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__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

gibbs

Alias for field number 1

index(value, start=0, stop=9223372036854775807, /)

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

class schrodinger.application.jaguar.utils.LewisStructure(charges, bonds, score, unpaired)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

bonds

Alias for field number 1

charges

Alias for field number 0

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

score

Alias for field number 2

unpaired

Alias for field number 3

class schrodinger.application.jaguar.utils.ChgAt(index, charge)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

charge

Alias for field number 1

count(value, /)

Return number of occurrences of value.

index

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.basic_windows_path(dos_path)

Convert extended length Windows path to standard. Does nothing on other OS’s.

Parameters

dos_path (string) – a (Windows) file path, which may have WINDOWS_EXTENDED_PATH_TAG to indicate extended path length

Return type

string

Returns

A file path which has not extended length tags

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. This is useful after calling mmjag_connect to reset bonding. We check atomic number and XYZ coordinates to classify which atoms are the “same” or “different”. But note for dummy atoms, we do not require XYZ to be the same.

We then try to sync the two structures by handling 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.

2. Non-existence of dummy atoms at any location in ref_st compared to st; they will be deleted from st.

Otherwise, an AssertionError is raised.

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, mode=0)

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 mode is PRINT, the lewis structure determination information will be returned

If mode is RINGCHAIN, special Lewis structure scoring for ring-chain tautomers will be used (and lewis structure information will be returned)

If mode if THOROUGH, the lewis structure search will be lengthened

If mode if FINDALL, the lewis structure search will be lengthened and suboptimal results will be included in the output data (which is sorted to have the best first).

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

Parameters

• st (Structure object) – structure to clean up

• mode (int) – specifies if std or ring-chain scoring should be used and whether or not the data is returned from lewis.cpp. Only STD, PRINT, RINGCHAIN, THOROUGH, and FINDALL are acceptable values

Return type

list of LewisStructure namedtuples

Returns

If mode is PRINT, RINGCHAIN, THOROUGH, or FINDALL, parsed lewis structure data is returned as namedtuple; an empty list is returned if mode is STD.

schrodinger.application.jaguar.utils.parse_lewis_data(lewis_data)

Parse the string-formatted Lewis data from mmjag into a data structure for easy use.

Parameters

lewis_data (list of strings:) – the line-by-line output of mmjag/lewis.cpp run on a structure

Return type

list of LewisStructure namedtuples

Returns

Namedtuples containing charge, multiple bond, and score

schrodinger.application.jaguar.utils.get_charges(lewis_output)

Parse charges from lewis code string output

Parameters

lewis_output (list of strings) – the line-by-line output of mmjag/lewis.cpp run on a structure

Return type

(list of list of ChgAt namedtuples, list of bools)

Returns

For each structure in the lewis_output (the length of the list), list of the charged atom and their charges, whether or not structure contains unpaired spins

schrodinger.application.jaguar.utils.get_bonds(lewis_output)

Parse bonds from lewis code string output

Parameters

lewis_output (list of strings) – the line-by-line output of mmjag/lewis.cpp run on a structure

Return type

list of list of 2-tuples of ints

Returns

For each structure in the lewis_output (the length of the list), list of the multiple bonds in the structure (NB: a triple bond is noted by being present in the list twice)

schrodinger.application.jaguar.utils.get_scores(lewis_output)

Parse scores from lewis code string output

Parameters

lewis_output (list of strings) – the line-by-line output of mmjag/lewis.cpp run on a structure

Return type

list of floats

Returns

For each structure in the lewis_output (the length of the list), that structures score according to the mmjag/lewis.cpp code (see there for more details)

schrodinger.application.jaguar.utils.apply_lewis(st, lewis_st)

Return a copy of a structure with a Lewis structure as described by the LewisStructure given.

Parameters

• st (Structure instance) – structure on which to apply Lewis structure

• lewis_st (LewisStructure namedtuple) – Namedtuple containing charge, multiple bond, and score

Return type

Structure instance

Returns

a structure with the desired Lewis structure applied