kinoml.docking.OEDocking

Module Contents

kinoml.docking.OEDocking.resids_to_box_molecule(protein: openeye.oechem.OEMolBase, resids: List[int]) → openeye.oechem.OEGraphMol

Retrieve a box molecule spanning the given protein residue IDs.

Parameters

  • protein (oechem.OEMolBase) – An OpenEye molecule holding a protein structure.

  • resids (list of int) – A list of resids defining the residues of interest.

Returns

box_molecule – Rectangular box molecule spanning the region of the given protein defined by the given residue IDs.

Return type

oechem.OEGraphMol

kinoml.docking.OEDocking.pose_molecules(design_unit: openeye.oechem.OEDesignUnit, molecules: List[openeye.oechem.OEMolBase], pKa_norm: bool = True, score_pose: bool = False) → Union[List[openeye.oechem.OEGraphMol], None]

Generate a binding pose of molecules in a prepared receptor with OpenEye’s Posit method.

Parameters

  • design_unit (oechem. OEDesignUnit) – A design unit with a receptor object.

  • molecules (list of oechem.OEMolBase) – A list of OpenEye molecules holding prepared molecules for docking.

  • pKa_norm (bool, default=True) – Assign the predominant ionization state at pH ~7.4.

  • score_pose (bool, default=False) – Score the best docking pose per ligand and add the proper SD tag.

Returns

posed_molecules – A list of OpenEye molecules holding the docked molecules.

Return type

list of oechem.OEGraphMol or None

kinoml.docking.OEDocking.run_docking(design_unit: openeye.oechem.OEDesignUnit, molecules: List[openeye.oechem.OEMolBase], dock_method: int, num_poses: int = 1, pKa_norm: bool = True) → Union[List[openeye.oechem.OEGraphMol], None]

Dock molecules into a prepared design unit containing a receptor object.

Parameters

  • design_unit (oechem.OEDesignUnit) – A design unit with a receptor object.

  • molecules (list of oechem.OEMolBase) – A list of OpenEye molecules holding prepared molecules for docking.

  • dock_method (int) – Constant defining the docking method.

  • num_poses (int) – Number of docking poses to generate per molecule.

  • pKa_norm (bool, default=True) – Assign the predominant ionization state at pH ~7.4.

Returns

docked_molecules – A list of OpenEye molecules holding the docked molecules.

Return type

list of oechem.OEGraphMol or None

kinoml.docking.OEDocking.hybrid_docking(design_unit: openeye.oechem.OEDesignUnit, molecules: List[openeye.oechem.OEMolBase], num_poses: int = 1, pKa_norm: bool = True) → Union[List[openeye.oechem.OEGraphMol], None]

Dock molecules into a prepared design unit containing a hybrid receptor object.

Parameters

  • design_unit (oechem.OEDesignUnit) – A design unit with a hybrid receptor object.

  • molecules (list of oechem.OEMolBase) – A list of OpenEye molecules holding prepared molecules for docking.

  • num_poses (int) – Number of docking poses to generate per molecule.

  • pKa_norm (bool, default=True) – Assign the predominant ionization state at pH ~7.4.

Returns

docked_molecules – A list of OpenEye molecules holding the docked molecules.

Return type

list of oechem.OEGraphMol or None

kinoml.docking.OEDocking.fred_docking(design_unit: openeye.oechem.OEDesignUnit, molecules: List[openeye.oechem.OEMolBase], num_poses: int = 1, pKa_norm: bool = True) → Union[List[openeye.oechem.OEGraphMol], None]

Dock molecules into a prepared design unit containing a receptor object.

Parameters

  • design_unit (oechem.OEDesignUnit) – A design unit with a receptor object.

  • molecules (list of oechem.OEMolBase) – A list of OpenEye molecules holding prepared molecules for docking.

  • num_poses (int) – Number of docking poses to generate per molecule.

  • pKa_norm (bool, default=True) – Assign the predominant ionization state at pH ~7.4.

Returns

docked_molecules – A list of OpenEye molecules holding the docked molecules.

Return type

list of oechem.OEGraphMol or None