10 #ifndef _RD_MOLFRAGMENTER_H__ 11 #define _RD_MOLFRAGMENTER_H__ 17 namespace MolFragmenter{
52 const std::vector< std::pair<unsigned int,unsigned int> > *dummyLabels=0,
53 const std::vector< Bond::BondType > *bondTypes=0,
54 std::vector<unsigned int> *nCutsPerAtom=0);
57 const std::map<unsigned int,ROMOL_SPTR> *atomEnvirons=0,
58 std::vector<unsigned int> *nCutsPerAtom=0);
60 std::vector<ROMOL_SPTR> &resMols,
61 unsigned int maxToCut=1,
63 const std::vector< std::pair<unsigned int,unsigned int> > *dummyLabels=0,
64 const std::vector< Bond::BondType > *bondTypes=0,
65 std::vector<std::vector<unsigned int> > *nCutsPerAtom=0);
77 std::string comment=
"//",
bool validate=
true,
78 std::map<unsigned int,ROMOL_SPTR> *environs=0);
80 std::string comment=
"//",
bool validate=
true,
81 std::map<unsigned int,ROMOL_SPTR> *environs=0);
83 std::map<unsigned int,ROMOL_SPTR> *environs=0);
85 const std::map<unsigned int,std::string> &atomTypes,
86 std::vector<FragmenterBondType> &defs,
87 std::string comment=
"//",
bool validate=
true,
88 bool labelByConnector=
true);
90 const std::map<unsigned int,std::string> &atomTypes,
91 std::vector<FragmenterBondType> &defs,
92 std::string comment=
"//",
bool validate=
true,
93 bool labelByConnector=
true);
ROMol * fragmentOnBRICSBonds(const ROMol &mol)
Fragments a molecule by breaking all BRICS bonds.
void fragmentOnSomeBonds(const ROMol &mol, const std::vector< unsigned int > &bondIndices, std::vector< ROMOL_SPTR > &resMols, unsigned int maxToCut=1, bool addDummies=true, const std::vector< std::pair< unsigned int, unsigned int > > *dummyLabels=0, const std::vector< Bond::BondType > *bondTypes=0, std::vector< std::vector< unsigned int > > *nCutsPerAtom=0)
Defines the primary molecule class ROMol as well as associated typedefs.
ROMol is a molecule class that is intended to have a fixed topology.
void constructBRICSBondTypes(std::vector< FragmenterBondType > &defs)
ROMol * fragmentOnBonds(const ROMol &mol, const std::vector< unsigned int > &bondIndices, bool addDummies=true, const std::vector< std::pair< unsigned int, unsigned int > > *dummyLabels=0, const std::vector< Bond::BondType > *bondTypes=0, std::vector< unsigned int > *nCutsPerAtom=0)
Fragments a molecule by breaking a set of bonds.
void constructBRICSAtomTypes(std::map< unsigned int, std::string > &defs, std::map< unsigned int, ROMOL_SPTR > *environs=0)
void constructFragmenterAtomTypes(std::istream *inStream, std::map< unsigned int, std::string > &defs, std::string comment="//", bool validate=true, std::map< unsigned int, ROMOL_SPTR > *environs=0)
boost::shared_ptr< ROMol > ROMOL_SPTR
Includes a bunch of functionality for handling Atom and Bond queries.
void constructFragmenterBondTypes(std::istream *inStream, const std::map< unsigned int, std::string > &atomTypes, std::vector< FragmenterBondType > &defs, std::string comment="//", bool validate=true, bool labelByConnector=true)