 void parseQueryDefFile(std::string filename,std::map<std::string,ROMOL_SPTR> &queryDefs,
184 bool standardize=
true,std::string delimiter=
"\t",std::string comment=
"//",
185 unsigned int nameColumn=0,
unsigned int smartsColumn=1);
187 void parseQueryDefFile(std::istream *inStream,std::map<std::string,ROMOL_SPTR> &queryDefs,
188 bool standardize=
true,std::string delimiter=
"\t",std::string comment=
"//",
189 unsigned int nameColumn=0,
unsigned int smartsColumn=1);
191 void parseQueryDefText(
const std::string &queryDefText,std::map<std::string,ROMOL_SPTR> &queryDefs,
192 bool standardize=
true,std::string delimiter=
"\t",std::string comment=
"//",
193 unsigned int nameColumn=0,
unsigned int smartsColumn=1);
void parseQueryDefFile(std::string filename, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, std::string delimiter="\t", std::string comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1)
parses a query definition file and sets up a set of definitions suitable for use by addRecursiveQueri...
ROMol * combineMols(const ROMol &mol1, const ROMol &mol2, RDGeom::Point3D offset=RDGeom::Point3D(0, 0, 0))
Combined two molecules to create a new one.
void addRecursiveQueries(ROMol &mol, const std::map< std::string, ROMOL_SPTR > &queries, std::string propName, std::vector< std::pair< unsigned int, std::string > > *reactantLabels=NULL)
Adds named recursive queries to a molecule's atoms based on atom labels.
ROMol is a molecule class that is intended to have a fixed topology.
ROMol * replaceCore(const ROMol &mol, const ROMol &coreQuery, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false)
Returns a copy of an ROMol with the atoms and bonds that do fall within a substructure match removed...
ROMol * MurckoDecompose(const ROMol &mol)
Carries out a Murcko decomposition on the molecule provided.
ROMol * deleteSubstructs(const ROMol &mol, const ROMol &query, bool onlyFrags=false)
Returns a copy of an ROMol with the atoms and bonds that match a pattern removed. ...
boost::shared_ptr< ROMol > ROMOL_SPTR
void parseQueryDefText(const std::string &queryDefText, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, std::string delimiter="\t", std::string comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1)
equivalent to parseQueryDefFile() but the query definitions are explicitly passed in ...
Includes a bunch of functionality for handling Atom and Bond queries.
std::vector< ROMOL_SPTR > replaceSubstructs(const ROMol &mol, const ROMol &query, const ROMol &replacement, bool replaceAll=false, unsigned int replacementConnectionPoint=0)
Returns a list of copies of an ROMol with the atoms and bonds that match a pattern replaced with the ...
ROMol * replaceSidechains(const ROMol &mol, const ROMol &coreQuery)
Returns a copy of an ROMol with the atoms and bonds that don't fall within a substructure match remov...