schrodinger.application.jaguar.utils module¶
Jaguar utility functions.
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.application.jaguar.utils.
append_outfiles_to_recover_file
(recover_file, outfiles)¶ Append list of output file paths to a YAML-format .recover file.
Parameters: - recover_file (str) – .recover file name
- outfiles (list of str) – list of output file paths
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schrodinger.application.jaguar.utils.
elmnt_mult_dict
()¶ make a dictionary of element:multiplicity for all neutral elements up to Lawrencium
The values are from the ground state term symbol as reported by NIST at http://physics.nist.gov/PhysRefData/Elements/index.html as of 4.2014
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schrodinger.application.jaguar.utils.
get_jobname
(prefix, str_to_hash)¶ Construct a jobname based on the given string prefix (typically the backend script name) and a string to be hashed (typically based on the cmdline being used to invoke the job.)
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schrodinger.application.jaguar.utils.
get_number_electrons
(st)¶ Count the number of electrons disregarding charges.
Parameters: st (Structure instance) – the structure Return type: int Returns: the number of electrons
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schrodinger.application.jaguar.utils.
get_stoichiometry_string
(atom_list)¶ Take atom list and return stoichiometry string. For example, atom_list = [‘H’, ‘H’, ‘O’] yields stoichimetry string = ‘H2O’.
Parameters: atom_list (list) – list of strings Returns: stoichiometry string Return type: str
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schrodinger.application.jaguar.utils.
get_total_charge
(structure)¶ Return the total charge of the structure If the property i_m_Molecular_charge is defined we use that, else we sum the formal charges
Parameters: structure (Structure object) – whose total charge must be calculated Returns: total charge of structure Return type: int
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schrodinger.application.jaguar.utils.
validate_stoichiometry
(reactants, products)¶ This function validates stoichiometry for a reaction defined by the list of reactants and products. If stoichiometry is not valid this function return text string explaining what was wrong. In case of valid stoichiometry returns None.
Parameters: - reactants (list) – list of
JaguarInput
objects for reactants - products (list) – list of
JaguarInput
objects products
Returns: string with warning message or None
Return type: - reactants (list) – list of