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:
g_var.box_vec = box_vec_initial
box_shift = np.array([0, 0, 0])
read_in.real_box_vectors(g_var.box_vec)
#### pbc fix and residue truncation if required
#!/usr/bin/env python3
import os, sys
import numpy as np
from shutil import copyfile
from time import gmtime
import datetime
sys.path.append(
os.path.dirname(os.path.realpath(__file__)) + '/database/script_files')
import gen, gro, at_mod, at_mod_p, at_mod_np, cg_mod, g_var, f_loc
initialisation_time = np.array(gmtime()[3:6])
user_at_input = gro.collect_input(g_var.c, g_var.a)
print('\nThis script is now hopefully doing the following (Good luck):\n')
#### read in CG file
print('Reading in your CG representation\n')
cg_residues, box_vec = cg_mod.read_initial_pdb()
cg_residues = cg_mod.fix_pbc(cg_residues, box_vec)
read_in_time = np.array(gmtime()[3:6])
system = {}
### convert protein to atomistic
if 'PROTEIN' in cg_residues:
p_system, backbone_coords, final_coordinates_atomistic, sequence = at_mod_p.build_protein_atomistic_system(
cg_residues['PROTEIN'], box_vec)
system['PROTEIN'] = p_system['PROTEIN']
protein_de_novo_time = np.array(gmtime()[3:6])
if user_at_input and 'PROTEIN' in system:
#### reads in atomistic structure