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, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_md Ndx2resttopGenerate 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_md.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:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
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, **kwargs) → int[source]¶ Create
Ndx2resttop
class and execute thelaunch()
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, properties: dict = None, **kwargs)[source]¶ Bases:
biobb_common.generic.biobb_object.BiobbObject
biobb_md AppendLigandThis 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.
Examples
This is a use example of how to use the building block from Python:
from biobb_md.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:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
AppendLigand
object.
- input_top_zip_path (str) –
-
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, properties: dict = None, **kwargs) → int[source]¶ Create
AppendLigand
class and execute thelaunch()
method.