def main():
args = read_args()
ncs, msg = find_ncs(args.ncs, script_path)
if not ncs:
print(msg)
exit()
result, blocks, ncs_name, deuterated = read_blocks(args.elb_file)
if result:
exit()
product_finder = ProductFinder(blocks, args.samples, args.min_patterns)
products = product_finder.find_products()
schemes_total = sum([len(product) for product in products])
blocks_total = {}
print("{} products found".format(schemes_total))
output = "[NCS = {}]\n".format(ncs_name)
output += "[Deuterated = {}]\n".format(deuterated)
for product in products:
for scheme in product:
scheme.simplify()
blocks_total = add_block(blocks_total, scheme.samples,
len(scheme.patterns))
output += scheme.full_str()
output += "\n"
stats_total = make_block_stats(blocks_total)
if args.output:
with open(args.output, mode="w") as f:
f.write(output)
print("{} blocks were written to the file \'{}\'".format(
schemes_total, args.output))
else:
print(output)
print("Statistics of generated blocks:")
print(stats_total["str"])
def get_params(args, logger):
ncs, msg = find_ncs(args.ncs, script_path)
if not ncs:
logger.error(msg)
exit()
else:
logger.info(msg)
samples = args.samples
if samples < 1 or samples > 9:
logger.error(
"Number of samples '{}' is not in range 1-9".format(samples))
exit()
min_patterns = 0
exact_patterns = False
if args.minpatterns:
min_patterns = args.minpatterns
exact_patterns = True
min_t_free = -1
check_t_free = False
if args.min_t_free:
if args.min_t_free >= 0:
min_t_free = args.min_t_free
check_t_free = True
else:
min_t_free = -1
if check_t_free:
exact_patterns = True
params = {
"ncs": ncs,
"samples": samples,
"exact_patterns": exact_patterns,
"min_patterns": min_patterns,
"check_t_free": check_t_free,
"min_t_free": min_t_free,
"verbose": args.verbose,
"silent": args.silent
}
return params
def read_parameters(args, logger):
ncs, msg = find_ncs(args.ncs, script_path)
if not ncs:
logger.error(msg)
exit()
result, blocks, ncs_name, deuterated = read_blocks(args.elb_file, logger)
if result:
exit()
prices = {}
if os.path.isfile(args.price_file):
prices, msg = read_prices(args.price_file)
if not prices:
logger.error(msg)
exit()
else:
logger.error("Error! Price file '{}' not found".format(args.price_file))
max_block_samples = max(blocks.keys())
jobname = args.jobname
if args.aminoacids:
residues = extract_residues(args.aminoacids)
else:
residues = Constants.RES_TYPES_LIST
if args.notaminoacids:
not_residues = extract_residues(args.notaminoacids)
else:
not_residues = []
final_residues = []
for res in residues:
if res not in not_residues:
final_residues.append(res)
if not jobname:
jobname = "{}_{}".format(ncs.name, max_block_samples)
parameters = {
"blocks": blocks,
"ncs": ncs,
"prices": prices,
"residues": final_residues,
"jobname": jobname,
"verbose": args.verbose,
"silent": args.silent
}
return parameters
def get_params(args):
script_path = os.path.split(os.path.realpath(__file__))[0]
ncs, msg = find_ncs(args.ncs, script_path)
if not ncs:
print(msg)
exit()
print("NCS '{}' read".format(ncs.name))
protein_sequence, msg = read_sequence(args.sequence)
print("Protein sequence: {}".format(protein_sequence))
if len(protein_sequence) == 0:
exit()
if len(protein_sequence) < 3:
print("Protein sequence is too short({})".format(
len(protein_sequence)))
exit()
sequence = CLSequence(protein_sequence)
print("Protein sequence file '{}' read".format(args.sequence))
solution = read_solution(args.solution)
if not solution:
exit()
solution = add_unlabeled_residues(solution, sequence)
print("Solution file '{}' read".format(args.solution))
label_options = get_stock_from_solution(solution)
pairs_table = PairsTable(sequence, label_options)
all_label_options = set(sum(list(label_options.values()), []))
new_label_types = []
for label_type in Constants.BASIC_TYPES:
if label_type in all_label_options or label_type in ncs.label_types:
new_label_types.append(label_type)
show_price = False
price_dict = {}
if args.prices:
show_price = True
price_dict, msg = read_prices(args.prices)
if not price_dict:
print(msg)
exit()
new_ncs = NCS("",
ncs.spec_list,
new_label_types,
deuterated=ncs.deuterated)
new_ncs.name = auto_name_ncs(new_ncs)
name = "{}_{}".format(args.sequence.split(".")[0], new_ncs.name)
output_solution = name + "_solution_c.txt"
output_dictionary = name + "_dictionary_c.txt"
params = {
"ncs": new_ncs,
"name": name,
"label_options": label_options,
"sequence": sequence,
"solution": solution,
"pairs_table": pairs_table,
"show_price": show_price,
"price_dict": price_dict,
"output_solution": output_solution,
"output_dictionary": output_dictionary
}
return params
def read_parameters(args, logger):
logger.info("Reading NCS")
ncs, msg = find_ncs(args.ncs, script_path)
if not ncs:
logger.error(msg)
exit()
logger.info("NCS: {}".format(ncs.name))
sequence = ""
logger.info("Reading sequence: '{}'".format(args.sequence_file))
if os.path.isfile(args.sequence_file):
sequence, msg = read_sequence(args.sequence_file)
if not sequence:
logger.error(msg)
exit()
else:
logger.error("Error! Sequence file '{}' not found".format(args.sequence_file))
if len(sequence) < 3:
print("Sequence length ({}) is too short".format(len(sequence)))
exit()
logger.info("Sequence length - {} residues".format(len(sequence)))
stock = {}
if os.path.isfile(args.stock_file):
logger.info("Reading stock: '{}'".format(args.stock_file))
stock, msg = read_stock(args.stock_file)
if not stock:
logger.error(msg)
exit()
else:
logger.error("Error! Stock file '{}' not found".format(args.stock_file))
logger.info("Stock - OK")
optimize_price = True
if not args.price:
optimize_price = False
prices = {}
if optimize_price:
logger.info("Reading prices: '{}'".format(args.price))
if os.path.isfile(args.price):
prices, msg = read_prices(args.price)
if not prices:
logger.error(msg)
exit()
else:
logger.error("Error! Price file '{}' not found".format(args.price))
exit()
logger.info("Prices - OK")
assignment = True
if not args.assignment:
assignment = False
assignment_numbers = set()
if assignment:
logger.info("Reading assignment: '{}'".format(args.assignment))
if os.path.isfile(args.assignment):
assignment_numbers, msg = read_assignment(args.assignment)
else:
logger.error("Error! Assignment file '{}' not found".format(args.assignment))
for assignment_num in assignment_numbers:
if assignment_num > len(sequence):
warning_msg = "Warning! Residue number {} is exceeding sequence length ({})".format(assignment_num,
len(sequence))
logger.error(warning_msg)
if assignment:
logger.info("{} backbone assignments read".format(len(assignment_numbers)))
jobname = args.jobname
seq_name = args.sequence_file.split(".")[0]
if not jobname:
jobname = "{}_{}".format(seq_name, ncs.name)
samples = args.number_samples # default value is 1
if samples < 1 or samples > 9:
msg = "Error! Number of samples is not in range 1-9"
logger.error(msg)
exit()
parameters = {
"ncs": ncs,
"sequence": sequence,
"stock": stock,
"optimize_price": optimize_price,
"prices": prices,
"samples": samples,
"jobname": jobname,
"verbose": args.verbose,
"silent": args.silent,
"assignment": assignment_numbers
}
return parameters