def main():
parser = argparse.ArgumentParser(description='')
parser.add_argument('-r', '--residue', help='investigated residue')
parser.add_argument(
'-i',
'--input',
nargs='?',
help=
'list of inputs (e.g. "model1.prmtop model1.incprd mutation.prmtop prod_1.nc 1 20, ...")'
)
parser.add_argument('-f',
'--output_folder',
nargs='?',
help='set output folder (default: "occupancies")')
parser.add_argument(
'-m1',
'--mask1',
nargs='?',
help='mask for calculation of average occupancies (e.g. '
'1-582; default: solute-solute contacts excluded)')
parser.add_argument(
'-m2',
'--mask2',
nargs='?',
help='second mask determines what residues are used to '
'calculate occupancies with (default: 1-50000')
parser.add_argument('-a',
'--avrgs',
help='calculate averages',
action='store_true')
parser.add_argument('-w', '--wat', help='strip water', action='store_true')
parser.add_argument('-hy',
'--hydro',
help='strip hydrogen',
action='store_true')
args = parser.parse_args()
# parse inputs into input object
ip = Input(sys.argv)
# create output folder
os.create_output_folder(ip.folder)
# copy input trajectories and topology files to output folder
for item in ip.input:
os.copy_to_folder(item[0], ip.folder)
os.copy_to_folder(item[1], ip.folder)
# change to results folder
os.change_to_folder(ip.folder)
# set new file paths
ip.set_file_paths_to_output_folder()
##### calculate occupancies #####
initial_contact_atoms = cpp.get_residue_contacting_atoms(
ip.input[0][0], ip.input[0][1], ip.input[0][2], ip.input[0][3],
ip.mutation, ip.strip_water, ip.strip_hydro)
occupancies = []
for item in ip.input:
occupancies.append(
cpp.get_occupancy_of_atoms(item[0], item[1], item[2], item[3],
initial_contact_atoms, ip.strip_water,
ip.strip_hydro))
##### calculate average occupancies #####
if ip.calc_averages:
# generate pdb
pdb_file_name = cpp.generate_pdb(ip.input[0][0], ip.input[0][1], "1",
"1", 0, 1)
pdb = Pdb(pdb_file_name)
# get non solvent residue numbers from pdb to create mask to exclude solvent in calculation of averages
# (solute-solvent contacts will be calculated, but no solvent-solvent contacts)
if not ip.mask1:
non_solvent_residues = pdb.get_non_solvent_residue_numbers()
ip.mask1 = str(non_solvent_residues[0]) + "-" + str(
non_solvent_residues[-1])
if not ip.mask2:
ip.mask2 = "1-" + str(max(pdb.get_residue_numbers()))
# get types of contacting atoms
contacting_atoms_types = pdb.get_atom_types(initial_contact_atoms)
averages = []
for item in ip.input:
averages.append(
cpp.get_contact_averages_of_types(
item[0], item[1], item[2], item[3], contacting_atoms_types,
ip.mask1, ip.mask2, ip.strip_water, ip.strip_hydro))
##### reformat data #####
occupancies = reformat_occupancies_list(occupancies)
if ip.calc_averages:
for item in averages:
occupancies = add_averages_column(occupancies, item)
# add headers
output = add_headers(occupancies, ip.calc_averages)
# format output
output = output_2D_list(output)
output = prepare_output(output, ip.calc_averages)
##### write data #####
input_file_names = ip.get_file_names()
write_output(output, ip.mutation + '_occupancies.dat')
output_to_pdf(output, ip.mutation + '_occupancies.dat', ip.calc_averages,
ip.strip_water, ip.strip_hydro, input_file_names,
ip.mutation)
if ip.calc_averages:
write_percentages_quotients(output,
ip.mutation + "_percentage_quotients.dat")
def main():
parser = argparse.ArgumentParser(description='')
parser.add_argument('-r', '--residue', help='investigated residue')
parser.add_argument(
'-i',
'--input',
nargs='?',
help=
'list of inputs (e.g. "model1.prmtop model1.incprd mutation.prmtop prod_1.nc 1 20, ...")'
)
# parser.add_argument('-f', '--output_folder', nargs='?', help='set output folder (default: "occupancies")')
parser.add_argument(
'-m1',
'--mask1',
nargs='?',
help='mask for calculation of average occupancies (e.g. '
'1-582; default: solute-solute contacts excluded)')
parser.add_argument(
'-m2',
'--mask2',
nargs='?',
help='second mask determines what residues are used to '
'calculate occupancies with (default: 1-50000')
parser.add_argument('-a',
'--avrgs',
help='calculate averages',
action='store_true')
parser.add_argument('-w', '--wat', help='strip water', action='store_true')
parser.add_argument('-hy',
'--hydro',
help='strip hydrogen',
action='store_true')
parser.add_argument('-m',
'--mapping',
nargs='?',
help='add file to recalculate residue numbers')
args = parser.parse_args()
# parse inputs into input object
ip = Input(sys.argv)
# create output folder
# os.create_output_folder(ip.folder)
# copy input trajectories and topology files to output folder
# for item in ip.input:
# os.copy_to_folder(item[0], ip.folder)
# os.copy_to_folder(item[1], ip.folder)
# change to results folder
# os.change_to_folder(ip.folder)
# set new file paths
# ip.set_file_paths_to_output_folder()
##### calculate occupancies #####
initial_contact_atoms = cpp.get_residue_contacting_atoms(
ip.input[0][0], ip.input[0][1], ip.input[0][2], ip.input[0][3],
ip.mutation, ip.strip_water, ip.strip_hydro)
# set up multiprocessing
pool = multiprocessing.Pool()
input_list = copy.deepcopy(ip.input)
occupancies = []
for item in input_list:
item += [initial_contact_atoms, ip.strip_water, ip.strip_hydro]
occupancies.append(pool.map(cpp.get_occupancy_of_atoms, input_list))
##### calculate average occupancies #####
if ip.calc_averages:
# generate pdb
pdb_file_name = cpp.generate_pdb(ip.input[0][0], ip.input[0][1], "1",
"1", 0, 1)
pdb = Pdb(pdb_file_name)
# get non solvent residue numbers from pdb to create mask to exclude solvent in calculation of averages
# (solute-solvent contacts will be calculated, but no solvent-solvent contacts)
if not ip.mask1:
non_solvent_residues = pdb.get_non_solvent_residue_numbers()
ip.mask1 = str(non_solvent_residues[0]) + "-" + str(
non_solvent_residues[-1])
if not ip.mask2:
ip.mask2 = "1-" + str(max(pdb.get_residue_numbers()))
# get types of contacting atoms
contacting_atoms_types = pdb.get_atom_types(initial_contact_atoms)
averages = []
input_list = []
# item[0], item[1], item[2], item[3], contacting_atoms_types, ip.mask1, ip.mask2, ip.strip_water, ip.strip_hydro
for item2 in ip.input:
input_list.append([
item2[0], item2[1], item2[2], item2[3], contacting_atoms_types,
ip.mask1, ip.mask2, ip.strip_water, ip.strip_hydro
])
averages.append(pool.map(cpp.get_contact_averages_of_types,
input_list))
pool.close()
pool.join()
##### reformat data #####
occupancies = reformat_occupancies_list(occupancies[0])
if ip.calc_averages:
for item in averages[0]:
occupancies = add_averages_column(occupancies, item)
# add headers
output = add_headers(occupancies, ip.calc_averages)
# use the mapping file to transform residue numbering
if ip.mapping:
map_residues(ip.mapping, output)
# format output
output = output_2D_list(output)
output = prepare_output(output, ip.calc_averages)
##### write data #####
input_file_names = ip.get_file_names()
write_output(output, ip.mutation + '_occupancies.dat')
if ip.mapping:
investigated_residue = map_mutation_residue(ip.mapping, ip.mutation)
if len(ip.input) < 23:
output_to_pdf(output, ip.calc_averages, ip.strip_water, ip.strip_hydro,
input_file_names, investigated_residue)
else:
print(
"No pdf gets generated if there are more than 22 trajectories. Please refer to "
+ ip.mutation + '_occupancies.dat to retrieve occupancy values')
if ip.calc_averages:
totals, percentages = write_percentages_quotients(
output, ip.mutation + "_percentage_quotients.dat")
trajectories = ip.get_trajectories()
plot_total_values(totals, percentages, trajectories, ip.calc_averages)
