def run(args):
if (len(args) != 2):
raise Usage("""\
cctbx.python space_subgroups.py max_index space_group_symbol
Example: cctbx.python space_subgroups.py 2 P41212""")
#
max_index = int(args[0])
print("max_index:", max_index)
assert max_index >= 1
print()
space_group_t_den = 144
sginfo = sgtbx.space_group_info(symbol=args[1],
space_group_t_den=space_group_t_den)
sginfo.show_summary()
print()
cb_op_to_p = sginfo.change_of_basis_op_to_primitive_setting()
sginfo_p = sginfo.change_basis(cb_op=cb_op_to_p)
if (sginfo_p.group() != sginfo.group()):
print("Primitive setting:")
sginfo_p.show_summary()
print()
#
all_subgroups = dict_with_default_0()
sg_p = sginfo_p.group()
sg_p_a = sg_p.build_derived_acentric_group()
if (sg_p.is_centric()):
inv_mx = sg_p(0, 1, 0).t()
else:
inv_mx = None
for symx1 in sg_p_a:
subgr1 = sgtbx.space_group(hall_symbol="P1", t_den=space_group_t_den)
subgr1.expand_smx(symx1)
for symx2 in sg_p_a:
subgr2 = sgtbx.space_group(subgr1)
subgr2.expand_smx(symx2)
loop_over_super_cells(max_index=max_index,
all_subgroups=all_subgroups,
subgroup=subgr2)
if (inv_mx is not None):
subgr3 = sgtbx.space_group(subgr2)
subgr3.expand_inv(inv_mx)
loop_over_super_cells(max_index=max_index,
all_subgroups=all_subgroups,
subgroup=subgr3)
#
show_sorted_by_counts(label_count_pairs=list(all_subgroups.items()))
def run(args):
if (len(args) != 2):
raise Usage("""\
cctbx.python space_subgroups.py max_index space_group_symbol
Example: cctbx.python space_subgroups.py 2 P41212""")
#
max_index = int(args[0])
print "max_index:", max_index
assert max_index >= 1
print
space_group_t_den = 144
sginfo = sgtbx.space_group_info(
symbol=args[1], space_group_t_den=space_group_t_den)
sginfo.show_summary()
print
cb_op_to_p = sginfo.change_of_basis_op_to_primitive_setting()
sginfo_p = sginfo.change_basis(cb_op=cb_op_to_p)
if (sginfo_p.group() != sginfo.group()):
print "Primitive setting:"
sginfo_p.show_summary()
print
#
all_subgroups = dict_with_default_0()
sg_p = sginfo_p.group()
sg_p_a = sg_p.build_derived_acentric_group()
if (sg_p.is_centric()):
inv_mx = sg_p(0, 1, 0).t()
else:
inv_mx = None
for symx1 in sg_p_a:
subgr1 = sgtbx.space_group(hall_symbol="P1", t_den=space_group_t_den)
subgr1.expand_smx(symx1)
for symx2 in sg_p_a:
subgr2 = sgtbx.space_group(subgr1)
subgr2.expand_smx(symx2)
loop_over_super_cells(
max_index=max_index, all_subgroups=all_subgroups, subgroup=subgr2)
if (inv_mx is not None):
subgr3 = sgtbx.space_group(subgr2)
subgr3.expand_inv(inv_mx)
loop_over_super_cells(
max_index=max_index, all_subgroups=all_subgroups, subgroup=subgr3)
#
show_sorted_by_counts(label_count_pairs=all_subgroups.items())
def exercise():
from libtbx.test_utils import show_diff, Exception_expected
from six.moves import cPickle as pickle
#
from libtbx.str_utils import split_keeping_spaces
assert split_keeping_spaces(s="") == []
assert split_keeping_spaces(s=" ") == [" "]
assert split_keeping_spaces(s="a") == ["a"]
assert split_keeping_spaces(s="abc") == ["abc"]
assert split_keeping_spaces(s=" a") == [" ", "a"]
assert split_keeping_spaces(s=" a") == [" ", "a"]
assert split_keeping_spaces(s=" abc") == [" ", "abc"]
assert split_keeping_spaces(s=" abc ") == [" ", "abc", " "]
assert split_keeping_spaces(s=" abc ") == [" ", "abc", " "]
assert split_keeping_spaces(s="a ") == ["a", " "]
assert split_keeping_spaces(s="a ") == ["a", " "]
assert split_keeping_spaces(s="abc ") == ["abc", " "]
assert split_keeping_spaces(s="a b") == ["a", " ", "b"]
assert split_keeping_spaces(s="a b") == ["a", " ", "b"]
assert split_keeping_spaces(s=" a b c d ") == [
" ", "a", " ", "b", " ", "c", " ", "d", " "
]
#
from libtbx.str_utils import size_as_string_with_commas
assert size_as_string_with_commas(0) == "0"
assert size_as_string_with_commas(1) == "1"
assert size_as_string_with_commas(-1) == "-1"
assert size_as_string_with_commas(10) == "10"
assert size_as_string_with_commas(100) == "100"
assert size_as_string_with_commas(1000) == "1,000"
assert size_as_string_with_commas(12345) == "12,345"
assert size_as_string_with_commas(12345678) == "12,345,678"
assert size_as_string_with_commas(-12345678) == "-12,345,678"
#
from libtbx.str_utils import show_string
assert show_string("abc") == '"abc"'
assert show_string("a'c") == '"a\'c"'
assert show_string('a"c') == "'a\"c'"
assert show_string('\'"c') == '"\'\\"c"'
#
from libtbx.str_utils import prefix_each_line
assert prefix_each_line(prefix="^",
lines_as_one_string="""\
hello
world""") == """\
^hello
^world"""
#
from libtbx.str_utils import prefix_each_line_suffix
assert prefix_each_line_suffix(prefix="^",
lines_as_one_string="""\
hello
world""",
suffix=" ") == """\
^hello
^world"""
assert prefix_each_line_suffix(prefix="^",
lines_as_one_string="""\
hello
world""",
suffix=" ",
rstrip=False) == """\
^hello%s
^world """ % " "
#
from libtbx.str_utils import show_sorted_by_counts
from six.moves import cStringIO
out = cStringIO()
assert show_sorted_by_counts(label_count_pairs=[("b", 3), ("a", 3),
("c", -2)],
out=out,
prefix="%")
assert not show_diff(out.getvalue(), """\
%"a" 3
%"b" 3
%"c" -2
""")
out = cStringIO()
assert show_sorted_by_counts(label_count_pairs=[("b", -3), ("a", -3),
("c", 2)],
reverse=False,
out=out,
prefix="%",
annotations=[None, "", "x"])
assert not show_diff(out.getvalue(), """\
%"a" -3
%"b" -3
%"c" 2 x
""")
#
from libtbx.str_utils import line_breaker
for string, expected_result in [
("", [""]), ("this is", ["this is"]), ("this is a", ["this is", "a"]),
("this is a sentence", ["this is", "a", "sentence"]),
("this is a longer sentence", ["this is", "a", "longer", "sentence"]),
("this is a very long sentence indeed",
["this is", "a very", "long", "sentence", "indeed"])
]:
assert [block
for block in line_breaker(string, width=7)] == expected_result
#
from libtbx.str_utils import StringIO
out1 = cStringIO()
out2 = StringIO()
out3 = StringIO("Hello world!\n")
print("Hello world!", file=out1)
print("Hello world!", file=out2)
try:
print("Hello world!", file=out3)
except AttributeError:
pass
else:
raise Exception_expected
out4 = pickle.loads(pickle.dumps(out2))
out5 = pickle.loads(pickle.dumps(out3))
assert out4.getvalue() == out1.getvalue() == out2.getvalue(
) == out5.getvalue()
#
from libtbx.str_utils import reformat_terminal_text
txt1 = """
This is some
terminal-formatted
text which needs
to be reset.
"""
assert (reformat_terminal_text(txt1) ==
"This is some terminal-formatted text which needs to be reset.")
txt2 = """
This is more
terminal-formatted
text which needs
to be reset.
"""
#
from libtbx.str_utils import strip_lines, rstrip_lines
lines = [" This is more ", " terminal-formatted ", " text "]
assert (
strip_lines(txt2) ==
"\nThis is more\nterminal-formatted\ntext which needs\nto be reset.")
assert (
rstrip_lines(txt2) ==
"\n This is more\n terminal-formatted\n text which needs\n to be reset."
)
#
from libtbx.str_utils import expandtabs_track_columns
def check(s):
es, js = expandtabs_track_columns(s=s)
assert len(js) == len(s)
assert es == s.expandtabs()
sr = "".join([es[j] for j in js])
assert sr == s.replace("\t", " ")
check("")
check("\t")
check("\t\t")
check("\ty")
check("x\ty")
check("x\ty\tz")
check("\txy\t\tz")
check("abcdefg\txy\t\tz")
check("ab defgh\txyz\t\tu")
#
from libtbx.str_utils import format_value
assert format_value("%.4f", 1.2345678) == "1.2346"
assert format_value("%.4f", None) == " None"
assert format_value("%.4f", None, replace_none_with="---") == " ---"
#
from libtbx.str_utils import make_header
out = StringIO()
make_header("Header 1", out=out)
assert (out.getvalue() == """
=================================== Header 1 ==================================
""")
out = StringIO()
make_header("Header 2", out=out)
assert (out.getvalue() == """
=================================== Header 2 ==================================
""")
#
import sys
from libtbx.str_utils import string_representation
iset = list(range(130)) + list(range(250, 256))
for i in iset:
s = chr(i)
for j in iset:
ss = s + chr(j)
sr = string_representation(string=ss,
preferred_quote="'",
alternative_quote='"')
if sys.hexversion < 0x03000000:
assert sr == repr(ss)
else:
assert eval(sr) == ss
from libtbx.str_utils import framed_output
out = StringIO()
box = framed_output(out, frame='#')
print("Hello, world!", file=box)
box.close()
assert (out.getvalue() == """
#################
# Hello, world! #
#################
""")
out = StringIO()
box = framed_output(out,
frame='-',
width=80,
center=True,
title="Refinement stats")
box.write("r_free = 0.1234")
box.write(" ")
box.write("r_work = 0.1567")
box.close()
assert (out.getvalue() == """
|--------------------------------Refinement stats------------------------------|
| r_free = 0.1234 r_work = 0.1567 |
|------------------------------------------------------------------------------|
""")
out = StringIO()
box = framed_output(out,
frame='-',
width=72,
prefix=" ",
title="Validation summary")
print("Overall MolProbity score: 2.56", file=box)
box.add_separator()
print("""\
Ramachandran favored: 97.5 %
outliers: 2.5 %
Rotamer outliers: 5.9 %
Clashscore: 10.9""",
file=box)
assert (out.getvalue() == "")
del box
assert (out.getvalue() == """
|-Validation summary---------------------------------------------------|
| Overall MolProbity score: 2.56 |
|----------------------------------------------------------------------|
| Ramachandran favored: 97.5 % |
| outliers: 2.5 % |
| Rotamer outliers: 5.9 % |
| Clashscore: 10.9 |
|----------------------------------------------------------------------|
""")
from libtbx.str_utils import print_message_in_box
out = StringIO()
print_message_in_box(
message="This is some terminal-formatted text which needs to be reset.",
out=out,
width=32,
center=True,
prefix=" ",
frame='*')
assert (out.getvalue() == """
********************************
* This is some *
* terminal-formatted text *
* which needs to be reset. *
********************************
""")
from libtbx.str_utils import make_big_header
out = StringIO()
make_big_header("Section title", out=out)
assert (out.getvalue() == """
################################################################################
# Section title #
################################################################################
""")
def run(args):
assert len(args) in [0,2], "n_sites, n_trials"
if (len(args) == 0):
n_sites, n_trials = 3, 2
out = null_out()
else:
n_sites, n_trials = [int(arg) for arg in args]
out = sys.stdout
#
show_times_at_exit()
class type_info(object):
def __init__(O, type, use_analytical_gradients):
O.type = type
O.use_analytical_gradients = use_analytical_gradients
def __str__(O):
return "%s(use_analytical_gradients=%s)" % (
O.type.__name__, str(O.use_analytical_gradients))
spherical_types = [
type_info(euler_params, False),
type_info(euler_params, True),
type_info(euler_angles_xyz, False),
type_info(euler_angles_xyz, True),
type_info(euler_angles_zxz, False),
type_info(euler_angles_zxz, True),
type_info(euler_angles_yxyz, False),
type_info(euler_angles_xyzy, False),
type_info(inf_euler_params, False),
type_info(inf_axis_angle, False)]
nfun_accu = {}
n_failed = {}
for ti in spherical_types:
nfun_accu[str(ti)] = flex.size_t()
n_failed[str(ti)] = 0
mersenne_twister = flex.mersenne_twister(seed=0)
for i_trial in xrange(n_trials):
sites = [matrix.col(s) for s in flex.vec3_double(
mersenne_twister.random_double(size=n_sites*3)*2-1)]
c = center_of_mass_from_sites(sites)
r = matrix.sqr(mersenne_twister.random_double_r3_rotation_matrix())
wells = [r*(s-c)+c for s in sites]
for ti in spherical_types:
r = refinery(spherical_type_info=ti, sites=sites, wells=wells, out=out)
nfun_accu[str(ti)].append(r.nfun)
if (r.failed):
n_failed[str(ti)] += 1
nfun_sums = []
annotations = []
for ti in spherical_types:
print >> out, ti
nfuns = nfun_accu[str(ti)]
stats = nfuns.as_double().min_max_mean()
stats.show(out=out, prefix=" ")
nfun_sums.append((str(ti), flex.sum(nfuns)))
if (n_failed[str(ti)] == 0):
annotations.append(None)
else:
annotations.append("failed: %d" % n_failed[str(ti)])
print >> out
show_sorted_by_counts(
label_count_pairs=nfun_sums,
reverse=False,
out=out,
annotations=annotations)
print >> out
print "OK"
def run(args):
assert len(args) in [0, 2], "n_sites, n_trials"
if (len(args) == 0):
n_sites, n_trials = 3, 2
out = null_out()
else:
n_sites, n_trials = [int(arg) for arg in args]
out = sys.stdout
#
show_times_at_exit()
class type_info(object):
def __init__(O, type, use_analytical_gradients):
O.type = type
O.use_analytical_gradients = use_analytical_gradients
def __str__(O):
return "%s(use_analytical_gradients=%s)" % (
O.type.__name__, str(O.use_analytical_gradients))
spherical_types = [
type_info(euler_params, False),
type_info(euler_params, True),
type_info(euler_angles_xyz, False),
type_info(euler_angles_xyz, True),
type_info(euler_angles_zxz, False),
type_info(euler_angles_zxz, True),
type_info(euler_angles_yxyz, False),
type_info(euler_angles_xyzy, False),
type_info(inf_euler_params, False),
type_info(inf_axis_angle, False)
]
nfun_accu = {}
n_failed = {}
for ti in spherical_types:
nfun_accu[str(ti)] = flex.size_t()
n_failed[str(ti)] = 0
mersenne_twister = flex.mersenne_twister(seed=0)
for i_trial in xrange(n_trials):
sites = [
matrix.col(s) for s in flex.vec3_double(
mersenne_twister.random_double(size=n_sites * 3) * 2 - 1)
]
c = center_of_mass_from_sites(sites)
r = matrix.sqr(mersenne_twister.random_double_r3_rotation_matrix())
wells = [r * (s - c) + c for s in sites]
for ti in spherical_types:
r = refinery(spherical_type_info=ti,
sites=sites,
wells=wells,
out=out)
nfun_accu[str(ti)].append(r.nfun)
if (r.failed):
n_failed[str(ti)] += 1
nfun_sums = []
annotations = []
for ti in spherical_types:
print >> out, ti
nfuns = nfun_accu[str(ti)]
stats = nfuns.as_double().min_max_mean()
stats.show(out=out, prefix=" ")
nfun_sums.append((str(ti), flex.sum(nfuns)))
if (n_failed[str(ti)] == 0):
annotations.append(None)
else:
annotations.append("failed: %d" % n_failed[str(ti)])
print >> out
show_sorted_by_counts(label_count_pairs=nfun_sums,
reverse=False,
out=out,
annotations=annotations)
print >> out
print "OK"
def exercise():
from libtbx.test_utils import show_diff, Exception_expected
import cPickle
#
from libtbx.str_utils import split_keeping_spaces
assert split_keeping_spaces(s="") == []
assert split_keeping_spaces(s=" ") == [" "]
assert split_keeping_spaces(s="a") == ["a"]
assert split_keeping_spaces(s="abc") == ["abc"]
assert split_keeping_spaces(s=" a") == [" ", "a"]
assert split_keeping_spaces(s=" a") == [" ", "a"]
assert split_keeping_spaces(s=" abc") == [" ", "abc"]
assert split_keeping_spaces(s=" abc ") == [" ", "abc", " "]
assert split_keeping_spaces(s=" abc ") == [" ", "abc", " "]
assert split_keeping_spaces(s="a ") == ["a", " "]
assert split_keeping_spaces(s="a ") == ["a", " "]
assert split_keeping_spaces(s="abc ") == ["abc", " "]
assert split_keeping_spaces(s="a b") == ["a", " ", "b"]
assert split_keeping_spaces(s="a b") == ["a", " ", "b"]
assert split_keeping_spaces(s=" a b c d ") == [
" ", "a", " ", "b", " ", "c", " ", "d", " "]
#
from libtbx.str_utils import size_as_string_with_commas
assert size_as_string_with_commas(0) == "0"
assert size_as_string_with_commas(1) == "1"
assert size_as_string_with_commas(-1) == "-1"
assert size_as_string_with_commas(10) == "10"
assert size_as_string_with_commas(100) == "100"
assert size_as_string_with_commas(1000) == "1,000"
assert size_as_string_with_commas(12345) == "12,345"
assert size_as_string_with_commas(12345678) == "12,345,678"
assert size_as_string_with_commas(-12345678) == "-12,345,678"
#
from libtbx.str_utils import show_string
assert show_string("abc") == '"abc"'
assert show_string("a'c") == '"a\'c"'
assert show_string('a"c') == "'a\"c'"
assert show_string('\'"c') == '"\'\\"c"'
#
from libtbx.str_utils import prefix_each_line
assert prefix_each_line(prefix="^", lines_as_one_string="""\
hello
world""") == """\
^hello
^world"""
#
from libtbx.str_utils import prefix_each_line_suffix
assert prefix_each_line_suffix(prefix="^", lines_as_one_string="""\
hello
world""", suffix=" ") == """\
^hello
^world"""
assert prefix_each_line_suffix(prefix="^", lines_as_one_string="""\
hello
world""", suffix=" ", rstrip=False) == """\
^hello%s
^world """ % " "
#
from libtbx.str_utils import show_sorted_by_counts
import cStringIO
out = cStringIO.StringIO()
assert show_sorted_by_counts(
label_count_pairs=[("b", 3), ("a", 3), ("c", -2)],
out=out, prefix="%")
assert not show_diff(out.getvalue(), """\
%"a" 3
%"b" 3
%"c" -2
""")
out = cStringIO.StringIO()
assert show_sorted_by_counts(
label_count_pairs=[("b", -3), ("a", -3), ("c", 2)], reverse=False,
out=out, prefix="%", annotations=[None, "", "x"])
assert not show_diff(out.getvalue(), """\
%"c" 2 x
%"a" -3
%"b" -3
""")
#
from libtbx.str_utils import line_breaker
for string, expected_result in [
("", [""]),
("this is", ["this is"]),
("this is a", ["this is", "a"]),
("this is a sentence", ["this is", "a", "sentence"]),
("this is a longer sentence", ["this is", "a", "longer", "sentence"]),
("this is a very long sentence indeed",
["this is", "a very", "long", "sentence", "indeed"])]:
assert [block for block in line_breaker(string, width=7)]==expected_result
#
from libtbx.str_utils import StringIO
out1 = cStringIO.StringIO()
out2 = StringIO()
out3 = StringIO("Hello world!\n")
print >> out1, "Hello world!"
print >> out2, "Hello world!"
try :
print >> out3, "Hello world!"
except AttributeError :
pass
else :
raise Exception_expected
out4 = cPickle.loads(cPickle.dumps(out2))
out5 = cPickle.loads(cPickle.dumps(out3))
assert out4.getvalue()==out1.getvalue()==out2.getvalue()==out5.getvalue()
#
from libtbx.str_utils import reformat_terminal_text
txt1 = """
This is some
terminal-formatted
text which needs
to be reset.
"""
assert (reformat_terminal_text(txt1) ==
"This is some terminal-formatted text which needs to be reset.")
txt2 = """
This is more
terminal-formatted
text which needs
to be reset.
"""
#
from libtbx.str_utils import strip_lines, rstrip_lines
lines = [" This is more ", " terminal-formatted ", " text "]
assert (strip_lines(txt2) ==
"\nThis is more\nterminal-formatted\ntext which needs\nto be reset.")
assert (rstrip_lines(txt2) ==
"\n This is more\n terminal-formatted\n text which needs\n to be reset."
)
#
from libtbx.str_utils import expandtabs_track_columns
def check(s):
es,js = expandtabs_track_columns(s=s)
assert len(js) == len(s)
assert es == s.expandtabs()
sr = "".join([es[j] for j in js])
assert sr == s.replace("\t", " ")
check("")
check("\t")
check("\t\t")
check("\ty")
check("x\ty")
check("x\ty\tz")
check("\txy\t\tz")
check("abcdefg\txy\t\tz")
check("ab defgh\txyz\t\tu")
#
from libtbx.str_utils import format_value
assert format_value("%.4f", 1.2345678) == "1.2346"
assert format_value("%.4f", None) == " None"
assert format_value("%.4f", None, replace_none_with="---") == " ---"
#
from libtbx.str_utils import make_header
out = StringIO()
make_header("Header 1", out=out)
assert (out.getvalue() == """
=================================== Header 1 ==================================
""")
out = StringIO()
make_header("Header 2", out=out)
assert (out.getvalue() == """
=================================== Header 2 ==================================
""")
#
from libtbx.str_utils import string_representation
iset = range(130) + range(250,256)
for i in iset:
s = chr(i)
for j in iset:
ss = s + chr(j)
assert string_representation(
string=ss, preferred_quote="'", alternative_quote='"') == repr(ss)
from libtbx.str_utils import framed_output
out = StringIO()
box = framed_output(out, frame='#')
print >> box, "Hello, world!"
box.close()
assert (out.getvalue() == """
#################
# Hello, world! #
#################
""")
out = StringIO()
box = framed_output(out, frame='-', width=80, center=True,
title="Refinement stats")
box.write("r_free = 0.1234")
box.write(" ")
box.write("r_work = 0.1567")
box.close()
assert (out.getvalue() == """
|--------------------------------Refinement stats------------------------------|
| r_free = 0.1234 r_work = 0.1567 |
|------------------------------------------------------------------------------|
""")
out = StringIO()
box = framed_output(out, frame='-', width=72, prefix=" ",
title="Validation summary")
print >> box, "Overall MolProbity score: 2.56"
box.add_separator()
print >> box, """\
Ramachandran favored: 97.5 %
outliers: 2.5 %
Rotamer outliers: 5.9 %
Clashscore: 10.9"""
assert (out.getvalue() == "")
del box
assert (out.getvalue() == """
|-Validation summary---------------------------------------------------|
| Overall MolProbity score: 2.56 |
|----------------------------------------------------------------------|
| Ramachandran favored: 97.5 % |
| outliers: 2.5 % |
| Rotamer outliers: 5.9 % |
| Clashscore: 10.9 |
|----------------------------------------------------------------------|
""")
from libtbx.str_utils import print_message_in_box
out = StringIO()
print_message_in_box(
message="This is some terminal-formatted text which needs to be reset.",
out=out,
width=32,
center=True,
prefix=" ",
frame='*')
assert (out.getvalue() == """
********************************
* This is some *
* terminal-formatted text *
* which needs to be reset. *
********************************
""")
def check_comp(file_name):
result = 0
print "file name:", file_name
cif_object = mmtbx.monomer_library.server.read_cif(file_name)
for comp_comp_id in mmtbx.monomer_library.server.convert_comp_list(
source_info=file_name, cif_object=cif_object):
result += 1
atom_names = set()
for atom in comp_comp_id.atom_list:
atom_name = atom.atom_id
assert atom_name.count(" ") == 0
if (atom_name in atom_names):
raise RuntimeError("Duplicate atom name: %s" %
show_string(atom_name))
atom_names.add(atom_name)
print " number of atoms:", len(atom_names)
#
bond_atom_ids = set()
for bond in comp_comp_id.bond_list:
atom_ids = [bond.atom_id_1, bond.atom_id_2]
for atom_name in atom_ids:
if (atom_name not in atom_names):
raise RuntimeError("Unknown bond atom name: %s" %
show_string(atom_name))
atom_ids = tuple(sorted(atom_ids))
if (atom_ids in bond_atom_ids):
raise RuntimeError("Duplicate bond: %s - %s" %
tuple([show_string(s) for s in atom_ids]))
bond_atom_ids.add(atom_ids)
print " number of bonds:", len(bond_atom_ids)
#
angle_atom_ids = set()
for angle in comp_comp_id.angle_list:
atom_ids = [angle.atom_id_1, angle.atom_id_2, angle.atom_id_3]
for atom_name in atom_ids:
if (atom_name not in atom_names):
raise RuntimeError("Unknown angle atom name: %s" %
show_string(atom_name))
atom_ids = tuple(sorted(atom_ids))
if (atom_ids in angle_atom_ids):
raise RuntimeError("Duplicate angle: %s - %s - %s" %
tuple([show_string(s) for s in atom_ids]))
angle_atom_ids.add(atom_ids)
print " number of angles:", len(angle_atom_ids)
#
tor_atom_ids = set()
for tor in comp_comp_id.tor_list:
atom_ids = [
tor.atom_id_1, tor.atom_id_2, tor.atom_id_3, tor.atom_id_4
]
for atom_name in atom_ids:
if (atom_name not in atom_names):
raise RuntimeError("Unknown tor atom name: %s" %
show_string(atom_name))
atom_ids = tuple(sorted(atom_ids))
if (atom_ids in tor_atom_ids):
raise RuntimeError("Duplicate tor: %s - %s - %s - %s" %
tuple([show_string(s) for s in atom_ids]))
tor_atom_ids.add(atom_ids)
print " number of tors:", len(tor_atom_ids)
tor_atom_ids = {}
for tor in comp_comp_id.tor_list:
atom_ids = tuple(sorted([tor.atom_id_2, tor.atom_id_3]))
tor_atom_ids.setdefault(atom_ids, []).append(tor)
for atom_ids, tors in tor_atom_ids.items():
if (len(tors) != 1):
print " redundant tors:", ", ".join(
[tor.id for tor in tors])
#
chir_atom_ids = set()
for chir in comp_comp_id.chir_list:
atom_ids = [
chir.atom_id_1, chir.atom_id_2, chir.atom_id_3,
chir.atom_id_centre
]
for atom_name in atom_ids:
if (atom_name not in atom_names):
raise RuntimeError("Unknown chir atom name: %s" %
show_string(atom_name))
atom_ids = tuple(sorted(atom_ids))
if (atom_ids in chir_atom_ids):
raise RuntimeError("Duplicate chir: %s - %s - %s - %s" %
tuple([show_string(s) for s in atom_ids]))
chir_atom_ids.add(atom_ids)
print " number of chirs:", len(chir_atom_ids)
#
plane_atom_counts = dict_with_default_0()
for plane_atom in comp_comp_id.plane_atom_list:
if (plane_atom.atom_id not in atom_names):
raise RuntimeError("Unknown plane atom name: %s" %
show_string(plane_atom.atom_id))
plane_atom_counts[plane_atom.plane_id] += 1
print " number of planes:", len(plane_atom_counts)
if (len(plane_atom_counts) != 0):
show_sorted_by_counts(label_count_pairs=plane_atom_counts.items(),
prefix=" ")
assert min(plane_atom_counts.values()) >= 3
#
rotamer_info = comp_comp_id.rotamer_info()
if (rotamer_info is not None):
print " rotamer_info.tor_ids:", rotamer_info.tor_ids
for tor_id in rotamer_info.tor_ids:
assert tor_id.strip() == tor_id
assert tor_id.split() == [tor_id]
for tor_atom_ids in rotamer_info.tor_atom_ids:
assert len(tor_atom_ids) == 5
assert tor_atom_ids[0] in rotamer_info.tor_ids
for atom_id in tor_atom_ids[1:]:
assert atom_id.strip() == atom_id
assert atom_id.split() == [atom_id]
atom_ids = rotamer_info.atom_ids_not_handled
if (atom_ids is not None):
for atom_id in atom_ids:
assert atom_id.strip() == atom_id
assert atom_id.split() == [atom_id]
assert (
rotamer_info.
constrain_dihedrals_with_sigma_less_than_or_equal_to is None
or rotamer_info.
constrain_dihedrals_with_sigma_less_than_or_equal_to > 0)
print " number of rotamers:", len(rotamer_info.rotamer)
n_missing_frequencies = 0
for rotamer in rotamer_info.rotamer:
assert rotamer.id is not None
assert len(rotamer.id.strip()) == len(rotamer.id)
assert len(rotamer.id.split()) == 1
if (rotamer.frequency is None):
if (rotamer.frequency_annotation !=
"for more uniform sampling"):
n_missing_frequencies += 1
else:
assert rotamer.frequency > 0
assert rotamer.frequency < 1
assert rotamer.angles is not None
assert len(rotamer.angles) == len(rotamer_info.tor_ids)
for angle in rotamer.angles:
assert angle is None or -180 < angle <= 180
if (n_missing_frequencies != 0):
print " WARNING: number of missing frequencies:", \
n_missing_frequencies
return result
def check_comp(file_name):
result = 0
print "file name:", file_name
cif_object = mmtbx.monomer_library.server.read_cif(file_name)
for comp_comp_id in mmtbx.monomer_library.server.convert_comp_list(
source_info=file_name, cif_object=cif_object):
result += 1
atom_names = set()
for atom in comp_comp_id.atom_list:
atom_name = atom.atom_id
assert atom_name.count(" ") == 0
if (atom_name in atom_names):
raise RuntimeError(
"Duplicate atom name: %s" % show_string(atom_name))
atom_names.add(atom_name)
print " number of atoms:", len(atom_names)
#
bond_atom_ids = set()
for bond in comp_comp_id.bond_list:
atom_ids = [bond.atom_id_1, bond.atom_id_2]
for atom_name in atom_ids:
if (atom_name not in atom_names):
raise RuntimeError(
"Unknown bond atom name: %s" % show_string(atom_name))
atom_ids = tuple(sorted(atom_ids))
if (atom_ids in bond_atom_ids):
raise RuntimeError(
"Duplicate bond: %s - %s" % tuple([show_string(s)
for s in atom_ids]))
bond_atom_ids.add(atom_ids)
print " number of bonds:", len(bond_atom_ids)
#
angle_atom_ids = set()
for angle in comp_comp_id.angle_list:
atom_ids = [angle.atom_id_1, angle.atom_id_2, angle.atom_id_3]
for atom_name in atom_ids:
if (atom_name not in atom_names):
raise RuntimeError(
"Unknown angle atom name: %s" % show_string(atom_name))
atom_ids = tuple(sorted(atom_ids))
if (atom_ids in angle_atom_ids):
raise RuntimeError(
"Duplicate angle: %s - %s - %s" % tuple([show_string(s)
for s in atom_ids]))
angle_atom_ids.add(atom_ids)
print " number of angles:", len(angle_atom_ids)
#
tor_atom_ids = set()
for tor in comp_comp_id.tor_list:
atom_ids = [tor.atom_id_1, tor.atom_id_2, tor.atom_id_3, tor.atom_id_4]
for atom_name in atom_ids:
if (atom_name not in atom_names):
raise RuntimeError(
"Unknown tor atom name: %s" % show_string(atom_name))
atom_ids = tuple(sorted(atom_ids))
if (atom_ids in tor_atom_ids):
raise RuntimeError(
"Duplicate tor: %s - %s - %s - %s" % tuple([show_string(s)
for s in atom_ids]))
tor_atom_ids.add(atom_ids)
print " number of tors:", len(tor_atom_ids)
tor_atom_ids = {}
for tor in comp_comp_id.tor_list:
atom_ids = tuple(sorted([tor.atom_id_2, tor.atom_id_3]))
tor_atom_ids.setdefault(atom_ids, []).append(tor)
for atom_ids,tors in tor_atom_ids.items():
if (len(tors) != 1):
print " redundant tors:", ", ".join([tor.id for tor in tors])
#
chir_atom_ids = set()
for chir in comp_comp_id.chir_list:
atom_ids = [
chir.atom_id_1, chir.atom_id_2, chir.atom_id_3, chir.atom_id_centre]
for atom_name in atom_ids:
if (atom_name not in atom_names):
raise RuntimeError(
"Unknown chir atom name: %s" % show_string(atom_name))
atom_ids = tuple(sorted(atom_ids))
if (atom_ids in chir_atom_ids):
raise RuntimeError(
"Duplicate chir: %s - %s - %s - %s" % tuple([show_string(s)
for s in atom_ids]))
chir_atom_ids.add(atom_ids)
print " number of chirs:", len(chir_atom_ids)
#
plane_atom_counts = dict_with_default_0()
for plane_atom in comp_comp_id.plane_atom_list:
if (plane_atom.atom_id not in atom_names):
raise RuntimeError(
"Unknown plane atom name: %s" % show_string(plane_atom.atom_id))
plane_atom_counts[plane_atom.plane_id] += 1
print " number of planes:", len(plane_atom_counts)
if (len(plane_atom_counts) != 0):
show_sorted_by_counts(
label_count_pairs=plane_atom_counts.items(),
prefix=" ")
assert min(plane_atom_counts.values()) >= 3
#
rotamer_info = comp_comp_id.rotamer_info()
if (rotamer_info is not None):
print " rotamer_info.tor_ids:", rotamer_info.tor_ids
for tor_id in rotamer_info.tor_ids:
assert tor_id.strip() == tor_id
assert tor_id.split() == [tor_id]
for tor_atom_ids in rotamer_info.tor_atom_ids:
assert len(tor_atom_ids) == 5
assert tor_atom_ids[0] in rotamer_info.tor_ids
for atom_id in tor_atom_ids[1:]:
assert atom_id.strip() == atom_id
assert atom_id.split() == [atom_id]
atom_ids = rotamer_info.atom_ids_not_handled
if (atom_ids is not None):
for atom_id in atom_ids:
assert atom_id.strip() == atom_id
assert atom_id.split() == [atom_id]
assert (
rotamer_info.constrain_dihedrals_with_sigma_less_than_or_equal_to
is None
or rotamer_info.constrain_dihedrals_with_sigma_less_than_or_equal_to
> 0)
print " number of rotamers:", len(rotamer_info.rotamer)
n_missing_frequencies = 0
for rotamer in rotamer_info.rotamer:
assert rotamer.id is not None
assert len(rotamer.id.strip()) == len(rotamer.id)
assert len(rotamer.id.split()) == 1
if (rotamer.frequency is None):
if (rotamer.frequency_annotation != "for more uniform sampling"):
n_missing_frequencies += 1
else:
assert rotamer.frequency > 0
assert rotamer.frequency < 1
assert rotamer.angles is not None
assert len(rotamer.angles) == len(rotamer_info.tor_ids)
for angle in rotamer.angles:
assert angle is None or -180 < angle <= 180
if (n_missing_frequencies != 0):
print " WARNING: number of missing frequencies:", \
n_missing_frequencies
return result
