gen.forcefield_selection()
gen.fragment_selection()
gen.check_water_molecules()
if g_var.args.posre != None and len(g_var.np_directories) > 0:
check_library.add_posres_file()
if g_var.args.compare != None and len(g_var.np_directories) > 0:
check_library.compare_forcefield_to_database()
if g_var.args.info:
gen.database_information()
if g_var.args.v >= 1:
print(gen.fragments_in_use())
gen.fetch_fragment_multi()
gen.fetch_fragment_single()
gen.fetch_chain_groups()
gen.sort_swap_group()
print(gen.print_swap_residues())
###
#### collects initial structures into INPUT folder
gro.collect_input()
#### saves flags used into INPUT folder
gen.flags_used()
g_var.tc['i_t_e'] = time.time()
#### reads in CG file and separates into residue types
box_vec_initial = read_in.read_initial_cg_pdb()
#### box size update
if g_var.args.box != None:
print('box cutting only works for cubic boxes currently')
g_var.box_vec, box_shift = gen.new_box_vec(box_vec_initial,
g_var.args.box)
else:
if g_var.fg != None:
print('Cannot find fragment library: ' + frag +
' please select library from below\n')
fragment_number = gen.database_selection(fragments_available, 'fragments')
p_directories_unsorted, mod_directories_unsorted, np_directories_unsorted = gen.fetch_residues(
fragments_available, fragment_number)
np_residues, p_residues, mod_residues, np_directories, p_directories, mod_directories = gen.sort_directories(
p_directories_unsorted, mod_directories_unsorted, np_directories_unsorted)
chiral = gen.fetch_chiral(np_directories, p_directories)
if not g_var.at2cg:
### reads in water molecules
water_dir, water = gen.check_water_molecules(g_var.w, np_directories)
### return backbone information
backbone, sorted_connect, hydrogen, heavy_bond = gen.fetch_fragment(
p_residues, p_directories, mod_directories, np_directories,
forcefield_location + forcefield, mod_residues)
swap_dict = gen.sort_swap_group()
### finds initial rotation matrices
x_rot, y_rot, z_rot = [], [], []
for angle in range(0, 360, 5):
angle = np.radians(angle)
x_rot.append(gen.eulerAnglesToRotationMatrix([angle, 0, 0]))
y_rot.append(gen.eulerAnglesToRotationMatrix([0, angle, 0]))
z_rot.append(gen.eulerAnglesToRotationMatrix([0, 0, angle]))