PDB2GMXParameters

Module

viennaptm.gromacs.pdb2gmx

class PDB2GMXParameters(*, input: Path, output_gro: Path = PosixPath('conf.gro'), topology: Path = PosixPath('topol.top'), posre_itp: Path | None = PosixPath('posre.itp'), index_file: Path | None = None, clean_pdb: Path | None = None, forcefield: str | None = None, water: str | None = None, chainsep: str | None = None, merge: str | None = None, ignore_h: bool = False, verbose: bool = False)

Bases: BaseModel

Parameter model for the GROMACS pdb2gmx command.

This model defines all input and output paths as well as optional command-line flags controlling force-field selection, water model, chain handling, and verbosity.

All path-like parameters are normalized to pathlib.Path instances after validation.

Parameters:

• input (pathlib.Path) – Input PDB structure file.

• output_gro (pathlib.Path) – Output GRO structure file.

• topology (pathlib.Path) – Output topology file.

• posre_itp (pathlib.Path or None) – Position restraint include file.

• index_file (pathlib.Path or None) – Optional index file.

• clean_pdb (pathlib.Path or None) – Optional cleaned PDB output file.

• forcefield (str or None) – Force-field identifier passed to pdb2gmx.

• water (str or None) – Water model identifier.

• chainsep (str or None) – Chain separation mode.

• merge (str or None) – Chain merge behavior.

• ignore_h (bool) – Ignore hydrogen atoms present in the input structure.

• verbose (bool) – Enable verbose output.

chainsep: str | None

clean_pdb: Path | None

classmethod ensure_paths(v)

forcefield: str | None

ignore_h: bool

index_file: Path | None

input: Path

merge: str | None

model_config = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

output_gro: Path

posre_itp: Path | None

topology: Path

verbose: bool

water: str | None

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, ...])
ensure_paths(v)
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, ...])
schema([by_alias, ref_template])
schema_json(*[, by_alias, ref_template])
update_forward_refs(**localns)
validate(value)