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(const OEFragmentOptions& opts = OEFragmentOptions())

Default constructor.

Add

bool Add(OEChem::OEMCMolBase& frag)
bool Add(OESystem::OEIter<OEChem::OEMCMolBase>& frag)
bool Add(const std::string& smiles)
bool Add(const std::vector<std::string>& vecSmiles)

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

AddCSV

bool AddCSV(const std::vector<std::string>& vecSmiles)

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

Expand

bool Expand(const OEConfGen::OEFlipperOptions& opts)

Expands the database by stereo-enumerating currently contained fragments.

Filter

bool Filter(OEMolProp::OEFilter& filter)

Filters currently contained database fragments.

Generate

bool Generate(const OEChem::OEMolBase& mol)

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

GetFrag

bool GetFrag(OEChem::OEMCMolBase& mol, const std::string& smiles) const

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

std::vector<std::string> GetFragSmiles() const
bool GetFragSmiles(std::vector<std::string>&) const

Returns SMILES strings corresponding to the current database.

GetFragSmilesCSV

std::vector<std::string> GetFragSmilesCSV() const
bool GetFragSmilesCSV(std::vector<std::string>&) const

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

GetFrags

OESystem::OEIterBase<OEChem::OEMCMolBase>* GetFrags() const

Returns two-dimensional fragments corresponding to the current database.

NumFrags

unsigned NumFrags() const

Returns the number of fragments corresponding to the current database.

Screen

bool Screen(const OEDBScreenOptions& opts)

Screens the fragments in the current database.