kinoml.docking.SCHRODINGERDocking

Module Contents

kinoml.docking.SCHRODINGERDocking.logger
kinoml.docking.SCHRODINGERDocking.run_glide(schrodinger_directory: Union[pathlib.Path, str], input_file_mae: Union[pathlib.Path, str], output_file_sdf: Union[pathlib.Path, str], mols_smiles: List[str], ligand_resname: Union[str, None], n_poses: int = 1, mols_names: Union[List[str], None] = None, shape_restrain: bool = True, macrocyles: bool = False, precision: str = 'XP', cache_dir: Union[pathlib.Path, str] = user_cache_dir())

Run glide for protein ligand docking.

Parameters

  • schrodinger_directory (Path or str) – The path to the directory of the Schrodinger installation.

  • input_file_mae (Path or str) – The path to the input file in MAE format containing the protein structure to dock to and a co-crystallized ligand in the binding pocket of interest.

  • output_file_sdf (Path or str) – The path to the output file of the generated in docking poses in SDF format.

  • mols_smiles (list of str) – The molecules to dock as SMILES representation.

  • ligand_resname (str or None) – The resname of the co-crystallized ligand, which will be used for pocket definition.

  • mols_names (None or list of str, default=None) – The names of the molecules to dock. Will be used as molecule title in the SDF file. If None, names will be numbers (1,..,len(mols_smiles).

  • n_poses (int, default=1) – Number of poses to generate per molecule.

  • shape_restrain (bool, default=True) – If the co-crystallized ligand shell be used for shape restrained docking.

  • macrocyles (bool, default=False) – Macrocycle conformations will be sampled with an appropriate algorithm. All non- macrocyclic molecules by detected by SCHRODINGER will be skipped.

  • precision (str, default="XP") – The docking precision to use [“HTVS”, “SP”, “XP”].

  • cache_dir (Path or str, default=appdirs.user_cache_dir()) – Path to a directory for caching grids for docking.