batter.config.run.CreateArgs

class batter.config.run.CreateArgs(*, system_name: str | None = 'unnamed_system', protein_input: Path | None = None, system_input: Path | None = None, system_coordinate: Path | None = None, protein_align: str | None = 'name CA', ligand_paths: dict[str, ~pathlib.Path | str]=<factory>, ligand_input: Path | None = None, ligand_ff: str = 'gaff2', retain_lig_prot: bool = True, param_method: Literal['amber', 'openff']='amber', param_charge: str = 'am1bcc', param_outdir: Path | None = None, anchor_atoms: list[str] = <factory>, lipid_mol: list[str] = <factory>, other_mol: list[str] = <factory>, overwrite: bool = True, extra_restraints: str | None = None, extra_restraint_fc: float = 10.0, extra_conformation_restraints: Path | None = None, receptor_ff: str = 'protein.ff14SB', lipid_ff: str = 'lipid21', solv_shell: float = 15.0, cation: str = 'Na+', anion: str = 'Cl-', ion_conc: float = 0.15, neutralize_only: Literal['yes', 'no']='no', water_model: str = 'TIP3P', l1_range: float = 6.0, min_adis: float = 3.0, max_adis: float = 7.0)

Inputs for system creation and staging.

Notes

This section mirrors the create block in the run YAML file.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

__init__(**data: Any) → None

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Methods

__init__(**data)	Create a new model by parsing and validating input data from keyword arguments.
construct([_fields_set])
copy(*[, include, exclude, update, deep])	Returns a copy of the model.
dict(*[, include, exclude, by_alias, ...])
from_orm(obj)
json(*[, include, exclude, by_alias, ...])
model_construct([_fields_set])	Creates a new instance of the Model class with validated data.
model_copy(*[, update, deep])	!!! abstract "Usage Documentation"
model_dump(*[, mode, include, exclude, ...])	!!! abstract "Usage Documentation"
model_dump_json(*[, indent, ensure_ascii, ...])	!!! abstract "Usage Documentation"
model_json_schema(by_alias, ref_template, ...)	Generates a JSON schema for a model class.
model_parametrized_name(params)	Compute the class name for parametrizations of generic classes.
model_post_init(context, /)	Override this method to perform additional initialization after __init__ and model_construct.
model_rebuild(*[, force, raise_errors, ...])	Try to rebuild the pydantic-core schema for the model.
model_validate(obj, *[, strict, extra, ...])	Validate a pydantic model instance.
model_validate_json(json_data, *[, strict, ...])	!!! abstract "Usage Documentation"
model_validate_strings(obj, *[, strict, ...])	Validate the given object with string data against the Pydantic model.
parse_file(path, *[, content_type, ...])
parse_obj(obj)
parse_raw(b, *[, content_type, encoding, ...])
resolve_paths(base)	Return a copy where path fields are absolute relative to base.
schema([by_alias, ref_template])
schema_json(*[, by_alias, ref_template])
update_forward_refs(**localns)
validate(value)

Attributes

model_computed_fields
model_config	Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
model_extra	Get extra fields set during validation.
model_fields
model_fields_set	Returns the set of fields that have been explicitly set on this model instance.
system_name
protein_input
system_input
system_coordinate
protein_align
ligand_paths
ligand_input
ligand_ff
retain_lig_prot
param_method
param_charge
param_outdir
anchor_atoms
lipid_mol
other_mol
overwrite
extra_restraints
extra_restraint_fc
extra_conformation_restraints
receptor_ff
lipid_ff
solv_shell
cation
anion
ion_conc
neutralize_only
water_model
l1_range
min_adis
max_adis