11 #ifndef _RD_MOLFRAGMENTER_H__ 12 #define _RD_MOLFRAGMENTER_H__ 18 namespace MolFragmenter {
51 const ROMol &mol,
const std::vector<unsigned int> &bondIndices,
52 bool addDummies =
true,
53 const std::vector<std::pair<unsigned int, unsigned int> > *dummyLabels = 0,
54 const std::vector<Bond::BondType> *bondTypes = 0,
55 std::vector<unsigned int> *nCutsPerAtom = 0);
58 const ROMol &mol,
const std::vector<FragmenterBondType> &bondPatterns,
59 const std::map<unsigned int, ROMOL_SPTR> *atomEnvirons = 0,
60 std::vector<unsigned int> *nCutsPerAtom = 0);
62 const ROMol &mol,
const std::vector<unsigned int> &bondIndices,
63 std::vector<ROMOL_SPTR> &resMols,
unsigned int maxToCut = 1,
64 bool addDummies =
true,
65 const std::vector<std::pair<unsigned int, unsigned int> > *dummyLabels = 0,
66 const std::vector<Bond::BondType> *bondTypes = 0,
67 std::vector<std::vector<unsigned int> > *nCutsPerAtom = 0);
78 std::istream *inStream, std::map<unsigned int, std::string> &defs,
79 const std::string &comment =
"//",
bool validate =
true,
80 std::map<unsigned int, ROMOL_SPTR> *environs = 0);
82 const std::string &str, std::map<unsigned int, std::string> &defs,
83 const std::string &comment =
"//",
bool validate =
true,
84 std::map<unsigned int, ROMOL_SPTR> *environs = 0);
86 std::map<unsigned int, ROMOL_SPTR> *environs = 0);
88 std::istream *inStream,
89 const std::map<unsigned int, std::string> &atomTypes,
90 std::vector<FragmenterBondType> &defs,
const std::string &comment =
"//",
91 bool validate =
true,
bool labelByConnector =
true);
93 const std::string &str,
94 const std::map<unsigned int, std::string> &atomTypes,
95 std::vector<FragmenterBondType> &defs,
const std::string &comment =
"//",
96 bool validate =
true,
bool labelByConnector =
true);
RDKIT_CHEMTRANSFORMS_EXPORT void constructBRICSAtomTypes(std::map< unsigned int, std::string > &defs, std::map< unsigned int, ROMOL_SPTR > *environs=0)
Defines the primary molecule class ROMol as well as associated typedefs.
RDKIT_CHEMTRANSFORMS_EXPORT void constructFragmenterAtomTypes(std::istream *inStream, std::map< unsigned int, std::string > &defs, const std::string &comment="//", bool validate=true, std::map< unsigned int, ROMOL_SPTR > *environs=0)
RDKIT_CHEMTRANSFORMS_EXPORT void constructBRICSBondTypes(std::vector< FragmenterBondType > &defs)
boost::shared_ptr< ROMol > ROMOL_SPTR
RDKIT_CHEMTRANSFORMS_EXPORT void constructFragmenterBondTypes(std::istream *inStream, const std::map< unsigned int, std::string > &atomTypes, std::vector< FragmenterBondType > &defs, const std::string &comment="//", bool validate=true, bool labelByConnector=true)
#define RDKIT_CHEMTRANSFORMS_EXPORT
RDKIT_CHEMTRANSFORMS_EXPORT 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)
RDKIT_CHEMTRANSFORMS_EXPORT ROMol * fragmentOnBRICSBonds(const ROMol &mol)
Fragments a molecule by breaking all BRICS bonds.
RDKIT_CHEMTRANSFORMS_EXPORT 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.