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