def merge_indivdual_chain_pdbs(file, end, res_type):
#### reads in each chain into merge list
merge, merged_coords = [], []
count = 0
restraint_count = -1
for chain in range(0, g_var.system[res_type]):
merge_temp = []
if os.path.exists(file + '_' + str(chain) + end):
with open(file + '_' + str(chain) + end, 'r') as pdb_input:
merge_temp += read_in.filter_input(pdb_input.readlines(),
False)
else:
sys.exit('cannot find chain: ' + file + '_' + str(chain) + end)
if res_type + '_aligned' in file:
count, restraint_count = at_mod_p.write_disres(
merge_temp, chain, file, count, restraint_count)
merge, merge_coords = fix_chirality(merge, merge_temp, merged_coords,
res_type)
if res_type + '_aligned' not in file:
coords, index_conversion = index_conversion_generate(
merge, merge_coords)
if 'aligned' in file.split('/')[-1]:
write_pdb(merge, merge_coords, {},
g_var.working_dir + 'PROTEIN/PROTEIN_aligned_merged.pdb')
else:
write_pdb(
merge, coords, index_conversion, g_var.working_dir + res_type +
'/' + res_type + '_de_novo_merged.pdb')
def read_in_merged_pdbs(merge, merge_coords, location):
if os.path.exists(location):
#### opens pdb files and writes straight to merged_cg2at pdb
with open(location, 'r') as pdb_input:
read_in_atoms = read_in.filter_input(pdb_input.readlines(), False)
merge_coords += [[line_sep['x'],line_sep['y'],line_sep['z']] for line_sep in read_in_atoms ]
return merge+read_in_atoms, merge_coords
else:
sys.exit('cannot find minimised residue: \n'+ location)