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

__add__

Return self+value.

__class__

alias of builtins.type

__contains__

Return key in self.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__

Return self[key].

__getnewargs__()

Return self as a plain tuple. Used by copy and pickle.

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__iter__

Implement iter(self).

__le__

Return self<=value.

__len__

Return len(self).

__lt__

Return self<value.

__module__ = 'schrodinger.application.jaguar.utils'
__mul__

Return self*value.n

__ne__

Return self!=value.

static __new__(_cls, temp, gibbs, property_key)

Create new instance of FreeEnergy(temp, gibbs, property_key)

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__()

Return a nicely formatted representation string

__rmul__

Return self*value.

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()
__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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