Input

enzymm.jess_run.load_molecules(molecule_paths: List[Path], conservation_cutoff: float = 0, warn: bool = False) → List[Molecule]

Load query molecules from a list of paths to PDB or CIF/mmCIF structure files.

Parameters:

  • molecule_paths – List of Path: List of PDB or CIF structure file paths to load

  • conservation_cutoff – float: Load only Atoms with a B-factor above this value Default 0

  • warn – bool If warnings about issues during matching should be printed. Default False

Note

This function will try to auto-detect the format of the files (PDB or CIF)

Note

This function can also handle gz, bz2, lz4 and xz compressed files

enzymm.template.load_templates(template_dir: Path | None = None, warn: bool = False, verbose: bool = False, with_annotations: bool = True) → Iterator[Template | AnnotatedTemplate]

Load templates from a given directory, recursively.

Parameters:

  • template_dir – Path | None Directory which to search recursively for files with the ‘.pdb’ extension. By default, set to None, it will load templates included in this library.

  • warn – bool If warnings about annoation issues in templates should be printed. Default False

  • verbose – bool If loading should be verbose. Default False

  • with_annotations – bool If True (default) M-CSA derived templates with a PDB-id and M-CSA id will be annotated with extra information.

Yields:

Template | AnnotatedTemplate