Python normalize_areas Examples

Example #1

File: test1_2v2.py Project: alejandrovr/Protein-orientation-in-cell-membrane

}

mol = Molecule(molecule_id)
for element in conditions:
    try:
        filtering = filtering + " or (" + element + ")"
    except NameError:
        if len(conditions) > 1:
            element = "(" + element + ")"
        filtering = element
if asa == True:
    import asa_config
    import asa_module
    atoms = asa_module.generate_atom_list(mol)
    areas_dict = asa_module.calculate_asa(atoms, asa_config.distance)
    scale_dict = asa_module.normalize_areas(areas_dict)
elif asa == False:
    scale_dict = None

(mol, z_1, z_2) = apply_main(mol, filtering, f_structure_a_n,
                             my_normalized_hydrophobicies, mem_window,
                             scale_dict, solvation, max_it)

mem1 = dummy_leaflet(pmin, pmax, z_1)
mem2 = dummy_leaflet(pmin, pmax, z_2)
allmol = mol.copy()
allmol.append(mem1)
allmol.append(mem2)
allmol.center()
if opm_molecule_path != None:
    opm = Molecule(opm_molecule_path)

Example #2

File: test1_2v2_it_20_0.py Project: alejandrovr/Protein-orientation-in-cell-membrane

                               'PRO': -0.46, 'ASP': -0.55}

mol=Molecule(molecule_id)
for element in conditions:
    try:
        filtering = filtering + " or (" + element + ")"
    except NameError:
        if len(conditions) > 1:
            element = "(" + element + ")"
        filtering = element
if asa == True:
    import asa_config
    import asa_module
    atoms = asa_module.generate_atom_list(mol)
    areas_dict = asa_module.calculate_asa(atoms, asa_config.distance)
    scale_dict = asa_module.normalize_areas(areas_dict)
elif asa == False:
    scale_dict = None

(mol, z_1, z_2) = apply_main(mol, filtering, f_structure_a_n, my_normalized_hydrophobicies, mem_window, scale_dict, solvation, max_it, 0)

mem1 = dummy_leaflet(pmin,pmax,z_1)
mem2 = dummy_leaflet(pmin,pmax,z_2)
allmol=mol.copy()
allmol.append(mem1)
allmol.append(mem2)
allmol.center()
if opm_molecule_path != None:
    opm=Molecule(opm_molecule_path)
    opm.center()
    if superpose != True: