def get_args(cmd_args):
parser = utils.get_basic_parser(
usage='used to calculate unun, neighbour residues are excluded')
parser.add_argument(
'--query',
required=True,
help=
'query for selecting atoms used for calculating non-polar interactions'
)
parser.add_argument('--h5',
required=True,
help='written to hdf5 file directory')
parser.add_argument(
'-c',
'--cutoff',
default=0.55,
type=float,
help=
'cutoff in nm (will be converted to angstrom in the code so as to work with MDAnalysis)'
)
parser.add_argument(
'--nres-away',
default=2,
type=int,
help='the atoms should be nres away to avoid neigbor interactions)')
args = parser.parse_args(cmd_args)
return args
def get_args():
p = utils.get_basic_parser(usage='used to calculate unun, neighbour residues are excluded')
p.add_argument('-c', '--cutoff', type=float, required=True,
help='cutoff in nm (will be converted to angstrom in the code so as to work with MDAnalysis)')
p.add_argument('--debug', dest='debug', default=False, action='store_true',
help='for debugging, verbose info will be printted to the screen')
args = p.parse_args()
return args
def parse_cmd():
usage='used to calculate sequence spacing'
p = utils.get_basic_parser(usage=usage)
p.add_argument('--pl', type=int, dest='peptide_length', default=None, required=True,
help='specify the peptide_length')
p.add_argument('--atom-selection', type=str, dest='atom_sel', default='resid {0} and not type H',
help=("atom selection, the default is 'resid {0} and not type H': {0}"
"will be substituted with a number, the atom selection option only"
"applies to each resid! I know, it's WIRED and UGLY, let me know"
"if you have a better way. Thanks! 2011-12-12"))
args = p.parse_args()
return args
def get_args(cmd_args):
parser = utils.get_basic_parser(usage='used to calculate unun, neighbour residues are excluded')
parser.add_argument('--query', required=True,
help='query for selecting atoms used for calculating non-polar interactions')
parser.add_argument('--h5', required=True,
help='written to hdf5 file directory')
parser.add_argument('-c', '--cutoff', default=0.55, type=float,
help='cutoff in nm (will be converted to angstrom in the code so as to work with MDAnalysis)')
parser.add_argument('--nres-away', default=2, type=int,
help='the atoms should be nres away to avoid neigbor interactions)')
args = parser.parse_args(cmd_args)
return args
def parse_arguments(args):
"""
Parse program arguments
"""
parser = utils.get_basic_parser()
parser.add_argument('--nz', type=int, default=100, help='size of the latent z vector')
parser.add_argument('--ngf', type=int, default=64,
help='the depth of feature maps carried through the generator')
parser.add_argument('--ndf', type=int, default=64,
help='the depth of feature maps propagated through the discriminator')
opt = parser.parse_args(args)
opt.device = utils.get_device(opt)
return opt
def parse_arguments(args):
""" Parse program arguments
Arguments:
args {[string]} -- Arguments to parse
Returns:
[argparse.Namespace] -- parsed arguments
"""
parser = utils.get_basic_parser()
parser.add_argument("--latent_dim",
type=int,
default=100,
help="dimensionality of the latent space")
opt = parser.parse_args(args)
opt.device = utils.get_device(opt)
return opt
def main(args):
parser = utils.get_basic_parser()
opt = parser.parse_args(args)
batch_sizes = []
for epoch in range(opt.n_epochs):
batch_sizes.append(utils.get_batch_sizes(opt, epoch))
df = pd.DataFrame(batch_sizes, columns=['real_batch', 'fake_batch'])
max_size = max(df.max())
ax = df.plot(ylim=(0, int(1.05 * max_size)),
xlim=(0, opt.n_epochs),
alpha=0.6)
ax.set_xlabel("epoch")
plt.savefig("{}_{}_{}_{}.png".format(opt.policy, opt.batch_size,
opt.batch_interval, opt.n_epochs),
dpi=1000)
def get_args():
p = utils.get_basic_parser(
usage='used to calculate unun, neighbour residues are excluded')
p.add_argument(
'-c',
'--cutoff',
type=float,
required=True,
help=
'cutoff in nm (will be converted to angstrom in the code so as to work with MDAnalysis)'
)
p.add_argument(
'--debug',
dest='debug',
default=False,
action='store_true',
help='for debugging, verbose info will be printted to the screen')
args = p.parse_args()
return args
def parse_cmd():
usage = 'used to calculate sequence spacing'
p = utils.get_basic_parser(usage=usage)
p.add_argument('--pl',
type=int,
dest='peptide_length',
default=None,
required=True,
help='specify the peptide_length')
p.add_argument(
'--atom-selection',
type=str,
dest='atom_sel',
default='resid {0} and not type H',
help=(
"atom selection, the default is 'resid {0} and not type H': {0}"
"will be substituted with a number, the atom selection option only"
"applies to each resid! I know, it's WIRED and UGLY, let me know"
"if you have a better way. Thanks! 2011-12-12"))
args = p.parse_args()
return args
tets = select_dihedrals(univer) # there should be a better name for tet
# Write headers, hdr: header
hdrs = []
for k, tet in enumerate(tets):
# ca1 + ca2 + (NO. peptide-bond)
hdr = (utils.swap_aa_name(tet[0].resname) +
utils.swap_aa_name(tet[-1].resname) + "{0:02d}".format(k + 1))
# hdrs.append("{0:8s}".format(hdr))
hdrs.append("{0:4s}".format(hdr))
yield '#{0:8s}{1}\n'.format('t(ps)', ' '.join(hdrs))
if not xtcf:
yield calc_dih(tets)
else:
for ts in univer.trajectory:
if btime > ts.time:
continue
if etime > 0 and etime < ts.time:
break
res = calc_dih(tets, ts.time)
yield res
utils.print_progress(ts)
if __name__ == "__main__":
parser = utils.get_basic_parser()
args = parser.parse_args()
main(args)
tets = select_dihedrals(univer) # there should be a better name for tet
# Write headers, hdr: header
hdrs = []
for k, tet in enumerate(tets):
# ca1 + ca2 + (NO. peptide-bond)
hdr = (utils.swap_aa_name(tet[0].resname) +
utils.swap_aa_name(tet[-1].resname) +
"{0:02d}".format(k+1))
# hdrs.append("{0:8s}".format(hdr))
hdrs.append("{0:4s}".format(hdr))
yield '#{0:8s}{1}\n'.format('t(ps)', ' '.join(hdrs))
if not xtcf:
yield calc_dih(tets)
else:
for ts in univer.trajectory:
if btime > ts.time:
continue
if etime > 0 and etime < ts.time:
break
res = calc_dih(tets, ts.time)
yield res
utils.print_progress(ts)
if __name__ == "__main__":
parser = utils.get_basic_parser()
args = parser.parse_args()
main(args)
def get_args():
p = U.get_basic_parser(
usage='used to calculate unun, neighbour residues are excluded')
args = p.parse_args()
return args
def get_args():
p = U.get_basic_parser(usage='used to calculate unun, neighbour residues are excluded')
args = p.parse_args()
return args