schrodinger.application.transforms.epikx module¶

EpikX transform for enumerating protonation and tautomeric states.

This module provides Apache Beam transforms for running EpikX on molecular structures to enumerate their protonation and tautomeric states at a given pH.

class schrodinger.application.transforms.epikx.EpikXResult(*, source_id: ~schrodinger.seam.io.sourceid.SourceID, input_structure: ~schrodinger.structure._structure.Structure, success: bool, output_structures: list[schrodinger.structure._structure.Structure] = <factory>, error_message: str | None = None)¶

Bases: BaseModel

Result of running EpikX on a single structure.

Parameters:

source_id – Source ID for tracking the input structure.
input_structure – The input structure (preserved for downstream use).
success – Whether EpikX processing succeeded.
output_structures – List of enumerated protonation/tautomeric states.
error_message – Error message if processing failed.

source_id: SourceID¶

input_structure: Structure¶

success: bool¶

output_structures: list[Structure]¶

error_message: str | None¶

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'frozen': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class schrodinger.application.transforms.epikx.EpikXConfig(*, legacy_arg_string: str | None = None, ph: float = 7.4, pht: float = 2.0, population_cutoff: float | None = None, max_structures: int = 16, max_tautomers: int = 8, max_atoms: int = 200, max_atoms_pka: int = 500, charge_low: int = -2, charge_high: int = 2, highest_pka: float = 14.0, lowest_pka: float = 0.0, query_only: bool = False, taut_only: bool = False, no_tautomerize: bool = False, best_neutral: bool = False, best_neutral_zwit: bool = False, metal_binding: bool = False, racemize: bool = False, retain_input_state: bool = False, refine: bool = True, add_hydrogen_coords: bool = False, single_model: bool = False, custom_model: str | None = None, cpu_only: bool = False, match_exp: str | None = None, report: bool = False)¶

Bases: BaseModel

Configuration for EpikX transforms.

Parameters:

legacy_arg_string – Legacy CLI argument string (mutually exclusive with other parameters).
ph – Query pH for protonation state prediction.
pht – pH tolerance for generated structures (mutually exclusive with population_cutoff).
population_cutoff – State population cutoff (mutually exclusive with pht).
max_structures – Maximum number of returned structures per input.
max_tautomers – Maximum number of tautomers to enumerate.
max_atoms – Max atoms for state enumeration.
max_atoms_pka – Max atoms for pKa prediction.
charge_low – Lower bound for the charge level window.
charge_high – Upper bound for the charge level window.
highest_pka – Highest pKa value to display.
lowest_pka – Lowest pKa value to display.
query_only – Query pKas only, do not predict states.
taut_only – Tautomerize only, do not evaluate pKas.
no_tautomerize – Do not tautomerize.
best_neutral – Provide the most populated neutral tautomer.
best_neutral_zwit – Provide neutral tautomer and optionally a zwitterion.
metal_binding – Generate states appropriate for metal ion binding.
racemize – Enumerate and score individual racemers.
retain_input_state – Retain input ionization/tautomerization state.
refine – Refine prioritization step to remove unwanted states.
add_hydrogen_coords – Add coordinates to non-polar hydrogens.
single_model – Use single best model instead of ensemble.
custom_model – Path to custom model.
cpu_only – Run on CPU only (no GPU acceleration).
match_exp – Property label of experimental pKa value for matching.
report – Generate pKa report (single structure only).

legacy_arg_string: str | None¶

ph: float¶

pht: float¶

population_cutoff: float | None¶

max_structures: int¶

max_tautomers: int¶

max_atoms: int¶

max_atoms_pka: int¶

charge_low: int¶

charge_high: int¶

highest_pka: float¶

lowest_pka: float¶

query_only: bool¶

taut_only: bool¶

no_tautomerize: bool¶

best_neutral: bool¶

best_neutral_zwit: bool¶

metal_binding: bool¶

racemize: bool¶

retain_input_state: bool¶

refine: bool¶

add_hydrogen_coords: bool¶

single_model: bool¶

custom_model: str | None¶

cpu_only: bool¶

match_exp: str | None¶

report: bool¶

model_config: ClassVar[ConfigDict] = {'frozen': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

toArgList() → list[str]¶

Convert the config to a list of command line arguments.

Returns:: List of command line argument strings.

class schrodinger.application.transforms.epikx.RunEpikX(**kwargs)¶

Bases: PTransformWithConfig

Run EpikX on input structures.

Example usage:

>>> from schrodinger import adapter
>>> st1 = adapter.to_structure('CC(=O)O')
>>> st1.title = "acetic_acid"
>>> with beam.Pipeline() as p:
...     results = (p
...         | beam.Create([st1])
...         | RunEpikX(ph=7.0)
...         | beam.Map(lambda r: (r.source_id, r.success, len(r.output_structures)))
...         | beam.LogElements())

See EpikXConfig for available configuration options.

config_class¶: alias of EpikXConfig

class schrodinger.application.transforms.epikx.ProtonateLigands(**kwargs)¶

Bases: PTransformWithConfig

Enumerate protonation states and return output structures.

Example usage:

>>> from schrodinger import adapter
>>> st1 = adapter.to_structure('CC(=O)O')
>>> st1.title = "acetic_acid"
>>> with beam.Pipeline() as p:
...     structures = (p
...         | beam.Create([st1])
...         | ProtonateLigands(ph=7.0)
...         | beam.Map(lambda st: st.title)
...         | beam.LogElements())

See EpikXConfig for available configuration options.

config_class¶: alias of EpikXConfig

class schrodinger.application.transforms.epikx.EpikXWithProps(**kwargs)¶

Bases: PTransformWithConfig

Enumerate protonation states and annotate with derived pKa properties.

Example usage:

>>> from schrodinger import adapter
>>> st = adapter.to_structure('CC(=O)O')
>>> st.title = "acetic_acid"
>>> with beam.Pipeline() as p:
...     structures = (p
...         | beam.Create([st])
...         | EpikXWithProps(ph=7.0)
...         | beam.Map(lambda st: st.property.get('r_epik_Most_acidic_pKa'))
...         | beam.LogElements())

See EpikXConfig for available configuration options.

config_class¶: alias of EpikXConfig

class schrodinger.application.transforms.epikx.Neutralize(**kwargs)¶

Bases: PTransformWithConfig

Return the best neutral tautomer with state penalty annotated.

Raises RuntimeError if EpikX fails for any input structure.

Example usage:

>>> from schrodinger import adapter
>>> st = adapter.to_structure('CC(=O)O')
>>> with beam.Pipeline() as p:
...     structures = (p
...         | beam.Create([st])
...         | Neutralize())

See EpikXConfig for available configuration options.

config_class¶: alias of _NeutralizeConfig