schrodinger.application.jaguar.utils module

Jaguar utility functions.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.jaguar.utils.FreeEnergy(temp, gibbs, property_key)

Bases: tuple

gibbs

Alias for field number 1

property_key

Alias for field number 2

temp

Alias for field number 0

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
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

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.)

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
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
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
schrodinger.application.jaguar.utils.gibbs_energy_property_string(temp, inf_sep=False)

Construct the property key string for Gibbs energy at a particular temperature

Parameters:
  • temp (float) – temperature in Kelvin
  • inf_sep (bool) – True indicates infinitely separated energy
Returns:

a property key string
schrodinger.application.jaguar.utils.parse_gibbs_energies(st, inf_sep=False)

Search the structures property dict to find all Total_Free_Energy properties. Extract the temperature, gibbs energy and property keys and store these in a dict relating temperature to FreeEnergy instances.

Parameters:st (Structure) – the structure
Returns:a dict relating temperature to a FreeEnergy instance with attributes storing these data
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:

str or None