def __init__(self, args):
n = tst_tardy.n_test_models
command_line = (
libtbx_option_parser(
usage="""\
scitbx.python wx_tardy.py [options] model_index
model_index range: 0 ... %d\
"""
% (n - 1)
)
.option(
None, "--fixed_vertices", type="str", action="append", default=None, metavar="COMMA-SEPARATED-INTEGERS"
)
.option(None, "--i_seq_labels", action="store_true", default=False)
.option(None, "--velocity_scaling", action="store_true", default=False)
.option(None, "--e_kin_per_dof", type="float", default=1.0, metavar="FLOAT")
.option(None, "--view_scale", type="float", default=1.3, metavar="FLOAT")
).process(args=args, nargs=1)
co = command_line.options
self.fixed_vertex_lists = []
if co.fixed_vertices is not None:
for s in co.fixed_vertices:
self.fixed_vertex_lists.append(tuple(eval("[" + s + "]")))
self.i_seq_labels = co.i_seq_labels
self.velocity_scaling = co.velocity_scaling
self.e_kin_per_dof = co.e_kin_per_dof
self.view_scale = co.view_scale
self.model_index = int(command_line.args[0])
assert 0 <= self.model_index < n
super(App, self).__init__(title="wx_tardy")
def run(args):
if (len(args) == 0): args = ["--help"]
from libtbx.option_parser import libtbx_option_parser
import libtbx.load_env
command_line = (libtbx_option_parser(
usage="%s [options] space_group_symbol ..." % libtbx.env.dispatcher_name)
.option(None, "--primitive",
action="store_true",
help="Convert centred space groups to primitive setting.")
.option(None, "--symops",
action="store_true",
help="Show list of symmetry operations.")
).process(args=args)
co = command_line.options
from cctbx import sgtbx
args = command_line.args
if (args == ["all"]):
args = [str(no) for no in xrange(1,230+1)]
for symbol in args:
sgi = sgtbx.space_group_info(symbol=symbol)
if (co.primitive):
sgi = sgi.primitive_setting()
sgi.show_summary()
gr = sgi.group()
print " Crystal system:", gr.crystal_system()
print " Point group type:", gr.point_group_type()
print " Laue group type:", gr.laue_group_type()
print " Number of symmetry operations:", gr.order_z()
print " Lattice centering operations:", gr.n_ltr()
if (gr.n_ltr() != 1):
print " Number of symmetry operations in primitive setting:", \
gr.order_p()
if (gr.is_centric()): s = gr(0, 1, 0)
else: s = None
print " Center of inversion:", s
print " Dimensionality of continuous allowed origin shifts:", \
sgi.number_of_continuous_allowed_origin_shifts()
ssi_vm = sgi.structure_seminvariants().vectors_and_moduli()
print " Structure-seminvariant vectors and moduli:", \
len(ssi_vm)
if (len(ssi_vm) != 0):
for vm in ssi_vm:
print " (%2d, %2d, %2d)" % vm.v, "%2d" % vm.m
print " Direct-space asymmetric unit:"
dau = sgi.direct_space_asu()
print " Number of faces: %d" % len(dau.cuts)
for cut in dau.cuts:
print " " + cut.as_xyz()
print " ADP constraint matrix:"
_ = sgi.group().adp_constraints().gradient_sum_matrix()
from scitbx import matrix
print matrix.rec(tuple(_), _.focus()).mathematica_form(
one_row_per_line=True,
prefix=" ")
if (co.symops):
print " List of symmetry operations:"
for s in sgi.group():
print " %s" % str(s)
print
def __init__(O, args):
import libtbx.load_env
command_line = (libtbx_option_parser(
usage="%s [options] pdb_file" % libtbx.env.dispatcher_name
).option(
None,
"--model_id",
action="store",
type="str",
default=None,
help="only show model with given id",
metavar="STR"
).option(
None,
"--labels_threshold",
action="store",
type="int",
default=20,
help="do not show atom labels if more than given number of atoms",
metavar="INT").option(None,
"--serial_labels",
action="store_true",
default=False)).process(args=args, nargs=1)
O.co = command_line.options
file_name = command_line.args[0]
import iotbx.pdb
O.pdb_inp = iotbx.pdb.input(file_name=file_name)
O.pdb_hierarchy = O.pdb_inp.construct_hierarchy()
O.pdb_atoms = O.pdb_hierarchy.atoms()
print(file_name)
print(" number of models:", O.pdb_hierarchy.models_size())
print(" number of atoms:", O.pdb_atoms.size())
if (O.co.model_id is not None):
mid = O.co.model_id.strip()
from libtbx.str_utils import show_string
print("Selecting model with id %s" % show_string(mid))
for mdl in O.pdb_hierarchy.models():
if (mdl.id.strip() == mid):
O.pdb_hierarchy = iotbx.pdb.hierarchy.root()
O.pdb_hierarchy.append_model(mdl)
O.pdb_atoms = O.pdb_hierarchy.atoms()
print(" number of atoms:", O.pdb_atoms.size())
break
else:
raise RuntimeError("--model-id=%s is not in the pdb file." %
show_string(mid))
super(App, O).__init__(title=libtbx.env.dispatcher_name)
def __init__(O, args):
import libtbx.load_env
command_line = (libtbx_option_parser(
usage="%s [options] pdb_file" % libtbx.env.dispatcher_name)
.option(None, "--model_id",
action="store",
type="str",
default=None,
help="only show model with given id",
metavar="STR")
.option(None, "--labels_threshold",
action="store",
type="int",
default=20,
help="do not show atom labels if more than given number of atoms",
metavar="INT")
.option(None, "--serial_labels",
action="store_true",
default=False)
).process(args=args, nargs=1)
O.co = command_line.options
file_name = command_line.args[0]
import iotbx.pdb
O.pdb_inp = iotbx.pdb.input(file_name=file_name)
O.pdb_hierarchy = O.pdb_inp.construct_hierarchy()
O.pdb_atoms = O.pdb_hierarchy.atoms()
print file_name
print " number of models:", O.pdb_hierarchy.models_size()
print " number of atoms:", O.pdb_atoms.size()
if (O.co.model_id is not None):
mid = O.co.model_id.strip()
from libtbx.str_utils import show_string
print "Selecting model with id %s" % show_string(mid)
for mdl in O.pdb_hierarchy.models():
if (mdl.id.strip() == mid):
O.pdb_hierarchy = iotbx.pdb.hierarchy.root()
O.pdb_hierarchy.append_model(mdl)
O.pdb_atoms = O.pdb_hierarchy.atoms()
print " number of atoms:", O.pdb_atoms.size()
break
else:
raise RuntimeError(
"--model-id=%s is not in the pdb file." % show_string(mid))
super(App, O).__init__(title=libtbx.env.dispatcher_name)
def __init__(self, args):
n = tst_tardy.n_test_models
command_line = (libtbx_option_parser(usage="""\
scitbx.python wx_tardy.py [options] model_index
model_index range: 0 ... %d\
""" % (n - 1)).option(None,
"--fixed_vertices",
type="str",
action="append",
default=None,
metavar="COMMA-SEPARATED-INTEGERS").option(
None,
"--i_seq_labels",
action="store_true",
default=False).option(
None,
"--velocity_scaling",
action="store_true",
default=False).option(
None,
"--e_kin_per_dof",
type="float",
default=1.0,
metavar="FLOAT").option(
None,
"--view_scale",
type="float",
default=1.3,
metavar="FLOAT")).process(args=args,
nargs=1)
co = command_line.options
self.fixed_vertex_lists = []
if (co.fixed_vertices is not None):
for s in co.fixed_vertices:
self.fixed_vertex_lists.append(tuple(eval("[" + s + "]")))
self.i_seq_labels = co.i_seq_labels
self.velocity_scaling = co.velocity_scaling
self.e_kin_per_dof = co.e_kin_per_dof
self.view_scale = co.view_scale
self.model_index = int(command_line.args[0])
assert 0 <= self.model_index < n
super(App, self).__init__(title="wx_tardy")
def run(args):
if (len(args) == 0): args = ["--help"]
from libtbx.option_parser import libtbx_option_parser
import libtbx.load_env
command_line = (libtbx_option_parser(
usage="%s [options] space_group_symbol ..." %
libtbx.env.dispatcher_name).option(
None,
"--primitive",
action="store_true",
help="Convert centred space groups to primitive setting.").option(
None,
"--symops",
action="store_true",
help="Show list of symmetry operations.")).process(args=args)
co = command_line.options
from cctbx import sgtbx
args = command_line.args
if (args == ["all"]):
args = [str(no) for no in xrange(1, 230 + 1)]
for symbol in args:
sgi = sgtbx.space_group_info(symbol=symbol)
if (co.primitive):
sgi = sgi.primitive_setting()
sgi.show_summary()
gr = sgi.group()
print " Crystal system:", gr.crystal_system()
print " Point group type:", gr.point_group_type()
print " Laue group type:", gr.laue_group_type()
print " Number of symmetry operations:", gr.order_z()
print " Lattice centering operations:", gr.n_ltr()
if (gr.n_ltr() != 1):
print " Number of symmetry operations in primitive setting:", \
gr.order_p()
if (gr.is_centric()): s = gr(0, 1, 0)
else: s = None
print " Center of inversion:", s
print " Dimensionality of continuous allowed origin shifts:", \
sgi.number_of_continuous_allowed_origin_shifts()
ssi_vm = sgi.structure_seminvariants().vectors_and_moduli()
print " Structure-seminvariant vectors and moduli:", \
len(ssi_vm)
if (len(ssi_vm) != 0):
for vm in ssi_vm:
print " (%2d, %2d, %2d)" % vm.v, "%2d" % vm.m
print " Direct-space asymmetric unit:"
dau = sgi.direct_space_asu()
print " Number of faces: %d" % len(dau.cuts)
for cut in dau.cuts:
print " " + cut.as_xyz()
print " ADP constraint matrix:"
_ = sgi.group().adp_constraints().gradient_sum_matrix()
from scitbx import matrix
print matrix.rec(tuple(_),
_.focus()).mathematica_form(one_row_per_line=True,
prefix=" ")
if (co.symops):
print " List of symmetry operations:"
for s in sgi.group():
print " %s" % str(s)
print