schrodinger.application.matsci.solvation_entropy_utils module

Utilities for solvation entropy in reaction workflow.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.solvation_entropy_utils.TempPressProp(temperature_K, pressure_atm, solvent_density_g_cm3)

Bases: tuple

pressure_atm

Alias for field number 1

solvent_density_g_cm3

Alias for field number 2

temperature_K

Alias for field number 0

class schrodinger.application.matsci.solvation_entropy_utils.StructurePropertyInfo(key, is_total_energy, is_logged, lnq_key)

Bases: tuple

is_logged

Alias for field number 2

is_total_energy

Alias for field number 1

key

Alias for field number 0

lnq_key

Alias for field number 3

schrodinger.application.matsci.solvation_entropy_utils.add_temp_press_parser_arguments(parser)

Add temperature and pressure related arguments to the parser.

Parameters:

parser (argparse.ArgumentParser) – the parser to add these arguments to

schrodinger.application.matsci.solvation_entropy_utils.get_jaguar_solvents_csv()

Return the Jaguar solvents in solvents.csv.

Return type:

list[str]

Returns:

the Jaguar solvents

schrodinger.application.matsci.solvation_entropy_utils.get_jaguar_solvents_xml()

Return the Jaguar solvents in jaguar_keywords.xml.

Return type:

list[str]

Returns:

the Jaguar solvents

schrodinger.application.matsci.solvation_entropy_utils.get_jaguar_solvents()

Return the Jaguar solvents.

Return type:

list[str]

Returns:

the Jaguar solvents

schrodinger.application.matsci.solvation_entropy_utils.add_solvation_entropy_arguments(parser)

Add solvation entropy related arguments to the parser.

Parameters:

parser (argparse.ArgumentParser) – the parser to add these arguments to

schrodinger.application.matsci.solvation_entropy_utils.get_solvent_params(solvent)

Return the solvent parameters for the given Jaguar-supported solvent.

Parameters:

solvent (str) – the Jaguar-supported solvent

Raises:

SolvationEntropyException – if there is an issue

Return type:

SolventParams

Returns:

the solvent parameters

schrodinger.application.matsci.solvation_entropy_utils.get_solvent_params_by_t_and_p(solvent, temp_press_data)

Return the solvent parameters for the given Jaguar-supported solvent keyed by temprature and pressure.

Parameters:

  • solvent (str) – the Jaguar-supported solvent

  • temp_press_data (rxnwfu.TempPressData) – the temperature and pressure data for thermochemical properties

Return type:

dict

Returns:

the solvent parameters keyed by temperature and pressure

schrodinger.application.matsci.solvation_entropy_utils.get_flags_from_solvent_params(solvent_params)

Return a list of flags from the given solvent parameters.

Parameters:

solvent_params (SolventParams) – the solvent parameters

Return type:

list[str]

Returns:

the flags

schrodinger.application.matsci.solvation_entropy_utils.get_lnQtot(temperature, energy)

Return ln(Q_tot) from the given Gibbs free energy.

Parameters:

  • temperature (float) – temperature in K

  • energy (float) – the Gibbs free energy in hartree

Return type:

float

Returns:

ln(Q_tot)

schrodinger.application.matsci.solvation_entropy_utils.get_gibbs_free_energy(temperature, lnqtot)

Return Gibbs free energy from the given ln(Q_tot).

Parameters:

  • temperature (float) – temperature in K

  • lnqtot (float) – ln(Q_tot)

Return type:

float

Returns:

Gibbs free energy in hartree

exception schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyException

Bases: Exception

class schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyProperties(st, stage_idx, out_fp)

Bases: object

S_TRANSLATION_START = 'Translation'
S_ROTATION_START = 'Rotation'
S_VIBRATION_START = 'Vibration'
S_CONCENTRATION_START = 'Concentration'
S_CAVITY_START = 'Cavity'
S_TOTAL_START = 'Total'
S_STARTERS = ['Translation', 'Rotation', 'Vibration', 'Concentration', 'Cavity', 'Total']
S_TRANSLATION_KEY = 'S_trans'
S_ROTATION_KEY = 'S_rot'
S_VIBRATION_KEY = 'S_vib'
S_CONCENTRATION_KEY = 'S_conc'
S_CAVITY_KEY = 'S_cav'
S_TOTAL_KEY = 'S_tot'
S_KEYS = ['S_trans', 'S_rot', 'S_vib', 'S_conc', 'S_cav', 'S_tot']
S_STARTERS_TO_KEYS = {'Cavity': 'S_cav', 'Concentration': 'S_conc', 'Rotation': 'S_rot', 'Total': 'S_tot', 'Translation': 'S_trans', 'Vibration': 'S_vib'}
G_TOTAL_OMEGA_START = 'Total Gibbs free energy with S_omega'
G_TOTAL_EPSILON_START = 'Total Gibbs free energy with S_epsilon'
G_TOTAL_EPSILON_ALPHA_START = 'Total Gibbs free energy with S_epsilon_alpha'
G_IDXS_TO_STARTERS = {1: 'Total Gibbs free energy with S_omega', 2: 'Total Gibbs free energy with S_epsilon', 3: 'Total Gibbs free energy with S_epsilon_alpha'}
G_TOTAL_KEY = 'G_tot'
LNQ_TOTAL_KEY = 'lnQ_tot'
OMEGA_KEY = 'omega'
EPSILON_KEY = 'epsilon'
EPSILON_ALPHA_KEY = 'epsilon_alpha'
TYPES_TO_IDXS = {'epsilon': 2, 'epsilon_alpha': 3, 'omega': 1}
SOLVATION_ENTROPY = 'solvation_entropy'
PROP_STARTER = 'r_matsci_solvation_entropy'
ENTROPY_STARTER = 'r_matsci_solvation_entropy_{type_key}_{s_key}_(cal/mol/K)'
ENTROPY_PROP = 'r_matsci_solvation_entropy_{type_key}_{s_key}_(cal/mol/K){temp_press}_stage_{idx}'
FREE_ENERGY_STARTER = 'r_matsci_solvation_entropy_{type_key}_G_tot_(au)'
FREE_ENERGY_PROP = 'r_matsci_solvation_entropy_{type_key}_G_tot_(au){temp_press}_stage_{idx}'
LNQ_STARTER = 'r_matsci_solvation_entropy_{type_key}_lnQ_tot'
LNQ_PROP = 'r_matsci_solvation_entropy_{type_key}_lnQ_tot{temp_press}_stage_{idx}'
__init__(st, stage_idx, out_fp)
Parameters:
parseTempPress(lines)

Parse the temperature and pressure.

Parameters:

lines (list[str]) – lines from the output

Raises:

SolvationEntropyException – if there is an issue

parseZPEEnergy(lines)

Parse the ZPE energy.

Parameters:

lines (list[str]) – lines from the output

Raises:

SolvationEntropyException – if there is an issue

parseSCFEnergy(lines)

Parse the SCF energy.

Parameters:

lines (list[str]) – lines from the output

Raises:

SolvationEntropyException – if there is an issue

parseSolvationEntropySection(lines)

Parse the solvation entropy section.

Parameters:

lines (list[str]) – lines from the output

Raises:

SolvationEntropyException – if there is an issue

Return type:

int

Returns:

the 0-based index of the line marking the start of the solvation entropy section

parseEntropies(lines, properties)

Parse the entropies.

Parameters:

  • lines (list[str]) – lines from the output

  • properties (dict) – dictionary to which to add properties

Raises:

SolvationEntropyException – if there is an issue

parseFreeEnergies(lines, properties)

Parse the Gibbs free energies.

Parameters:

  • lines (list[str]) – lines from the output

  • properties (dict) – dictionary to which to add properties

Raises:

SolvationEntropyException – if there is an issue

calculatelnQs(properties)

Calculate the lnQs.

Parameters:

properties (dict) – dictionary to which to add properties

parseFile()

Parse the solvation entropy output.

static getEntropyInfos(temperature, pressure, stage_idx)

Return a list of entropy StructurePropertyInfo.

Parameters:

  • temperature (float) – temperature in K

  • pressure (float) – pressure in atm

  • stage_idx (int) – the stage index

Return type:

list[StructurePropertyInfo]

Returns:

entropy properties

static getFreeEnergyInfos(temperature, pressure, stage_idx)

Return a list of free energy StructurePropertyInfo.

Parameters:

  • temperature (float) – temperature in K

  • pressure (float) – pressure in atm

  • stage_idx (int) – the stage index

Return type:

list[StructurePropertyInfo]

Returns:

free energy properties

static getlnQInfos(temperature, pressure, stage_idx)

Return a list of ln(Q) StructurePropertyInfo.

Parameters:

  • temperature (float) – temperature in K

  • pressure (float) – pressure in atm

  • stage_idx (int) – the stage index

Return type:

list[StructurePropertyInfo]

Returns:

ln(Q) properties

setStructureProperties()

Set the structure properties.

getOutMaeFileName()

Return the output mae file name.

Return type:

str

Returns:

the output mae file name

writeStructure()

Write the structure.

run()

Run it.

class schrodinger.application.matsci.solvation_entropy_utils.SolvationEntropyJob(st, stage_idx, out_fn, temperature, pressure, solvent_params, *args, **kwargs)

Bases: LoggingSubprocessJob

Manage a solvation entropy job.

__init__(st, stage_idx, out_fn, temperature, pressure, solvent_params, *args, **kwargs)

See parent class for documentation.

Parameters:

  • st (schrodinger.structure.Structure) – the structure

  • stage_idx (int) – the stage index

  • out_fn (str) – the Jaguar .out output file name

  • temperature (float) – the temperature in K

  • pressure (float) – the pressure in atm

  • solvent_params (SolventParams) – the solvent parameters

update()

See parent class for documentation.

exception schrodinger.application.matsci.solvation_entropy_utils.TempPressDataException

Bases: Exception

class schrodinger.application.matsci.solvation_entropy_utils.TempPressData(temp_start=298.15, temp_step=10.0, temp_n=1, press_start=1.0, press_step=1.0, press_n=1, temp_press_props_fn=None)

Bases: object

Manage temperatures and pressures and properties that depend them.

__init__(temp_start=298.15, temp_step=10.0, temp_n=1, press_start=1.0, press_step=1.0, press_n=1, temp_press_props_fn=None)
Parameters:

  • temp_start (float) – the starting temperature in K

  • temp_step (float) – the temperature step in K

  • temp_n (int) – the number of temperatures

  • press_start (float) – the starting pressure in atm

  • press_step (float) – the pressure step in atm

  • press_n (int) – the number of pressures

  • temp_press_props_fn (str) – csv file containing temperatures in K, pressures in atm, and any other properties, using column names TEMPERATURE_COL, PRESSURE_COL, and SOLVENT_DENSITY_COL

setFromOptions(options)

Set from options.

Parameters:

options (argparse.Namespace) – the object holding all the option values

setFromJaguarKeywords(keywords)

Set from Jaguar keywords.

Parameters:

keywords (dict) – Jaguar keywords

getCmd()

Return the command line.

Return type:

list[str]

Returns:

the command line

static getTempPressDataFromOptions(options)

Return TempPressData from the given options.

Parameters:

options (argparse.Namespace) – the object holding all the option values

Return type:

TempPressData

Returns:

the TempPressData from the given options

static getTempPressDataFromJaguarKeywords(keywords)

Return TempPressData from the given Jaguar keywords.

Parameters:

keywords (dict) – Jaguar keywords

Return type:

TempPressData

Returns:

the TempPressData from the given Jaguar keywords

getPressuresTemperatures()

Return the list of pressures and temepratures.

Return type:

list[float], list[float]

Returns:

pressures in atm, temperatures in K

getJaguarKeywords()

Return the Jaguar keywords.

Return type:

dict

Returns:

the Jaguar keywords

static removeFromJaguarKeywords(key_dict)

Remove the temperature and pressure keywords from the given dictionary of Jaguar keywords.

Parameters:

key_dict (dict) – the Jaguar keywords

setPropsByTAndP()

Set the temperature and pressure dependent properties dictionary.

Raises:

TempPressDataException – if there is an issue