def main():
parser = OptionParser(usage="usage: python %prog [options] file_name ...")
parser.add_option("-c", "--cutoff", type="float", default=6.05, metavar="FLOAT", help="maximum sin(theta)/lambda")
(options, args) = parser.parse_args()
if len(args) < 1:
parser.print_help()
return
cutoff = options.cutoff
for file_name in args:
tab = read_table(file_name)
if tab.element == "Es":
continue
wk = xray_scattering.wk1995(tab.element, True).fetch()
sel = tab.x <= cutoff
tab_x = tab.x.select(sel)
tab_y = tab.y.select(sel)
sigmas = flex.double(tab_x.size(), 0.0005)
wky = wk.at_x(tab_x)
errors_abs = flex.abs(wky - tab_y)
fit = scitbx.math.gaussian.fit(tab_x, tab_y, sigmas, wk)
errors_rel = fit.significant_relative_errors(1.0e-6)
print tab.element, tab.atomic_number,
print "max error < %.1fA-1 abs, rel: %7.4f %7.4f" % (cutoff, flex.max(errors_abs), flex.max(errors_rel))
for x, y, f, ea, er in zip(tab_x, tab_y, wky, errors_abs, errors_rel):
print "%7.4f %7.4f %7.4f %7.4f %7.4f" % (x, y, f, ea, er)
print
def main():
parser = OptionParser(usage="usage: python %prog [options] file_name ...")
parser.add_option("-c",
"--cutoff",
type="float",
default=6.05,
metavar="FLOAT",
help="maximum sin(theta)/lambda")
(options, args) = parser.parse_args()
if (len(args) < 1):
parser.print_help()
return
cutoff = options.cutoff
for file_name in args:
tab = read_table(file_name)
if (tab.element == "Es"): continue
wk = xray_scattering.wk1995(tab.element, True).fetch()
sel = tab.x <= cutoff
tab_x = tab.x.select(sel)
tab_y = tab.y.select(sel)
sigmas = flex.double(tab_x.size(), 0.0005)
wky = wk.at_x(tab_x)
errors_abs = flex.abs(wky - tab_y)
fit = scitbx.math.gaussian.fit(tab_x, tab_y, sigmas, wk)
errors_rel = fit.significant_relative_errors(1.e-6)
print(tab.element, tab.atomic_number, end=' ')
print("max error < %.1fA-1 abs, rel: %7.4f %7.4f" %
(cutoff, flex.max(errors_abs), flex.max(errors_rel)))
for x, y, f, ea, er in zip(tab_x, tab_y, wky, errors_abs, errors_rel):
print("%7.4f %7.4f %7.4f %7.4f %7.4f" % (x, y, f, ea, er))
print()
def main():
parser = OptionParser(
usage="usage: python %prog file_name [n_chunks,i_chunk] [scatterer...]")
parser.add_option("-v", "--verbose",
action="store_true", default=0,
help="show comparison table for each element")
parser.add_option("-c", "--cutoff",
type="float", default=6, metavar="FLOAT",
help="maximum sin(theta)/lambda")
parser.add_option("-n", "--max_n_terms",
type="int", default=5, metavar="INT",
help="maximum number of Gaussian terms")
parser.add_option("-s", "--six_term",
action="store_true", default=0,
help="fit six-term Gaussians using Golay based starts")
(options, args) = parser.parse_args()
if (len(args) < 1):
parser.print_help()
return
run_and_time(
args=args,
cutoff=options.cutoff,
max_n_terms=options.max_n_terms,
six_term=options.six_term,
verbose=options.verbose)
def main():
parser = OptionParser(
usage="usage: python %prog [options] itvc_table kissel_files ...")
parser.add_option("-c", "--cutoff",
type="float", default=6, metavar="FLOAT",
help="maximum sin(theta)/lambda")
parser.add_option("-g", "--high_resolution_only",
action="store_true", default=0,
help="analyze points beyond sin(theta)/lambda=2A-1 only")
(options, args) = parser.parse_args()
if (len(args) < 2):
parser.print_help()
return
run(
args=args,
cutoff=options.cutoff,
high_resolution_only=options.high_resolution_only)
def main():
parser = OptionParser(
usage="usage: python %prog [options] itvc_table kissel_files ...")
parser.add_option("-c", "--cutoff",
type="float", default=6, metavar="FLOAT",
help="maximum sin(theta)/lambda")
parser.add_option("-g", "--high_resolution_only",
action="store_true", default=0,
help="analyze points beyond sin(theta)/lambda=2A-1 only")
(options, args) = parser.parse_args()
if (len(args) < 2):
parser.print_help()
return
run(
args=args,
cutoff=options.cutoff,
high_resolution_only=options.high_resolution_only)
def setup_parser():
parser = OptionParser(
prog="phenix.perigee",
version="""
up-to-date version
""",
usage="""
phenix.perigee pdb_file_name=pdb3a37.ent
""",
)
# Input options
parser.add_option("",
"--show_defaults",
dest="show_defaults",
default=False,
action="store_true",
help="Display defaults",
)
return parser
def run(http_server_name=None, html_subdir="asu_gallery"):
parser = OptionParser(
usage="usage: python jv_asu.py [options] [numbers...]")
parser.add_option("-s",
"--server",
action="store",
type="string",
help="network name of http server",
metavar="NAME")
parser.add_option("-p", "--plane_group", action="store_true")
options, args = parser.parse_args()
if (options.server is not None):
http_server_name = options.server
if (not os.path.isdir(html_subdir)):
os.makedirs(html_subdir)
jv_index.write_html(open("%s/index.html" % html_subdir, "w"))
guide_to_notation.write_html(
open("%s/guide_to_notation.html" % html_subdir, "w"))
if (len(args) == 0):
if (options.plane_group):
args = ["1-17"]
else:
args = ["1-230"]
for arg in args:
numbers = [int(n) for n in arg.split('-')]
assert len(numbers) in (1, 2)
if (len(numbers) == 1): numbers *= 2
for group_type_number in xrange(numbers[0], numbers[1] + 1):
if (options.plane_group):
print "Plane group number:", group_type_number
from cctbx.sgtbx.direct_space_asu import plane_group_reference_table
asu = plane_group_reference_table.get_asu(group_type_number)
group_type_number *= -1
else:
print "Space group number:", group_type_number
asu = reference_table.get_asu(group_type_number)
for colored_grid_points in [None, []]:
asu_as_jvx(group_type_number=group_type_number,
asu=asu,
colored_grid_points=colored_grid_points,
http_server_name=http_server_name,
html_subdir=html_subdir)
def setup_parser():
parser = OptionParser(
prog="phenix.perigee",
version="""
up-to-date version
""",
usage="""
phenix.perigee pdb_file_name=pdb3a37.ent
""",
)
# Input options
parser.add_option(
"",
"--show_defaults",
dest="show_defaults",
default=False,
action="store_true",
help="Display defaults",
)
return parser
def run(http_server_name=None, html_subdir="asu_gallery"):
parser = OptionParser(usage="usage: python jv_asu.py [options] [numbers...]")
parser.add_option(
"-s", "--server", action="store", type="string", help="network name of http server", metavar="NAME"
)
parser.add_option("-p", "--plane_group", action="store_true")
options, args = parser.parse_args()
if options.server is not None:
http_server_name = options.server
if not os.path.isdir(html_subdir):
os.makedirs(html_subdir)
jv_index.write_html(open("%s/index.html" % html_subdir, "w"))
guide_to_notation.write_html(open("%s/guide_to_notation.html" % html_subdir, "w"))
if len(args) == 0:
if options.plane_group:
args = ["1-17"]
else:
args = ["1-230"]
for arg in args:
numbers = [int(n) for n in arg.split("-")]
assert len(numbers) in (1, 2)
if len(numbers) == 1:
numbers *= 2
for group_type_number in xrange(numbers[0], numbers[1] + 1):
if options.plane_group:
print "Plane group number:", group_type_number
from cctbx.sgtbx.direct_space_asu import plane_group_reference_table
asu = plane_group_reference_table.get_asu(group_type_number)
group_type_number *= -1
else:
print "Space group number:", group_type_number
asu = reference_table.get_asu(group_type_number)
for colored_grid_points in [None, []]:
asu_as_jvx(
group_type_number=group_type_number,
asu=asu,
colored_grid_points=colored_grid_points,
http_server_name=http_server_name,
html_subdir=html_subdir,
)
def main():
parser = OptionParser(usage="usage: python %prog [options] file_name ...")
parser.add_option("-t",
"--itvc",
action="store",
metavar="FILE",
help="file name for international tables data")
parser.add_option("-k",
"--kissel",
action="store",
metavar="DIRECTORY",
help="directory name for Kissel data")
parser.add_option("-c",
"--cross_check",
action="store_true",
default=0,
help="compare two quick_summary.pickle files")
(options, args) = parser.parse_args()
if (len(args) < 1):
parser.print_help()
return
assert not (options.itvc and options.kissel)
if (options.cross): assert len(args) == 2
if (not options.cross):
run(gaussian_fit_pickle_file_names=args,
itvc_file_name=options.itvc,
kissel_dir=options.kissel)
else:
cross_check(args)
def main():
parser = OptionParser(
usage="usage: python %prog [options] file_name ...")
parser.add_option("-t", "--itvc",
action="store", metavar="FILE",
help="file name for international tables data")
parser.add_option("-k", "--kissel",
action="store", metavar="DIRECTORY",
help="directory name for Kissel data")
parser.add_option("-c", "--cross_check",
action="store_true", default=0,
help="compare two quick_summary.pickle files")
(options, args) = parser.parse_args()
if (len(args) < 1):
parser.print_help()
return
assert not (options.itvc and options.kissel)
if (options.cross): assert len(args) == 2
if (not options.cross):
run(
gaussian_fit_pickle_file_names=args,
itvc_file_name=options.itvc,
kissel_dir=options.kissel)
else:
cross_check(args)
def setup_parser():
usage = """
elbow.generate_all_chemical_component_restraint_files only_code=NAG
"""
parser = OptionParser(
prog="elbow.generate_all_chemical_component_restraint_files",
version="""
up-to-date version
""",
usage=usage,
)
# Input options
parser.add_option(
"",
"--show_defaults",
dest="show_defaults",
default=False,
action="store_true",
help="Display defaults",
)
parser.add_option(
"",
"--dry-run",
dest="dry_run",
default=False,
action="store_true",
help="Display which residues will be processed",
)
if 0:
parser.add_option(
"",
"--verbose",
dest="verbose",
default=False,
action="store_true",
help="Verbose output",
)
parser.add_option(
"",
"--silent",
dest="silent",
default=False,
action="store_true",
help="No output to screen",
)
return parser
def setup_parser():
usage="""
elbow.generate_all_chemical_component_restraint_files only_code=NAG
"""
parser = OptionParser(
prog="elbow.generate_all_chemical_component_restraint_files",
version="""
up-to-date version
""",
usage=usage,
)
# Input options
parser.add_option("",
"--show_defaults",
dest="show_defaults",
default=False,
action="store_true",
help="Display defaults",
)
parser.add_option("",
"--dry-run",
dest="dry_run",
default=False,
action="store_true",
help="Display which residues will be processed",
)
if 0:
parser.add_option("",
"--verbose",
dest="verbose",
default=False,
action="store_true",
help="Verbose output",
)
parser.add_option("",
"--silent",
dest="silent",
default=False,
action="store_true",
help="No output to screen",
)
return parser
def main():
parser = OptionParser(
usage="usage: python %prog file_name [n_chunks,i_chunk] [scatterer...]"
)
parser.add_option("-v",
"--verbose",
action="store_true",
default=0,
help="show comparison table for each element")
parser.add_option("-c",
"--cutoff",
type="float",
default=6,
metavar="FLOAT",
help="maximum sin(theta)/lambda")
parser.add_option("-q",
"--quick",
action="store_true",
default=0,
help="quick mode for debugging")
parser.add_option("-n",
"--max_n_terms",
type="int",
default=5,
metavar="INT",
help="maximum number of Gaussian terms")
parser.add_option("-e",
"--max_max_error",
type="float",
default=0.01,
metavar="FLOAT",
help="max acceptable max_error")
parser.add_option("-s",
"--six_term",
action="store_true",
default=0,
help="fit six-term Gaussians using Golay based starts")
parser.add_option("-z",
"--zig_zag",
action="store_true",
default=0,
help="zig-zag fits starting from six-term Gaussians")
parser.add_option("-r",
"--full_fits",
action="store",
help="pickled six-term Gaussian fits")
(options, args) = parser.parse_args()
if (len(args) < 1):
parser.print_help()
return
assert [options.six_term, options.zig_zag, options.full_fits
].count(True) < 2
if (options.full_fits is not None):
full_fits = easy_pickle.load(options.full_fits)
else:
full_fits = None
params = cctbx.eltbx.gaussian_fit.fit_parameters(
max_n_terms=options.max_n_terms, max_max_error=options.max_max_error)
if (options.quick):
params = params.quick()
run_and_time(file_name=args[0],
args=args[1:],
cutoff=options.cutoff,
params=params,
zig_zag=options.zig_zag,
six_term=options.six_term,
full_fits=full_fits,
verbose=options.verbose)
def main():
parser = OptionParser(
usage="usage: python %prog file_name [n_chunks,i_chunk] [scatterer...]")
parser.add_option("-v", "--verbose",
action="store_true", default=0,
help="show comparison table for each element")
parser.add_option("-c", "--cutoff",
type="float", default=6, metavar="FLOAT",
help="maximum sin(theta)/lambda")
parser.add_option("-q", "--quick",
action="store_true", default=0,
help="quick mode for debugging")
parser.add_option("-n", "--max_n_terms",
type="int", default=5, metavar="INT",
help="maximum number of Gaussian terms")
parser.add_option("-e", "--max_max_error",
type="float", default=0.01, metavar="FLOAT",
help="max acceptable max_error")
parser.add_option("-s", "--six_term",
action="store_true", default=0,
help="fit six-term Gaussians using Golay based starts")
parser.add_option("-z", "--zig_zag",
action="store_true", default=0,
help="zig-zag fits starting from six-term Gaussians")
parser.add_option("-r", "--full_fits",
action="store",
help="pickled six-term Gaussian fits")
(options, args) = parser.parse_args()
if (len(args) < 1):
parser.print_help()
return
assert [options.six_term, options.zig_zag, options.full_fits].count(True) < 2
if (options.full_fits is not None):
full_fits = easy_pickle.load(options.full_fits)
else:
full_fits = None
params = cctbx.eltbx.gaussian_fit.fit_parameters(
max_n_terms=options.max_n_terms,
max_max_error=options.max_max_error)
if (options.quick):
params = params.quick()
run_and_time(
file_name=args[0],
args=args[1:],
cutoff=options.cutoff,
params=params,
zig_zag=options.zig_zag,
six_term=options.six_term,
full_fits=full_fits,
verbose=options.verbose)
def main():
parser = OptionParser(usage="usage: python %prog [options] file_name")
parser.add_option("-t",
"--table",
default="wk1995",
action="store",
dest="table_of_gaussians",
help="wk1995 or it1992")
parser.add_option("-q",
"--quiet",
action="store_true",
default=0,
help="do not show values for large errors, only stol")
parser.add_option("-v",
"--verbose",
action="store_true",
default=0,
help="show comparison table for each element")
parser.add_option("-l",
"--low_resolution_only",
action="store_true",
default=0,
help="analyze points up to sin(theta)/lambda=2A-1 only")
parser.add_option("-g",
"--high_resolution_only",
action="store_true",
default=0,
help="analyze points beyond sin(theta)/lambda=2A-1 only")
parser.add_option("-s",
"--significant_errors_only",
action="store_true",
default=0,
help="show errors greater than 1% only")
(options, args) = parser.parse_args()
if (len(args) != 1):
parser.print_help()
return
assert options.table_of_gaussians in ["wk1995", "it1992"]
if (options.table_of_gaussians == "wk1995"):
table_of_gaussians = xray_scattering.wk1995
plots_dir = "itvc_wk1995_plots"
cutoff = 6
else:
table_of_gaussians = xray_scattering.it1992
plots_dir = "itvc_it1992_plots"
cutoff = 2
assert not options.low_resolution_only
assert not options.high_resolution_only
print("table_of_gaussians:", options.table_of_gaussians)
run(file_name=args[0],
table_of_gaussians=table_of_gaussians,
cutoff=cutoff,
low_resolution_only=options.low_resolution_only,
high_resolution_only=options.high_resolution_only,
significant_errors_only=options.significant_errors_only,
plots_dir=plots_dir,
quiet=options.quiet,
verbose=options.verbose)
def main():
parser = OptionParser(usage="usage: python %prog [options] file_name")
parser.add_option(
"-t", "--table", default="wk1995", action="store", dest="table_of_gaussians", help="wk1995 or it1992"
)
parser.add_option(
"-q", "--quiet", action="store_true", default=0, help="do not show values for large errors, only stol"
)
parser.add_option("-v", "--verbose", action="store_true", default=0, help="show comparison table for each element")
parser.add_option(
"-l",
"--low_resolution_only",
action="store_true",
default=0,
help="analyze points up to sin(theta)/lambda=2A-1 only",
)
parser.add_option(
"-g",
"--high_resolution_only",
action="store_true",
default=0,
help="analyze points beyond sin(theta)/lambda=2A-1 only",
)
parser.add_option(
"-s", "--significant_errors_only", action="store_true", default=0, help="show errors greater than 1% only"
)
(options, args) = parser.parse_args()
if len(args) != 1:
parser.print_help()
return
assert options.table_of_gaussians in ["wk1995", "it1992"]
if options.table_of_gaussians == "wk1995":
table_of_gaussians = xray_scattering.wk1995
plots_dir = "itvc_wk1995_plots"
cutoff = 6
else:
table_of_gaussians = xray_scattering.it1992
plots_dir = "itvc_it1992_plots"
cutoff = 2
assert not options.low_resolution_only
assert not options.high_resolution_only
print "table_of_gaussians:", options.table_of_gaussians
run(
file_name=args[0],
table_of_gaussians=table_of_gaussians,
cutoff=cutoff,
low_resolution_only=options.low_resolution_only,
high_resolution_only=options.high_resolution_only,
significant_errors_only=options.significant_errors_only,
plots_dir=plots_dir,
quiet=options.quiet,
verbose=options.verbose,
)