GromacsMDProtocolResult

class openfe_gromacs.protocols.gromacs_md.GromacsMDProtocolResult(**data)

Dict-like container for the output of a Gromacs MDProtocol.

Provides access to simulation outputs including the pre-minimized system PDB and production trajectory files.

Methods

get_estimate	Since no results as output --> returns None
get_filenames_em	Get a list of paths to the files of the energy minimization Following file formats are stored in the dictionary under these keys: - "gro_em" - "tpr_em" - "trr_em" - "xtc_em" - "edr_em" - "log_em" - "cpt_em" - "grompp_mdp_em"
get_filenames_npt	Get a list of paths to the files of the NPT MD simulation Following file formats are stored in the dictionary under these keys: - "gro_npt" - "tpr_npt" - "trr_npt" - "xtc_npt" - "edr_npt" - "log_npt" - "cpt_npt" - "grompp_mdp_npt"
get_filenames_nvt	Get a list of paths to the files of the NVT equilibration Following file formats are stored in the dictionary under these keys: - "gro_nvt" - "tpr_nvt" - "trr_nvt" - "xtc_nvt" - "edr_nvt" - "log_nvt" - "cpt_nvt" - "grompp_mdp_nvt"
get_gro_em_filenames	Get a list of paths to the .gro file, last frame of the energy minimization
get_gro_filename	Get the path to the input coordinate .gro file.
get_gro_npt_filenames	Get a list of paths to the .gro file, last frame of the NPT MD simulation
get_gro_nvt_filenames	Get a list of paths to the .gro file, last frame of the NVT equilibration
get_mdp_filenames	Get a dictionary of paths to the .mdp files.
get_top_filename	Get the path to the .top file.
get_uncertainty	Since no results as output --> returns None
get_xtc_em_filenames	Get a list of paths to the .xtc file of the energy minimization
get_xtc_npt_filenames	Get a list of paths to the .xtc file of the NPT MD simulation
get_xtc_nvt_filenames	Get a list of paths to the .xtc file of the NVT equilibration

property data: dict[str, Any]

Aggregated data contents from multiple ProtocolDAGResult instances.

The structure of this data is specific to the Protocol subclass each ProtocolResult subclass corresponds to.

get_estimate()

Since no results as output –> returns None

Return type:

None

get_filenames_em() → dict[str, list[pathlib.Path]]

Get a list of paths to the files of the energy minimization Following file formats are stored in the dictionary under these keys: - “gro_em” - “tpr_em” - “trr_em” - “xtc_em” - “edr_em” - “log_em” - “cpt_em” - “grompp_mdp_em”

Returns:

dict_em – dictionary containing list of paths (pathlib.Path) to the output files

Return type:

Optional[dict[str, list[pathlib.Path]]]

get_filenames_npt() → dict[str, list[pathlib.Path]]

Get a list of paths to the files of the NPT MD simulation Following file formats are stored in the dictionary under these keys: - “gro_npt” - “tpr_npt” - “trr_npt” - “xtc_npt” - “edr_npt” - “log_npt” - “cpt_npt” - “grompp_mdp_npt”

Returns:

dict_npt – dictionary containing list of paths (pathlib.Path) to the output files

Return type:

Optional[dict[str, list[pathlib.Path]]]

get_filenames_nvt() → dict[str, list[pathlib.Path]]

Get a list of paths to the files of the NVT equilibration Following file formats are stored in the dictionary under these keys: - “gro_nvt” - “tpr_nvt” - “trr_nvt” - “xtc_nvt” - “edr_nvt” - “log_nvt” - “cpt_nvt” - “grompp_mdp_nvt”

Returns:

dict_nvt – dictionary containing list of paths (pathlib.Path) to the output files

Return type:

Optional[dict[str, list[pathlib.Path]]]

get_gro_em_filenames() → list[pathlib.Path]

Get a list of paths to the .gro file, last frame of the energy minimization

Returns:

gro – list of paths (pathlib.Path) to the output .gro file

Return type:

Optional[list[pathlib.Path]]

get_gro_filename() → Path

Get the path to the input coordinate .gro file. This returns a single path even if multiple repeats are run since the GromacsMDSetupUnit is only run once.

Returns:

gro – Path to the input coordinate .gro file

Return type:

pathlib.Path

get_gro_npt_filenames() → list[pathlib.Path]

Get a list of paths to the .gro file, last frame of the NPT MD simulation

Returns:

gro – list of paths (pathlib.Path) to the output .gro file

Return type:

Optional[list[pathlib.Path]]

get_gro_nvt_filenames() → list[pathlib.Path]

Get a list of paths to the .gro file, last frame of the NVT equilibration

Returns:

gro – list of paths (pathlib.Path) to the output .gro file

Return type:

Optional[list[pathlib.Path]]

get_mdp_filenames() → dict[str, pathlib.Path]

Get a dictionary of paths to the .mdp files. This returns a single dictionary with paths even if multiple repeats are run since the GromacsMDSetupUnit is only run once.

Returns:

mdps – dictionary of paths (pathlib.Path) to the mdp files for energy minimization, NVT and NPT MD runs

Return type:

dict[str, pathlib.Path]

get_top_filename() → Path

Get the path to the .top file. This returns a single path even if multiple repeats are run since the GromacsMDSetupUnit is only run once.

Returns:

top – Path to the input topology .top file

Return type:

pathlib.Path

get_uncertainty()

Since no results as output –> returns None

get_xtc_em_filenames() → list[pathlib.Path]

Get a list of paths to the .xtc file of the energy minimization

Returns:

file_path – list of paths (pathlib.Path) to the output .xtc file

Return type:

Optional[list[pathlib.Path]]

get_xtc_npt_filenames() → list[pathlib.Path]

Get a list of paths to the .xtc file of the NPT MD simulation

Returns:

file_path – list of paths (pathlib.Path) to the output .xtc file

Return type:

Optional[list[pathlib.Path]]

get_xtc_nvt_filenames() → list[pathlib.Path]

Get a list of paths to the .xtc file of the NVT equilibration

Returns:

file_path – list of paths (pathlib.Path) to the output .xtc file

Return type:

Optional[list[pathlib.Path]]

property n_protocol_dag_results: int