schrodinger.application.jaguar.autots_constants module¶

schrodinger.application.jaguar.autots_constants.get_unit_free_energy_prop(prop: str, unit: StandardUnits, temp: float = 298.15) → str¶

Return a Gibbs free energy property key with a standard-state unit label and temperature inserted before the _kcal suffix.

For example, "r_j_..._Gibbs_..._kcal" becomes "r_j_..._Gibbs_..._1M_298.15K_kcal" when unit is StandardUnits.STD_CONC and temp is 298.15.

Parameters:

prop – Base property key ending in _kcal and containing Gibbs.
unit – The standard-state unit to embed in the key.
temp – Temperature in Kelvin to embed in the key.

Returns:

The modified property key.

Raises:

AssertionError – If prop does not end with _kcal or does not contain Gibbs.

class schrodinger.application.jaguar.autots_constants.CriticalPointNames¶

Bases: StrEnum

REACTANT = 'reactant'¶

PRODUCT = 'product'¶

TS = 'transition_state'¶

APPROX_TS = 'approx_transition_state'¶

INTERMEDIATE = 'intermediate'¶

class schrodinger.application.jaguar.autots_constants.CriticalPointType¶

Bases: StrEnum

MINIMUM = 'minimum'¶

TS = 'ts'¶

APPROX_TS = 'approximate_ts'¶

UNKNOWN = 'unknown'¶

classmethod from_structure(st: Structure) → CriticalPointType¶

Determine the critical-point type of a structure.

Reads the s_j_AutoTS_critical_point_type property, which must be present.

Parameters:: st – The structure to classify.
Returns:: The critical-point type.

classmethod from_structure_with_fallback(st: Structure) → CriticalPointType¶

Determine the critical-point type of a structure, first by property, then fall back to infer_type_from_title if the property is missing.

This should only be used where it could be reasonably expected that the property be missing, e.g. where user input could be from old calculations.

Parameters:: st – The structure to classify.
Returns:: The critical-point type.

classmethod infer_type_from_title(st: Structure) → None¶

Set the s_j_AutoTS_critical_point_type property from the title.

Parameters:: st – The structure to annotate in place.

classmethod is_ts(st: Structure) → bool¶

Determine if the given structure is a TS or not.

Parameters:: st – The structure to be analysed.
Raises:: ValueError – If type cannot be identified from the title.
Returns:: True if the structure is a TS.

classmethod is_minimum(st: Structure) → bool¶

Determine if the given structure is a minimum.

Parameters:: st – The structure to classify.
Raises:: ValueError – If type cannot be identified from the title.
Returns:: True if the structure is a minimum.

class schrodinger.application.jaguar.autots_constants.ConnectionStatus¶

Bases: StrEnum

CONNECTED = 'CONNECTED'¶

DISCONNECTED = 'DISCONNECTED'¶

class schrodinger.application.jaguar.autots_constants.IndexString(at_index_str, mol_index_str, static_at_index_str, static_mol_index_str, input_at_index_str, input_mol_index_str)¶

Bases: tuple

at_index_str¶: Alias for field number 0

input_at_index_str¶: Alias for field number 4

input_mol_index_str¶: Alias for field number 5

mol_index_str¶: Alias for field number 1

static_at_index_str¶: Alias for field number 2

static_mol_index_str¶: Alias for field number 3

class schrodinger.application.jaguar.autots_constants.EnergyTypeSpec(key: str, label: str, complex_key: str, inf_sep_key: str | None)¶

Bases: object

Specification for one energy type available in an AutoTS reaction path.

Parameters:

key – Short identifier used as a dict key (e.g. 'electronic').
label – Human-readable label (e.g. 'Electronic Energy').
complex_key – Structure property key for the reaction-complex energy.
inf_sep_key – Structure property key for the infinitely-separated energy, or None if unavailable for this type.

key: str¶

label: str¶

complex_key: str¶

inf_sep_key: str | None¶

__init__(key: str, label: str, complex_key: str, inf_sep_key: str | None) → None¶

class schrodinger.application.jaguar.autots_constants.AvailableEnergyConfig(temperatures: tuple[float, ...], solution_phase: bool, has_inf_sep: bool, has_csrch: bool)¶

Bases: object

Energy types discovered from structure properties on a reaction path.

When no free energy data is found, temperatures will be empty and solution_phase defaults to True (its value is meaningless without temperature data).

Parameters:

temperatures – Sorted temperatures (K) at which free energy data is available. Empty when no free energy properties exist.
solution_phase – Whether solution-phase (1M) free energies are present. Only meaningful when temperatures is non-empty.
has_inf_sep – Whether infinitely-separated energies are available.
has_csrch – Whether conformational-search energies are available.

temperatures: tuple[float, ...]¶

solution_phase: bool¶

has_inf_sep: bool¶

has_csrch: bool¶

__init__(temperatures: tuple[float, ...], solution_phase: bool, has_inf_sep: bool, has_csrch: bool) → None¶

schrodinger.application.jaguar.autots_constants.detect_available_energy_config(sts: list[Structure]) → AvailableEnergyConfig¶

Scan structure properties to discover which energy types are available.

Collects all property keys across the given structures and checks for the presence of free energy, infinitely-separated, and conformational search energy properties.

Parameters:: sts – Structures to scan (typically the full reaction path).
Returns:: Discovered energy configuration.