OEDBBuilder

Attention

This is a preliminary API and may be improved based on user feedback. It is currently available in C++ and Python.

class OEDBBuilder

This class defines an interface for building a two-dimensional Brood fragment database.

The OEDBBuilder class defines the following public methods:

Add
AddCSV
Expand
Filter
Generate
GetFrag
GetFragSmiles
GetFragSmilesCSV
GetFrags
NumFrags
Screen

Constructors

OEDBBuilder(opts: OEFragmentOptions = OEFragmentOptions()) -> OEDBBuilder

Default constructor.

Add

Add(frag: OEMol) -> bool
Add(vecSmiles: OEStringVector) -> bool

Adds the specified fragment(s) to the database. In the SMILES-based overloads, fragment SMILES in the format obtained from GetFragSmiles are expected.

AddCSV

AddCSV(vecSmiles: OEStringVector) -> bool

Adds fragments from the specified CSV SMILES strings. SMILES as obtained from GetFragSmilesCSV are expected.

Expand

Expand(opts: OEFlipperOptions) -> bool

Expands the database by stereo-enumerating currently contained fragments.

Filter

Filter(filter: OEFilter) -> bool

Filters currently contained database fragments.

Generate

Generate(mol: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Generates fragments from the specified molecule and adds the generated fragment(s) to the database.

GetFrag

GetFrag(mol: OEMol, smiles: str) -> bool

Obtains the fragment defined by the specified SMILES string. Returns false if a fragment with the specified SMILES does not exist. SMILES in the format obtained from GetFragSmiles is expected.

GetFragSmiles

GetFragSmiles() -> OEStringVector

Returns SMILES strings corresponding to the current database.

GetFragSmilesCSV

GetFragSmilesCSV() -> OEStringVector
GetFragSmilesCSV(vecSmiles: OEStringVector) -> bool

Returns CSV SMILES strings corresponding to the current database. CSV SMILES contains fragment SMILES in a special comma-separated string format.

GetFrags

GetFrags() -> Iterable[OEMol]

Returns two-dimensional fragments corresponding to the current database.

NumFrags

NumFrags() -> int

Returns the number of fragments corresponding to the current database.

Screen

Screen(opts: OEDBScreenOptions) -> bool

Screens the fragments in the current database.