def get_close_residues_dict():
if os.path.isfile('.close_residues.pickle'):
with open('.close_residues.pickle', 'r') as f:
return pickle.load(f)
mut_data_dict = setup_alanine_scanning.parse_mutations_file()
close_residues_dict = {}
for pdb_id in mut_data_dict:
mut_data = mut_data_dict[pdb_id]
for i, pdb_res in enumerate(mut_data.pdb_res_list):
insertion_code = mut_data.insertion_code_list[i]
chain = mut_data.chain_list[i]
close_residues = find_resnums_around_mutation(pdb_id, int(pdb_res), insertion_code, chain)
print 'Mutation %s:%d%s has %d residues within %.1f angstroms' % (pdb_id, pdb_res, insertion_code, len(close_residues), cutoff_dist)
if pdb_id not in close_residues_dict:
close_residues_dict[pdb_id] = {}
reskey = (pdb_res, chain, insertion_code)
assert( reskey not in close_residues_dict[pdb_id] )
close_residues_dict[pdb_id][reskey] = close_residues
with open('.close_residues.pickle', 'w') as f:
pickle.dump(close_residues_dict, f)
return close_residues_dict
def get_close_residues_dict():
if os.path.isfile('.close_residues.pickle'):
with open('.close_residues.pickle', 'rb') as f:
return pickle.load(f)
mut_data_dict = setup_alanine_scanning.parse_mutations_file()
close_residues_dict = {}
for pdb_id in mut_data_dict:
mut_data = mut_data_dict[pdb_id]
for i, pdb_res in enumerate(mut_data.pdb_res_list):
insertion_code = mut_data.insertion_code_list[i]
chain = mut_data.chain_list[i]
close_residues = find_resnums_around_mutation(
pdb_id, int(pdb_res), insertion_code, chain)
print('Mutation %s:%d%s has %d residues within %.1f angstroms' %
(pdb_id, pdb_res, insertion_code, len(close_residues),
cutoff_dist))
if pdb_id not in close_residues_dict:
close_residues_dict[pdb_id] = {}
reskey = (pdb_res, chain, insertion_code)
assert (reskey not in close_residues_dict[pdb_id])
close_residues_dict[pdb_id][reskey] = close_residues
with open('.close_residues.pickle', 'wb') as f:
pickle.dump(close_residues_dict, f)
return close_residues_dict
def get_mutations_data_from_pdb_dict(pdb_data_dict, PDBPosID):
for m in pdb_data_dict.values():
if PDBPosID in m.PDBPosID_list:
return m
raise Exception("Couldn't match ID %s" % str(PDBPosID))
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('output_dirs',
nargs='*',
help = 'Output directories')
args = parser.parse_args()
mutations_data = parse_mutations_file()
for output_dir in args.output_dirs:
analysis_output_dir = os.path.join(global_analysis_output_dir, os.path.basename(output_dir))
if not os.path.isdir(analysis_output_dir):
os.makedirs(analysis_output_dir)
assert( os.path.isdir(output_dir) )
job_pickle_file = os.path.join(
output_dir, pickle_name
)
with open(job_pickle_file,'r') as p:
job_dict = pickle.load(p)
