Package schrodinger :: Package application :: Package jaguar :: Module utils

Module utils

Jaguar utility functions.

Functions

append_outfiles_to_recover_file(recover_file, outfiles)
Append list of output file paths to a .recover file.

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.)

str

get_stoichiometry_string(atom_list)
Take atom list and return stoichiometry string.

list

_get_atom_elements(jag_input)
This function returns list of elements for atoms stored in a given JaguarInput object.

tuple

_get_atoms_and_charge(inputs)
This function iterates over the list of given JaguarInput objects and creates a list of all atom element names as well as total charge.

str or None

validate_stoichiometry(reactants, products)
This function validates stoichiometry for a reaction defined by the list of reactants and products.

int

get_number_electrons(st)
Count the number of electrons disregarding charges.

int

get_total_charge(structure)
Return the total charge of the structure

elmnt_mult_dict()
make a dictionary of element:multiplicity for all neutral elements up to Lawrencium

Variables

[hide private]

__package__ = 'schrodinger.application.jaguar'

Function Details

[hide private]

append_outfiles_to_recover_file(recover_file, outfiles)

Append list of output file paths to a .recover file.

Parameters:

recover_file (str) - .recover file name
outfiles (list of str) - list of output file paths

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: str

stoichiometry string

_get_atom_elements(jag_input)

This function returns list of elements for atoms stored in a given JaguarInput object. This function is only used when calling validate_stoichiometry function.

Returns: list: list of atom elements

_get_atoms_and_charge(inputs)

This function iterates over the list of given JaguarInput objects and creates a list of all atom element names as well as total charge. This function is only used when calling validate_stoichiometry function.

Returns: tuple: tuple that contains list of atom elements and total charge

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: str or None

string with warning message or None

get_number_electrons(st)

Count the number of electrons disregarding charges.

Parameters:

st (Structure instance) - the structure

Returns: int

the number of electrons

get_total_charge(structure)

Return the total charge of the structure

Parameters:

structure (Structure object) - whose total charge must be calculated

Returns: int

total charge of structure

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