PDB2GMX

Module

viennaptm.gromacs.pdb2gmx

class PDB2GMX(params: PDB2GMXParameters, mpi: MPIConfig | None = None, workdir: Path | None = None, stdin: str | None = None, timeout: int | None = None, env: dict | None = None)

Bases: GromacsCommand

Wrapper for the GROMACS pdb2gmx topology generation command.

This command converts a PDB structure into a GROMACS-compatible coordinate file and topology using the provided force-field and water model settings.

Command-line arguments are derived from a PDB2GMXParameters instance.

Parameters:

• params (PDB2GMXParameters) – Parameter model defining all pdb2gmx options.

• mpi (MPIConfig or None) – MPI execution configuration.

• workdir (pathlib.Path or None) – Working directory in which the command is executed.

• stdin (str or None) – Optional standard input passed to the command.

• timeout (int or None) – Maximum execution time in seconds.

• env (dict[str, str] or None) – Environment variables to use for command execution.

build_gromacs_cmd() → List[str]

Construct the gmx pdb2gmx command invocation.

Command-line arguments are conditionally assembled based on the values provided in the associated parameter model.

Returns:

Command-line argument list suitable for execution.

Return type:

list[str]

expected_outputs() → List[Path]

Declare the files expected to be generated by this command.

Returns:

List containing the generated GRO structure file and topology file.

Return type:

list[pathlib.Path]

Methods

__init__(params[, mpi, workdir, stdin, ...])	Initialize a GROMACS command wrapper.
build_command()	Build the full command invocation.
build_gromacs_cmd()	Construct the gmx pdb2gmx command invocation.
expected_outputs()	Declare the files expected to be generated by this command.
inspect_result(result)	Inspect command output for fatal GROMACS errors.
mpi_prefix()	Construct the MPI command prefix.
post_run_checks()	Verify that expected output files were created.
run()	Execute the GROMACS command.