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

__contains__

Return key in self.

__init__

Initialize self. See help(type(self)) for accurate signature.

__len__

Return len(self).

count(value) → integer -- return number of occurrences of value
gibbs

Alias for field number 1

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

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.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_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.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
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_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.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.remove_gibbs_energies(st, allowed_temps=())

Remove gibbs energy properties from a structure but allow some exceptions. This allows one to ‘unclutter’ the project table.

Parameters:
  • st (Structure) – structure containing gibbs energy properties
  • allowed_temps (tuple) – temperatures that are allowed to remain as properties
schrodinger.application.jaguar.utils.parse_gibbs_energies(st, inf_sep=False, std_conc=False)

Extract the temperature, gibbs energy and property keys for free energy and store these in a dict relating temperature to FreeEnergy instances.

Parameters:
  • st (Structure) – the structure
  • std_con (bool) – True indicates Gibbs energy at std state concentration
Returns:

a dict relating temperature to a FreeEnergy instance with attributes storing these data
schrodinger.application.jaguar.utils.gibbs_energy_property_string(temp, inf_sep=False, std_conc=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
  • std_conc (bool) – True indicates Gibbs energy at std state concentration
Returns:

a property key string
schrodinger.application.jaguar.utils.convert_gibbs_energy_to_std_conc(st)

Convert std state (1 atm) Gibbs energies to a std state of 1 Molar concentration. The energies are returned as a dict relating temperature to FreeEnergy instances. The energies are also stored as structure level properties. This is intended to be used with AutoTS for rate calculations and we assume the free energies were computed at 1 atm of pressure.

Parameters:st (Structure) – the structure
Returns:a dict relating temperature to a FreeEnergy instance with attributes storing these data
schrodinger.application.jaguar.utils.compute_std_conc_gibbs_energy(gibbs, temp, press, con)

Convert Gibbs energy which was computed at a pressure of press to a concentration of con using the formula G = G_0 + kT log(CRT/P_0) where we’ve used the ideal gas law to relate P = CRT

Parameters:
  • gibbs (float) – Gibbs free energy in a.u. evaluated at a pressure of press
  • press (float) – Pressure at which the Gibbs energy was evaluated in atm
  • temp (float) – Temperature at which the Gibbs energy was evaluated in Kelvin
  • con (float) – Concentration which defines the standard state in moles/Liter
schrodinger.application.jaguar.utils.group_items(items, comparator, *args)

Put items into groups using a comparator. These will be returned as a list of lists, each list representing a group. The first item of the first group will be the first item in the list items. The groups have the property that Comparator(item1, item2, args) returns True for all pairs in a group.

Parameters:
  • items (list) – a list of items to group
  • comparator (function) – this function compares two items and returns a boolean indicating whether or not they are equivalent.
  • args (argument list) – arguments passed to the comparator which is called as comparator(item1, item2, *args)
Returns:

a list of lists of items
schrodinger.application.jaguar.utils.beta_au(temp)

Beta = 1/kT in a.u.

schrodinger.application.jaguar.utils.beta_kcalmol(temp)

Beta = 1/kT in kcal/mol

schrodinger.application.jaguar.utils.copy_structure_bonding(ref_st, updated_st)

Copy all bonding and formal charges from reference structure onto a structure instance we want to update. Also update FF atom-typing. Assumes number of atoms and atom numbering is the same in both structures.

Parameters:
  • ref_st (Structure object) – structure to copy bonding from
  • updated_st (Structure object) – structure to copy bonding to
schrodinger.application.jaguar.utils.sync_dummy_atoms(ref_st, st)

Sync dummy atoms in ref_st and st. It assumes all atoms are the same, except for two possibilities: (1) existence of new dummy atoms at the end of the atom list in ref_st

compared to st; they will be added to the end of st.
  1. non-existence of dummy atoms at any location in ref_st compared to st; they will be deleted from st.

If this is not true, an AssertionError will be raised.

This is useful after calling mmjag_connect to reset bonding.

Parameters:
  • ref_st (Structure object) – structure to copy atoms from
  • st (Structure object) – structure to copy atoms to
schrodinger.application.jaguar.utils.mmjag_reset_connectivity(st)

Reset connectivity and Lewis structure using mmjag algorithm. i.e input st is modified to have new bonds, bond orders and formal charges. All other properties should be preserved.

Parameters:st (Structure object) – structure to clean up
schrodinger.application.jaguar.utils.mmjag_update_lewis(st)

Update Lewis structure for a given connectivity using mmjag algorithm. This can be used instead of, or to complement, e.g. the mmlewis code. Unlike mmjag_reset_connectivity, the connectivity will be preserved.

If the mmjag Lewis code fails to update the bonding, the original bonding will be preserved.

Parameters:st (Structure object) – structure to clean up