schrodinger.application.jaguar.garza module¶

Holds functions relating to calculation of equations from Garza, A. J. Chem. Theory Comput. 2019, 15, 5, 3204–3214 DOI: 10.1021/acs.jctc.9b00214

These functions are used in thermochemical_properties.py to calculate solvation entropy quantities. The functions are closely related to those in jaguar-src/main/garza.f and should be kept in-sync.

Bases: object

Dataclass holding the various contributions to the solvation entropy totals. All values have units of Ha/K

trans: float | None = None¶

rot: float | None = None¶

vib: float | None = None¶

conc: float | None = None¶

omega_cav: float | None = None¶

epsilon_cav: float | None = None¶

eps_alpha_cav: float | None = None¶

__init__(trans: float | None = None, rot: float | None = None, vib: float | None = None, conc: float | None = None, omega_cav: float | None = None, epsilon_cav: float | None = None, eps_alpha_cav: float | None = None) → None¶

Bases: object

Solvent parameters for solvation entropy calculations. Extracted from output file or read in through cmdline arguments.

mol_weight: float | None = None¶

density: float | None = None¶

volume: float | None = None¶

surface_area: float | None = None¶

radius_of_gyr: float | None = None¶

acentric_factor: float | None = None¶

dielectric_constant: float | None = None¶

expansion_coeff: float | None = None¶

check_params() → bool¶: Check that enough solvent parameters are defined to allow calculation of at least one solvation entropy flavor.

__init__(mol_weight: float | None = None, density: float | None = None, volume: float | None = None, surface_area: float | None = None, radius_of_gyr: float | None = None, acentric_factor: float | None = None, dielectric_constant: float | None = None, expansion_coeff: float | None = None) → None¶

class schrodinger.application.jaguar.garza.SoluteParams(volume: float | None = None, surface_area: float | None = None, radius_of_gyr: float | None = None)¶

Bases: object

Solute parameters for solvation entropy calculations. Extracted from structure in output file.

volume: float | None = None¶

surface_area: float | None = None¶

radius_of_gyr: float | None = None¶

__init__(volume: float | None = None, surface_area: float | None = None, radius_of_gyr: float | None = None) → None¶

class schrodinger.application.jaguar.garza.CalculatedParams(v_free: float | None = None, v_c: float | None = None, r_c: float | None = None, n_c: float | None = None)¶

Bases: object

Parameters that are calculated during solvation entropy calculations. Used in multiple equations so it is useful to store them.

v_free: float | None = None¶

v_c: float | None = None¶

r_c: float | None = None¶

n_c: float | None = None¶

__init__(v_free: float | None = None, v_c: float | None = None, r_c: float | None = None, n_c: float | None = None) → None¶

class schrodinger.application.jaguar.garza.SolvEntropyParams(solvent: schrodinger.application.jaguar.garza.SolventParams = <factory>, solute: schrodinger.application.jaguar.garza.SoluteParams = <factory>, calculated: schrodinger.application.jaguar.garza.CalculatedParams = <factory>)¶

Bases: object

Dataclass holding all parameters for solvation entropy.

solvent: schrodinger.application.jaguar.garza.SolventParams¶

solute: schrodinger.application.jaguar.garza.SoluteParams¶

calculated: schrodinger.application.jaguar.garza.CalculatedParams¶

get_intermediate_args() → tuple[float, float, float, float]¶: Helper function to make calls to calc_intermediates() take less space

get_acentric_args() → tuple[float, float, float]¶: Helper function to make calls to calc_acentric() take less space

get_spt_args() → tuple[float, float, float, float]¶: Helper function to make calls to calc_spt() take less space

__init__(solvent: schrodinger.application.jaguar.garza.SolventParams = <factory>, solute: schrodinger.application.jaguar.garza.SoluteParams = <factory>, calculated: schrodinger.application.jaguar.garza.CalculatedParams = <factory>) → None¶

schrodinger.application.jaguar.garza.calc_st_params(st: schrodinger.structure._structure.Structure) → tuple[float, float, float]¶

Given a Structure, calculate parameters relevant to calculation of solvation entropy.

Returns: Volume (ang^3), surface area (ang^2), and radius of gyration (ang) of Structure

schrodinger.application.jaguar.garza.calc_entropy_translation(mass: float, temp: float, vol: float) → float¶

Calculate translational contribution of entropy according to ideal gas thermodynamic equations.

Parameters

temp – temperature in Kelvin
press – pressure in atomic units (Ha/bohr^3)
vol – volume in bohr^3

Returns

translational component of entropy

schrodinger.application.jaguar.garza.calc_intermediates(mol_weight: float, density: float, volume: float, solute_volume: float) → tuple[float, float, float, float]¶

Calculate intermediate values used in solvation entropy See Eq’s 5-9 Garza, A. J. Chem. Theory Comput. 2019, 15, 5, 3204–3214 DOI: 10.1021/acs.jctc.9b00214

Parameters

mol_weight – solvent molecule weight, g/mol
density – solvent density, g/ang^3
volume – solvent volume, ang^3
solute_volume – solute volume, ang^3

Returns v_free

Free volume per solvent molecule, ang^3,

Returns v_c

Solute cavity volume, ang^3

Returns r_c

Solute cavity radius, ang

Returns n_c

Number of hopping sites for solute in solvent, unitless

schrodinger.application.jaguar.garza.calc_rot_term(mass: float, temp: float, v_free: float, rad_gyr: float, r_c: float, n_c: float) → float¶

Calculates the additional rotational term for solvation entropy according to Garza for a solute See last two terms of Eq 11 Garza, A. J. Chem. Theory Comput. 2019, 15, 5, 3204–3214 DOI: 10.1021/acs.jctc.9b00214

Parameters

mass – Mass of solute in atomic units (electron mass’)
temp – Temperature, in Kelvin
rad_gyr – Solute radius of gyration, in ang
v_free – Free volume per solvent molecule, in ang^3
r_c – Radius of solute cavity, in ang
n_c – Average number of hopping sites, unitless

Returns garza_rot_entropy

additional rotational entropy term, Hartree/K

schrodinger.application.jaguar.garza.calc_accessible_cavities(v_free: float, v_solvent: float, v_solute: float, r_c: float) → float¶

Calculates the average number of accessible cavities, n_c See Eq’s 7-9 Garza, A. J. Chem. Theory Comput. 2019, 15, 5, 3204–3214 DOI: 10.1021/acs.jctc.9b00214

Parameters

v_free – Free volume per solvent molecule, ang^3
v_solvent – Volume of solvent molecule, ang^3
v_solute – Volume of solute molecule, ang^3
r_c – Solute cavity radius, ang

Returns n_c

number of accessible cavities

schrodinger.application.jaguar.garza.calc_shape_factor(surface_area: float) → float¶

Calculates the shape factor for a given surface area. Given surface area of a sphere, find it’s radius and use that to find minimum bounding box. See Eq 16 Garza, A. J. Chem. Theory Comput. 2019, 15, 5, 3204–3214 DOI: 10.1021/acs.jctc.9b00214

Parameters: surface_area – surface area, ang^2
Returns: Garza’s shape factor

schrodinger.application.jaguar.garza.calc_acentric(temp: float, solvent: schrodinger.application.jaguar.garza.SolventParams, solute: schrodinger.application.jaguar.garza.SoluteParams, v_free: float) → float | None¶

Calculate the cavity entropy using acentric factor approximation. See Eq 13-23 in Garza, A. J. Chem. Theory Comput. 2019, 15, 5, 3204–3214 DOI: 10.1021/acs.jctc.9b00214

Parameters

temp – Temperature, in Kelvin
solvent – Solvent parameters
solute – Solute parameters
v_free – Free volume per solvent molecule, ang^3

Returns garza_cavity_acentric

Cavity entropy using acentric factor approx, Ha/K

schrodinger.application.jaguar.garza.calc_spt(temp: float, volume: float, dielectric: float, exp_coeff: float, solute_volume: float) → tuple[float | None, float | None]¶

Calculate the epsilon and epsilon,alpha cavity entropies using Garza’s scaled particle theory (spt). See Eq 25-32 in Garza, A. J. Chem. Theory Comput. 2019, 15, 5, 3204–3214 DOI: 10.1021/acs.jctc.9b00214

Note that in communication with Garza, he mentioned that Eq 25 is missing a factor of “y” in the second term. The equations are correct in the ref.

Parameters

temp – Temperature, in K
volume – Solvent volume, in ang^3
dielectric – Solvent permittivity (dielectric constant), no units
exp_coeff – Solvent expansion coefficient, in 1/K
solute_volume – Solute volume, in ang^3

Returns epsilon_val

S_epsilon, Ha/K

Returns eps_alpha_val

S_epsilon,alpha in Ha/K

schrodinger.application.jaguar.garza.calc_concentration_term(temp: float, pressure: float) → float¶

Calculates concentration change contribution to solvation entropy. Assumes standard states, converting from given pressure to 1 M See Eq 33 Garza, A. J. Chem. Theory Comput. 2019, 15, 5, 3204–3214 DOI: 10.1021/acs.jctc.9b00214

Parameters

pressure – pressure in APU (Ha/bohr^3)
temp – temperature in K

Returns

concentration term of solvation entropy, Ha/K

schrodinger.application.jaguar.garza.print_solvation_entropy(temp: float, pressure: float, enthalpy: float, results: schrodinger.application.jaguar.garza.SolvEntropyProps)¶

Print solvation entropy results in a nice table

Parameters

temp – Temperature in Kelvin
pressure – pressure in APU
enthalpy – enthalpy in Hartree
results – solvation entropy values in Ha/K