batter.config.run.CreateArgs#

pydantic model batter.config.run.CreateArgs[source]#

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.

Config:

  • extra: str = forbid

Fields:
Validators:
field anchor_atoms: list[str] [Optional]#

List of anchor atom selections used for restraint placement.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field anion: str = 'Cl-'#

Anion species for ion placement.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field cation: str = 'Na+'#

Cation species for ion placement.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field extra_conformation_restraints: Path | None = None#

Path to conformational restraint JSON (used for NFE workflows).

Validated by:

  • _check_extra_restraints

  • _require_ligands

field extra_restraint_fc: float = 10.0#

Force constant (kcal/mol/Å^2) applied to extra_restraints.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field extra_restraints: str | None = None#

Optional positional restraint specification string.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field ion_conc: float = 0.15#

Target salt concentration (M).

Validated by:

  • _check_extra_restraints

  • _require_ligands

field l1_range: float = 6.0#

Radius (Å) for L1 search when identifying pocket positions.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field ligand_ff: str = 'gaff2'#

Ligand force field identifier passed to parameterization tools.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field ligand_input: Path | None = None#

Alternative JSON file describing ligands (dict or list).

Validated by:

  • _check_extra_restraints

  • _coerce_ligand_input

  • _require_ligands

field ligand_paths: dict[str, Path | str] [Optional]#

Mapping of ligand identifiers to structure files (relative paths are resolved at runtime).

Validated by:

  • _check_extra_restraints

  • _normalize_ligand_paths

  • _require_ligands

field lipid_ff: str = 'lipid21'#

Lipid force-field identifier.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field lipid_mol: list[str] [Optional]#

Names of lipid molecules present in the system.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field max_adis: float = 7.0#

Maximum anchor-atom distance used during pose selection (Å).

Validated by:

  • _check_extra_restraints

  • _require_ligands

field min_adis: float = 3.0#

Minimum anchor-atom distance used during pose selection (Å).

Validated by:

  • _check_extra_restraints

  • _require_ligands

field neutralize_only: Literal['yes', 'no'] = 'no'#

If "yes", neutralize the system without adding bulk salt.

Validated by:

  • _check_extra_restraints

  • _coerce_create_yes_no

  • _require_ligands

field other_mol: list[str] [Optional]#

Names of non-lipid cofactors or co-binders.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field overwrite: bool = True#

If true, overwrite existing artifacts in the staging directory.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field param_charge: str = 'am1bcc'#

Charge derivation method for ligands.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field param_method: Literal['amber', 'openff'] = 'amber'#

Parameterization backend to use for ligands.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field param_outdir: Path | None = None#

Optional override for the ligand parameter output directory.

Validated by:

  • _check_extra_restraints

  • _coerce_opt_paths

  • _require_ligands

field protein_align: str | None = 'name CA'#

Selection string used to align the protein prior to staging.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field protein_input: Path | None = None#

Path to the receptor structure (PDB/mmCIF).

Validated by:

  • _check_extra_restraints

  • _coerce_opt_paths

  • _require_ligands

field receptor_ff: str = 'protein.ff14SB'#

Protein force-field identifier.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field retain_lig_prot: bool = True#

Whether to retain ligand protomers generated during staging.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field solv_shell: float = 15.0#

Initial solvent shell radius (Å).

Validated by:

  • _check_extra_restraints

  • _require_ligands

field system_coordinate: Path | None = None#

Optional starting coordinates (e.g., INPCRD/RST7).

Validated by:

  • _check_extra_restraints

  • _coerce_opt_paths

  • _require_ligands

field system_input: Path | None = None#

Optional pre-built system topology (e.g., PRMTOP).

Validated by:

  • _check_extra_restraints

  • _coerce_opt_paths

  • _require_ligands

field system_name: str | None = 'unnamed_system'#

Logical system name; used to label outputs when not provided.

Validated by:

  • _check_extra_restraints

  • _require_ligands

field water_model: str = 'TIP3P'#

Water model used for solvation.

Validated by:

  • _check_extra_restraints

  • _require_ligands