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)
opm.center()
if superpose != True:
opm.moveBy([50, 0, 0])
allmol.append(opm)
allmol.reps.add(sel='protein', style='NewCartoon')
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:
opm.moveBy([50,0,0])
allmol.append(opm)
allmol.reps.add(sel='protein', style='NewCartoon')
allmol.reps.add(sel='resname DUM', style='Licorice')