Topologie related class

Top class

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

add_mol(mol_name, mol_itp_file, mol_num)

Add a molecule in the topologie (composition and itp_list)

add_posre(posre_name='CA', selec_dict={'atom_name': ['CA']}, fc=[1000, 1000, 1000])

Add position restraint based on the selection for each itp

charge(verbose=False)

Get the charge of the system

mol_num(name)

Get the number of the molecule “name”

prot_res_num(selection='Protein')

Compute the residue number of a selection

Itp class

class gromacs_py.gromacs.gmx5.Itp(name, fullname, path)

Itp topologie in gromacs format May contain several molecule definition, so itp class is a collection of top_mol object which are indivudial molecule topologies

Top Mol class

class gromacs_py.gromacs.gmx5.TopMol(name, nrexcl)

Individual molecule topologie

get_selection_index(selec_dict={'atom_name': ['CA']})

Return the atom index to add posre