kinoml.modeling.SCHRODINGERModeling

Module Contents

kinoml.modeling.SCHRODINGERModeling.logger
kinoml.modeling.SCHRODINGERModeling.run_prepwizard(schrodinger_directory: Union[pathlib.Path, str], input_file: Union[pathlib.Path, str], output_file: Union[pathlib.Path, str], cap_termini: bool = True, build_loops: bool = True, sequence: Union[str, None] = None, chain_id: str = '', protein_pH: str = 'neutral', propka_pH: float = 7.4, epik_pH: float = 7.4, force_field: str = '3')

Run the prepwizard utility to prepare a protein structure.

Parameters

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

  • input_file (Path or str) – The path to the input file.

  • output_file (Path or str) – The path to the output file.

  • cap_termini (bool, default=True) – If termini should be capped.

  • build_loops (bool, default=True) – If loops should be built.

  • sequence (str or None) – The amino acid sequence in single letter codes that should be used for loop building. Also needs the chain_id parameter to work correctly.

  • chain_id (str, default="") – The chain ID of the protein that should be modeled based on the given sequence.

  • protein_pH (str, default='neutral') – The pH used during protonation of the protein (‘very_low’, ‘low’, ‘neutral’, ‘high’).

  • propka_pH (float, default=7.4) – Run PROPKA at given pH.

  • epik_pH (float, default=7.4) – The pH used during protonation of the ligand.

  • force_field (str, default='3') – Force field to use during minimization (2005, 3)

kinoml.modeling.SCHRODINGERModeling.mae_to_pdb(schrodinger_directory: Union[str, pathlib.Path], mae_file_path: Union[str, pathlib.Path], pdb_file_path: Union[str, pathlib.Path])

Convert a structure file from MAE to PDB format.

Parameters

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

  • mae_file_path (str or pathlib.Path) – The path to the input file in MAE format.

  • pdb_file_path (str or pathlib.Path) – The path to the output file in PDB format.

kinoml.modeling.SCHRODINGERModeling.shape_screen(schrodinger_directory: Union[pathlib.Path, str], query_path: Union[str, pathlib.Path], library_path: Union[str, pathlib.Path], output_sdf_path: Union[str, pathlib.Path], flexible: bool = True, thorough_sampling: bool = True, keep_best_match_only: bool = True)

Run the shape_screen tool to align a library of small molecules to the given shape query.

Parameters

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

  • query_path (Path or str) – The path to a valid shape query, e.g. an SDF file with one or more small molecules.

  • library_path (Path or str) – The path to a valid ligand library for shape screening, e.g. and SDF file with one more small molecules.

  • output_sdf_path (Path or str) – The path to the output SDF file of the shape screening.

  • flexible (bool, default=True) – If conformers shell be generated for the small molecule library to screen.

  • thorough_sampling (bool, default=True) – If conformations shell thoroughly sampled.

  • keep_best_match_only (bool, default=True) – In case multiple shape queries, if only the results for best matching shape query shell be returned.