OECreateBroodQuery

Query Creation without Protein

Attention

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

OECreateBroodQuery(query: OEBroodQuery, mol: OEMol,
                   selection: OEAtomBondSet) -> int
OECreateBroodQuery(query: OEBroodQuery, mol: OEMol,
                   selection: OEMatchBase) -> int

Creates a BROOD query. The function returns a status code from OEBroodStatusCode.

query

The OEBroodQuery to be created.

mol

The input molecule from which a query is to be created by replacing a fragment of the molecule.

selection

Criteria for selecting atoms and bonds of the molecule that becomes the fragment to be replaced. The atoms and bonds must collectively become a single fragment.

Query Creation with Associated Protein

OECreateBroodQuery(query: OEBroodQuery, mol: OEMol,
                   selection: OEAtomBondSet, du: OEDesignUnit,
                   proteinMask: int,
                   passingProteinSelect: bool = False) -> int
OECreateBroodQuery(query: OEBroodQuery, mol: OEMol,
                   selection: OEMatchBase, du: OEDesignUnit,
                   proteinMask: int,
                   passingProteinSelect: bool = False) -> int

Creates a BROOD query. The function returns a status code from OEBroodStatusCode.

du

The OEDesignUnit corresponding to the protein target.

proteinMask

Mask to be applied with the OEDesignUnit to determine the protein target.

passingProteinSelect

To create a BROOD query with a protein select, this boolean needs to be true.

Query Creation with Associated Protein and Protein Select

OECreateBroodQuery(query: OEBroodQuery, mol: OEMol,
                   selection: OEAtomBondSet, protDu: OEDesignUnit,
                   proteinMask: int, protSelectDu: OEDesignUnit,
                   proteinSelectMask: int) -> int
OECreateBroodQuery(query: OEBroodQuery, mol: OEMol,
                   selection: OEMatchBase, protDu: OEDesignUnit,
                   proteinMask: int, protSelectDu: OEDesignUnit,
                   proteinSelectMask: int) -> int

Creates a BROOD query. The function returns a status code from OEBroodStatusCode.

protSelectDu

The OEDesignUnit corresponding to the protein select target.

proteinSelectMask

Mask to be applied with the OEDesignUnit to determine the protein select target.

Linker Query Creation with Two Molecules (Bridging) without Protein

OECreateBroodQuery(query: OEBroodQuery, firstMol: OEMol,
                   secondMol: OEMol, firstMolSelection: OEMatchBase,
                   secondMolSelection: OEMatchBase) -> int
OECreateBroodQuery(query: OEBroodQuery, firstMol: OEMol,
                   secondMol: OEMol, firstMolSelection: OEAtomBondSet,
                   secondMolSelection: OEAtomBondSet) -> int

Creates a BROOD query. The function returns a status code from OEBroodStatusCode.

firstMol & secondMol

Input molecules from which a query is to be created by bridging a fragment between them. Molecules need to prepared in proper relative coordinates and should not be clashing for optimum results.

firstMolSelection and secondMolSelection

Criteria for selecting atoms and bonds of each molecule that becomes part of the bridge fragment to be replaced. The atoms and bonds must collectively become a single fragment for each molecule.

Linker Query Creation with Two Molecules (Bridging) with Protein

OECreateBroodQuery(query: OEBroodQuery, firstMol: OEMol,
                   secondMol: OEMol, firstMolSelection: OEMatchBase,
                   secondMolSelection: OEMatchBase, du: OEDesignUnit,
                   proteinMask: int,
                   passingProteinSelect: bool = False) -> int
OECreateBroodQuery(query: OEBroodQuery, firstMol: OEMol,
                   secondMol: OEMol, firstMolSelection: OEAtomBondSet,
                   secondMolSelection: OEAtomBondSet,
                   du: OEDesignUnit, proteinMask: int,
                   passingProteinSelect: bool = False) -> int

Creates a BROOD query. The function returns a status code from OEBroodStatusCode.

Linker Query Creation with Two Molecules (Bridging) with Protein and Protein Select

OECreateBroodQuery(query: OEBroodQuery, firstMol: OEMol,
                   secondMol: OEMol, firstMolSelection: OEMatchBase,
                   secondMolSelection: OEMatchBase,
                   protDu: OEDesignUnit, proteinMask: int,
                   protSelectDu: OEDesignUnit, proteinSelectMask: int) -> int
OECreateBroodQuery(query: OEBroodQuery, firstMol: OEMol,
                   secondMol: OEMol, firstMolSelection: OEAtomBondSet,
                   secondMolSelection: OEAtomBondSet,
                   protDu: OEDesignUnit, proteinMask: int,
                   protSelectDu: OEDesignUnit, proteinSelectMask: int) -> int

Creates a BROOD query. The function returns a status code from OEBroodStatusCode.