def write_RMSD():
print('\nCalculating backbone RMSDs\n')
RMSD = {}
de_novo_atoms, chain_count = read_in.read_in_atomistic(
g_var.final_dir + 'final_cg2at_de_novo.pdb') ## reads in final pdb
if chain_count != g_var.system['PROTEIN']:
sys.exit('number of chains in atomistic protein input (' +
str(chain_count) + ') does not match CG representation (' +
str(g_var.system['PROTEIN']) + ')')
RMSD['de novo '] = RMSD_measure(de_novo_atoms) ## gets rmsd of de novo
if g_var.user_at_input and 'PROTEIN' in g_var.cg_residues:
if g_var.args.o in ['all', 'align']:
at_input_atoms, chain_count = read_in.read_in_atomistic(
g_var.final_dir + 'final_cg2at_aligned.pdb')
RMSD['at aligned'] = RMSD_measure(at_input_atoms)
with open(g_var.final_dir + 'structure_quality.dat', 'w') as qual_out:
qual_out.write('\n{0:^10}{1:^25}{2:^10}\n'.format(
'output ', 'chain', 'RMSD (' + chr(197) + ')'))
qual_out.write('{0:^10}{1:^25}{2:^10}\n'.format(
'-------', '-----', '---------'))
print('\n{0:^10}{1:^25}{2:^10}'.format('output ', 'chain',
'RMSD (' + chr(197) + ')'))
print('{0:^10}{1:^25}{2:^10}'.format('-------', '-----', '---------'))
for rmsd in RMSD:
for chain in RMSD[rmsd]:
qual_out.write('{0:^10}{1:^25}{2:^10}\n'.format(
rmsd, str(chain), float(RMSD[rmsd][chain])))
print('{0:^10}{1:^25}{2:^10}'.format(rmsd, str(chain),
float(RMSD[rmsd][chain])))
print('\nAll RMSDs have been saved in: \n' + g_var.final_dir +
'structure_quality.dat\n')
def write_RMSD():
print('\nCalculating backbone RMSDs\n')
RMSD={}
de_novo_atoms, chain_count = read_in.read_in_atomistic(g_var.final_dir+'final_cg2at_de_novo.pdb') ## reads in final pdb
if chain_count != g_var.system['PROTEIN']:
sys.exit('number of chains in atomistic protein input ('+str(chain_count)+') does not match CG representation ('+str(g_var.system['PROTEIN'])+')')
RMSD_de_novo = RMSD_measure_de_novo(de_novo_atoms) ## gets rmsd of de novo
if g_var.user_at_input and 'PROTEIN' in g_var.cg_residues:
if g_var.args.o in ['all', 'align']:
at_input_atoms, chain_count = read_in.read_in_atomistic(g_var.final_dir+'final_cg2at_aligned.pdb')
RMSD_aligned = RMSD_measure_de_novo(at_input_atoms)
seg_rmsd = RMSD_measure_aligned(at_input_atoms)
with open(g_var.final_dir+'structure_quality.dat', 'w') as qual_out:
line_1 = ' chain De novo BB RMSD ('+chr(197)+')'
line_2 = ' ----- -------------------'
if 'seg_rmsd' in locals():
line_1+= ' Aligned BB RMSD ('+chr(197)+') Seg backbone RMSD ('+chr(197)+')'
line_2+= ' ------------------- ---------------------'
qual_out.write(line_1+'\n'+line_2+'\n')
print(line_1+'\n'+line_2)
for chain in RMSD_de_novo:
line = ' {0:^5}{1:^28}'.format(str(chain), float(RMSD_de_novo[chain]))
if 'seg_rmsd' in locals():
line += '{0:^18}'.format(float(RMSD_aligned[chain]))
if chain in seg_rmsd:
line+= '{0:^28}'.format(', '.join(seg_rmsd[chain]))
print(line)
qual_out.write(line+'\n')
print('\n * Segment alignments may have minor deviations due to either clashes or structure hybridisation.\n\nAll RMSDs have been saved in: \n'+g_var.final_dir+'structure_quality.dat\n')
def create_aligned():
print('\nCreating aligned system')
at_mod.merge_system_pdbs(
'_aligned') ## create restraint positions for aligned system
aligned_atoms, chain_count = read_in.read_in_atomistic(
g_var.working_dir +
'PROTEIN/PROTEIN_aligned_merged.pdb') ## reads in final pdb
rmsd = at_mod_p.RMSD_measure_de_novo(
aligned_atoms) ## gets rmsd of de novo
for chain in rmsd:
if rmsd[chain] > 3:
print(
'Your aligned structure is quite far from the CG, therefore running gentle steering\n'
)
print_rmsd(rmsd)
steer = ['very_low', 'low', 'mid', 'high', 'very_high', 'ultra']
break
else:
steer = ['low', 'high', 'ultra']
final_file = run_steer(
steer, g_var.merged_directory + 'checked_ringed_lipid_de_novo')
if final_file:
gen.file_copy_and_check(
final_file, g_var.final_dir +
'final_cg2at_aligned.pdb') ## copy to final folder
else:
final_file = run_steer(
['very_low', 'low', 'mid', 'high', 'very_high', 'ultra'],
g_var.merged_directory + 'checked_ringed_lipid_de_novo')
print('Completed alignment, please find final aligned system: \n' +
g_var.final_dir + 'final_cg2at_aligned.pdb')
gen.file_copy_and_check(
final_file, g_var.final_dir +
'final_cg2at_aligned.pdb') ## copy to final folder
def RMSD_measure_aligned(Final_structure):
seg_rmsd = {}
total_initial, total_final = np.array([]), np.array([])
for chain in g_var.atomistic_protein_input_aligned:
initial_structure, chain_count = read_in.read_in_atomistic(
g_var.working_dir + 'PROTEIN/MIN/PROTEIN_aligned_' + str(chain) +
'.pdb')
P_R = []
for key in g_var.atomistic_protein_input_aligned[chain].keys():
P_R.append(
np.arange(int(key.split(':')[0]) - 1, int(key.split(':')[1])))
final_backbone = get_coordinates(Final_structure, P_R, chain)
initial_backbone = get_coordinates(initial_structure, P_R, 0)
seg_rmsd[chain] = []
for segment in range(len(final_backbone)):
initial_backbone_fitted = RMSD_align(
initial_backbone[segment][:, :3],
final_backbone[segment][:, :3])
total_initial = np.append(total_initial, initial_backbone_fitted)
total_final = np.append(total_final,
final_backbone[segment][:, :3])
RMSD_val = Calculate_RMSD(np.array(initial_backbone_fitted),
final_backbone[segment][:, :3])
if RMSD_val > 0.15:
seg_rmsd[chain].append(str(RMSD_val) + ' *')
else:
seg_rmsd[chain].append(str(RMSD_val))
# print(Calculate_RMSD(total_initial, total_final))
return seg_rmsd
read_in.fix_pbc(box_vec_initial, g_var.box_vec, box_shift)
#### checks if fragment database and input files match
at_mod.sanity_check()
### convert protein to atomistic representation
g_var.tc['r_i_t'] = time.time()
if 'PROTEIN' in g_var.cg_residues:
g_var.coord_atomistic = at_mod_p.build_multi_residue_atomistic_system(
g_var.cg_residues, 'PROTEIN') ## converts protein to atomistic
if not g_var.user_at_input and g_var.args.v >= 1: ## prints protein sequences
print(gen.print_sequnce_info('PROTEIN'))
## reads in user chain, runs a sequence alignment and finds existing disulphide bonds
g_var.tc['p_d_n_t'] = time.time()
if g_var.user_at_input:
for file_num, file_name in enumerate(g_var.args.a):
atomistic_protein_input_raw, g_var.chain_count = read_in.read_in_atomistic(
g_var.input_directory + 'AT_INPUT_' + str(file_num) +
'.pdb') ## reads in user structure
g_var.atomistic_protein_input_raw.update(
atomistic_protein_input_raw)
read_in.duplicate_chain() ## duplicates user chcains
at_mod_p.check_sequence() ## gets user sequence
at_mod_p.align_chain_sequence('PROTEIN') ## aligns chains
at_mod_p.find_disulphide_bonds_user_sup(
) ## finds user disulphide bonds
at_mod_p.find_disulphide_bonds_de_novo() ## finds CG disulphide bonds
g_var.coord_atomistic = at_mod_p.correct_disulphide_bonds(
g_var.coord_atomistic) ## fixes sulphur distances
final_coordinates_atomistic_de_novo = at_mod_p.finalise_novo_atomistic(
g_var.coord_atomistic,
'PROTEIN') ## fixes carbonyl oxygens, hydrogens and writes pdb
## aligns user chains to the CG system