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RDKit
Open-source cheminformatics and machine learning.
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Classes | |
struct | FragmenterBondType |
Functions | |
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. More... | |
ROMol * | fragmentOnBonds (const ROMol &mol, const std::vector< FragmenterBondType > &bondPatterns, const std::map< unsigned int, ROMOL_SPTR > *atomEnvirons=0, std::vector< unsigned int > *nCutsPerAtom=0) |
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) |
ROMol * | fragmentOnBRICSBonds (const ROMol &mol) |
Fragments a molecule by breaking all BRICS bonds. More... | |
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) |
void | constructFragmenterAtomTypes (const std::string &str, std::map< unsigned int, std::string > &defs, std::string comment="//", bool validate=true, std::map< unsigned int, ROMOL_SPTR > *environs=0) |
void | constructBRICSAtomTypes (std::map< unsigned int, std::string > &defs, std::map< unsigned int, ROMOL_SPTR > *environs=0) |
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) |
void | constructFragmenterBondTypes (const std::string &str, const std::map< unsigned int, std::string > &atomTypes, std::vector< FragmenterBondType > &defs, std::string comment="//", bool validate=true, bool labelByConnector=true) |
void | constructBRICSBondTypes (std::vector< FragmenterBondType > &defs) |
void RDKit::MolFragmenter::constructBRICSAtomTypes | ( | std::map< unsigned int, std::string > & | defs, |
std::map< unsigned int, ROMOL_SPTR > * | environs = 0 |
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void RDKit::MolFragmenter::constructBRICSBondTypes | ( | std::vector< FragmenterBondType > & | defs | ) |
void RDKit::MolFragmenter::constructFragmenterAtomTypes | ( | std::istream * | inStream, |
std::map< unsigned int, std::string > & | defs, | ||
std::string | comment = "//" , |
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bool | validate = true , |
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std::map< unsigned int, ROMOL_SPTR > * | environs = 0 |
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void RDKit::MolFragmenter::constructFragmenterAtomTypes | ( | const std::string & | str, |
std::map< unsigned int, std::string > & | defs, | ||
std::string | comment = "//" , |
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bool | validate = true , |
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std::map< unsigned int, ROMOL_SPTR > * | environs = 0 |
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void RDKit::MolFragmenter::constructFragmenterBondTypes | ( | std::istream * | inStream, |
const std::map< unsigned int, std::string > & | atomTypes, | ||
std::vector< FragmenterBondType > & | defs, | ||
std::string | comment = "//" , |
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bool | validate = true , |
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bool | labelByConnector = true |
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void RDKit::MolFragmenter::constructFragmenterBondTypes | ( | const std::string & | str, |
const std::map< unsigned int, std::string > & | atomTypes, | ||
std::vector< FragmenterBondType > & | defs, | ||
std::string | comment = "//" , |
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bool | validate = true , |
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bool | labelByConnector = true |
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ROMol* RDKit::MolFragmenter::fragmentOnBonds | ( | const ROMol & | mol, |
const std::vector< unsigned int > & | bondIndices, | ||
bool | addDummies = true , |
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const std::vector< std::pair< unsigned int, unsigned int > > * | dummyLabels = 0 , |
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const std::vector< Bond::BondType > * | bondTypes = 0 , |
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std::vector< unsigned int > * | nCutsPerAtom = 0 |
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Fragments a molecule by breaking a set of bonds.
mol | - the molecule to be modified |
bondIndices | - indices of the bonds to be broken |
optional:
addDummies | - toggles addition of dummy atoms to indicate where bonds were broken |
dummyLabels | - used to provide the labels to be used for the dummies. the first element in each pair is the label for the dummy that replaces the bond's beginAtom, the second is for the dummy that replaces the bond's endAtom. If not provided, the dummies are labeled with atom indices. |
bondTypes | - used to provide the bond type to use between the fragments and the dummy atoms. If not provided, defaults to single. |
nCutsPerAtom | - used to return the number of bonds that were cut at each atom. Should be nAtoms long. |
ROMol* RDKit::MolFragmenter::fragmentOnBonds | ( | const ROMol & | mol, |
const std::vector< FragmenterBondType > & | bondPatterns, | ||
const std::map< unsigned int, ROMOL_SPTR > * | atomEnvirons = 0 , |
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std::vector< unsigned int > * | nCutsPerAtom = 0 |
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
Fragments a molecule by breaking all BRICS bonds.
void RDKit::MolFragmenter::fragmentOnSomeBonds | ( | const ROMol & | mol, |
const std::vector< unsigned int > & | bondIndices, | ||
std::vector< ROMOL_SPTR > & | resMols, | ||
unsigned int | maxToCut = 1 , |
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bool | addDummies = true , |
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const std::vector< std::pair< unsigned int, unsigned int > > * | dummyLabels = 0 , |
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const std::vector< Bond::BondType > * | bondTypes = 0 , |
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std::vector< std::vector< unsigned int > > * | nCutsPerAtom = 0 |
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