schrodinger.application.jaguar.jaguar_keyword_utils module¶

Functions to help grab keywords from xml and jaguar input files

schrodinger.application.jaguar.jaguar_keyword_utils.required_basis(functional: str) → Optional[str]¶

Get the basis set that should be used for the given functional. If the functional is not in FUNCTIONAL_TO_BASIS, then None is returned, indicating that the functional does not require a specific basis set.

Parameters: functional – The functional to get the basis set for
Returns: The basis set that should be used or None if the functional does not require a specific basis set

schrodinger.application.jaguar.jaguar_keyword_utils.jaguar_keywords_xml_filename() → str¶: Find the jaguar_keywords.xml file in $SCHRODINGER/mmshare-v*/

schrodinger.application.jaguar.jaguar_keyword_utils.all_keywords() → List[str]¶: return a list of all keywords

schrodinger.application.jaguar.jaguar_keyword_utils.all_meaningful_keywords() → List[str]¶: return a partial list keywords excludes all iopt,opt,cut,ip

schrodinger.application.jaguar.jaguar_keyword_utils.dftnames_markup() → Dict[str, List]¶

Return dictionary of DFT names, a short description, and DOI’s to literature references if available, grouped by type. All information is taken from the levels_of_theory.csv file. This is intended for use by the documentation team for auto-doc’ing. See JAGUAR-9563.

{'Local': [
     ('HFS', 'a short description', ['doi:1']),
     ('XALPHA', 'another functional', ['do1:2', 'doi:3']),
     ('SVWN', None, None),
    ...
'Aposteriori-corrected': [
     ('PBE-ulg', None, None),
     ('B3LYP-MM', None, None),
    ...
'Recommended': [
     ('B3LYP', None, None),
     ('B3LYP-MM', None, None),
    ...
}

schrodinger.application.jaguar.jaguar_keyword_utils.all_dftnames() → List[str]¶: Return a list of all dftnames. Includes HF, which can be specified as a dftname in Jaguar.

schrodinger.application.jaguar.jaguar_keyword_utils.all_basisnames() → List[str]¶: return a list of all basis set names each basis set name is itself a list containing ‘base’ name, backup name, nplus, nstar

schrodinger.application.jaguar.jaguar_keyword_utils.jaguar_input_keywords(fname: str) → Dict[str, str]¶: return a dictionary of the keywords in fname that are non-default hf and mp2 are considered ‘dftname’ and dftname and basis are always included

schrodinger.application.jaguar.jaguar_keyword_utils.clean_basisname(basis: str) → str¶: return a cleaned up basis name with stars following pluses i.e. NAME+++****

schrodinger.application.jaguar.jaguar_keyword_utils.keyword_coverage(input_files: List[str], print_report: bool = True) → Tuple[float, float, float, List[str], List[str], List[str]]¶: given a list of input files return in this order (as return 1, 2, 3, 4, 5, 6) 1 - percent of keywords covered 2 - percent of basis sets covered 3 - percent of functionals covered 4 - list of uncovered keywords 5 - list of uncovered basis sets 6 - list of uncovered functionals

schrodinger.application.jaguar.jaguar_keyword_utils.supported_basis_sets(functional: str) → List[str]¶: returns the supported basis sets for a particular functional, only useful for B3LYP-MM/B3LYP-LOC

schrodinger.application.jaguar.jaguar_keyword_utils.basis_is_supported_for_functional(functional: str, basis: str) → bool¶: is this functional/basis set combination supported really just checks B3LYP-MM and B3LYP-LOC

schrodinger.application.jaguar.jaguar_keyword_utils.basisname_in_list(basis: str, lst: list, remove: bool = False) → bool¶: Inspect list to see if basisname is in it. Compares only by ‘basename’, i.e. no ‘*’s or ‘+’s optionally removes any matches from the list