schrodinger.application.glide.specs module

This module provides the specs that define the input keywords recognized by Glide.

schrodinger.application.glide.specs.read_yaml()

Read mmim_keywords.json and return a list of objects. The read_yaml() name was retained for compatibility.

schrodinger.application.glide.specs.read_keywords_file()

Read the mmim_keywords.json file from the mmshare data directory and return a list of objects.

schrodinger.application.glide.specs.read_keywords_file_as_dict()

Read the mmim_keywords.json file from the mmshare data directory and return a dict of dicts, where the key is the keyword name and the value is the spec for the keyword (see get_keyword for more details).

schrodinger.application.glide.specs.get_keyword(keyword)

Return the specification of a Glide keyword as a dictionary, with keys such as “keyword”, “type”, “default”, “allowed”, “min”, “max”, and “comment”. For the full list and description for each field, see the comments in mmim_keywords.yaml.

schrodinger.application.glide.specs.get_keywords_dicts(jobtypes, include_undocumented=False)

Return the raw mmim_keywords.yaml data filtered to include only the keywords for the requested job types.

schrodinger.application.glide.specs.keyword_spec(jobtypes, include_undocumented=False)

Return a string with the specification of the mmim keywords that are valid for the jobtypes given. Jobtypes should be an iterable with items such as ‘docking’, ‘multi_docking’, or ‘gridgen’. Keywords for jobtype ‘all’ are always included.

By default, undocumented keywords are not included in the return value, but that behavior can be overridden by setting ‘include_undocumented’ to True.

schrodinger.application.glide.specs.validation_specs(jobtype)

Return a list of validation specs for a given jobtype (e.g., ‘docking’ or ‘gridgen’) or list of jobtypes. This includes not only the keywords returned by keyword_spec(jobtype), but also some extra keywords that are supported by glide.py but not by mmim.

schrodinger.application.glide.specs.get_keywords_set(jobtypes)

Return the set of all keywords valid for the given job types.

schrodinger.application.glide.specs.is_gridgen_keyword(keyword)

Return True is a keyword is valid for gridgen jobs.

schrodinger.application.glide.specs.is_docking_keyword(keyword)

Return True is a keyword is valid for docking jobs.