Topologie related class¶
Top class¶
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class
gromacs_py.gromacs.gmx5.
TopSys
(top_in)¶ Topologie base on gromacs .top : #include forcefield
All name and full path of itp are save [ system ] -> Name [ molecules ] -> Composition
Parameters: - path (str) – topologie file path
- forcefield (str) – name of the focefield
- itp_list (list) – list of the itp object
- mol_comp (list) – molecular composition
- name – name of the system
- folder (str) – path of the top file folder
- include_itp (bool) – Flag indicating if the topologie include a molecule topologie
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add_mol
(mol_name, mol_itp_file, mol_num)¶ Add a molecule in the topologie (composition and itp_list)
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add_posre
(posre_name='CA', selec_dict={'atom_name': ['CA']}, fc=[1000, 1000, 1000])¶ Add position restraint based on the selection for each itp
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charge
(verbose=False)¶ Get the charge of the system
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mol_num
(name)¶ Get the number of the molecule “name”
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prot_res_num
(selection='Protein')¶ Compute the residue number of a selection