gromacs_extra package

Submodules

gromacs_extra.ndx2resttop module

Module containing the Ndx2resttop class and the command line interface.

class gromacs_extra.ndx2resttop.Ndx2resttop(input_ndx_path: str, input_top_zip_path: str, output_top_zip_path: str, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_gromacs Ndx2resttop
Generate a restrained topology from an index NDX file.
This module automatizes the process of restrained topology generation starting from an index NDX file.
Parameters:

  • input_ndx_path (str) – Path to the input NDX index file. File type: input. Sample file. Accepted formats: ndx (edam:format_2033).

  • input_top_zip_path (str) –

    Path the input TOP topology in zip format. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • output_top_zip_path (str) –

    Path the output TOP topology in zip format. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • force_constants (str) - (“500 500 500”) Array of three floats defining the force constants.

    • ref_rest_chain_triplet_list (str) - (None) Triplet list composed by (reference group, restrain group, chain) list.

Examples

This is a use example of how to use the building block from Python:

from biobb_gromacs.gromacs_extra.ndx2resttop import ndx2resttop
prop = { 'ref_rest_chain_triplet_list': '( Chain_A, Chain_A_noMut, A ), ( Chain_B, Chain_B_noMut, B ), ( Chain_C, Chain_C_noMut, C ), ( Chain_D, Chain_D_noMut, D )' }
ndx2resttop(input_ndx_path='/path/to/myIndex.ndx',
            input_top_zip_path='/path/to/myTopology.zip',
            output_top_zip_path='/path/to/newTopology.zip',
            properties=prop)
Info:
launch() → int[source]

Execute the Ndx2resttop object.

gromacs_extra.ndx2resttop.main()[source]

Command line execution of this building block. Please check the command line documentation.

gromacs_extra.ndx2resttop.ndx2resttop(input_ndx_path: str, input_top_zip_path: str, output_top_zip_path: str, properties: Dict | None = None, **kwargs) → int[source]

Create Ndx2resttop class and execute the launch() method.

gromacs_extra.append_ligand module

Module containing the AppendLigand class and the command line interface.

class gromacs_extra.append_ligand.AppendLigand(input_top_zip_path: str, input_itp_path: str, output_top_zip_path: str, input_posres_itp_path: str | None = None, properties: Dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_gromacs AppendLigand
This class takes a ligand ITP file and inserts it in a topology.
This module automatizes the process of inserting a ligand ITP file in a GROMACS topology.
Parameters:

  • input_top_zip_path (str) –

    Path the input topology TOP and ITP files zipball. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • input_itp_path (str) –

    Path to the ligand ITP file to be inserted in the topology. File type: input. Sample file. Accepted formats: itp (edam:format_3883).

  • output_top_zip_path (str) –

    Path/Name the output topology TOP and ITP files zipball. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

  • input_posres_itp_path (str) (Optional) – Path to the position restriction ITP file. File type: input. Accepted formats: itp (edam:format_3883).

  • properties (dic) –

    • posres_name (str) - (“POSRES_LIGAND”) String to be included in the ifdef clause.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

This is a use example of how to use the building block from Python:

from biobb_gromacs.gromacs_extra.append_ligand import append_ligand
prop = { 'posres_name': 'POSRES_LIGAND' }
append_ligand(input_top_zip_path='/path/to/myTopology.zip',
              input_itp_path='/path/to/myTopologyAddOn.itp',
              output_top_zip_path='/path/to/newTopology.zip',
              properties=prop)
Info:
launch() → int[source]

Execute the AppendLigand object.

gromacs_extra.append_ligand.append_ligand(input_top_zip_path: str, input_itp_path: str, output_top_zip_path: str, input_posres_itp_path: str | None = None, properties: Dict | None = None, **kwargs) → int[source]

Create AppendLigand class and execute the launch() method.

gromacs_extra.append_ligand.main()[source]

Command line execution of this building block. Please check the command line documentation.