def show_ncs_groups(self, out = None):
if(out is None): out = sys.stdout
pr = "REMARK 3 "
print >>out,pr+"NCS DETAILS."
print >>out,pr+" NUMBER OF NCS GROUPS : %-6d"%len(self.ncs_groups)
for i_group, ncs_group in enumerate(self.ncs_groups):
print >>out,pr+" NCS GROUP : %-6d"%(i_group+1)
selection_strings = ncs_group.group.selection_strings
for i_op,pair,mx,rms in zip(
count(1),
ncs_group.group.selection_pairs,
ncs_group.matrices,
ncs_group.rms):
print >> out,pr+" NCS OPERATOR : %-d" % i_op
lines = line_breaker(selection_strings[0], width=34)
for i_line, line in enumerate(lines):
if(i_line == 0):
print >> out, pr+" REFERENCE SELECTION: %s"%line
else:
print >> out, pr+" : %s"%line
lines = line_breaker(selection_strings[i_op], width=34)
for i_line, line in enumerate(lines):
if(i_line == 0):
print >> out, pr+" SELECTION : %s"%line
else:
print >> out, pr+" : %s"%line
print >> out,pr+" ATOM PAIRS NUMBER : %-d" % len(pair[0])
print >> out,pr+" RMSD : %-10.3f" % rms
def as_pdb(self, sites_cart, out):
result = out
ncs_groups = self.extract_ncs_groups(sites_cart=sites_cart)
pr = "REMARK 3 "
print >> result, pr + "NCS DETAILS."
print >> result, pr + " NUMBER OF NCS GROUPS : %-6d" % len(ncs_groups)
for i_group, ncs_group in enumerate(ncs_groups):
print >> result, pr + " NCS GROUP : %-6d" % (i_group + 1)
selection_strings = ncs_group.group.selection_strings
for i_op, pair, mx, rms in zip(count(1),
ncs_group.group.selection_pairs,
ncs_group.matrices, ncs_group.rms):
print >> result, pr + " NCS OPERATOR : %-d" % i_op
lines = line_breaker(selection_strings[0], width=34)
for i_line, line in enumerate(lines):
if (i_line == 0):
print >> result, pr + " REFERENCE SELECTION: %s" % line
else:
print >> result, pr + " : %s" % line
lines = line_breaker(selection_strings[i_op], width=34)
for i_line, line in enumerate(lines):
if (i_line == 0):
print >> result, pr + " SELECTION : %s" % line
else:
print >> result, pr + " : %s" % line
print >> result, pr + " ATOM PAIRS NUMBER : %-d" % len(
pair[0])
print >> result, pr + " RMSD : %-10.3f" % rms
return result.getvalue()
def as_pdb(self, sites_cart, out):
result = out
pr = "REMARK 3 "
print(pr + "NCS DETAILS.", file=result)
print(pr + " NUMBER OF NCS GROUPS : %-6d" % self.get_n_groups(),
file=result)
for i_group, group in enumerate(self.groups_list):
print(pr + " NCS GROUP : %-6d" % (i_group + 1), file=result)
selection_strings = group.selection_strings
for i_op, pair, mx, rms in zip(count(1), group.selection_pairs,
group.matrices, group.rms):
print(pr + " NCS OPERATOR : %-d" % i_op, file=result)
lines = line_breaker(selection_strings[0], width=34)
for i_line, line in enumerate(lines):
if (i_line == 0):
print(pr + " REFERENCE SELECTION: %s" % line,
file=result)
else:
print(pr + " : %s" % line,
file=result)
lines = line_breaker(selection_strings[i_op], width=34)
for i_line, line in enumerate(lines):
if (i_line == 0):
print(pr + " SELECTION : %s" % line,
file=result)
else:
print(pr + " : %s" % line,
file=result)
print(pr + " ATOM PAIRS NUMBER : %-d" % len(pair[0]),
file=result)
print(pr + " RMSD : %-10.3f" % rms,
file=result)
return result.getvalue()
def show_ncs_groups(self, out = None):
if(out is None): out = sys.stdout
pr = "REMARK 3 "
print >>out,pr+"NCS DETAILS."
print >>out,pr+" NUMBER OF NCS GROUPS : %-6d"%len(self.ncs_groups)
for i_group, ncs_group in enumerate(self.ncs_groups):
print >>out,pr+" NCS GROUP : %-6d"%(i_group+1)
selection_strings = ncs_group.group.selection_strings
for i_op,pair,mx,rms in zip(
count(1),
ncs_group.group.selection_pairs,
ncs_group.matrices,
ncs_group.rms):
print >> out,pr+" NCS OPERATOR : %-d" % i_op
lines = line_breaker(selection_strings[0], width=34)
for i_line, line in enumerate(lines):
if(i_line == 0):
print >> out, pr+" REFERENCE SELECTION: %s"%line
else:
print >> out, pr+" : %s"%line
lines = line_breaker(selection_strings[i_op], width=34)
for i_line, line in enumerate(lines):
if(i_line == 0):
print >> out, pr+" SELECTION : %s"%line
else:
print >> out, pr+" : %s"%line
print >> out,pr+" ATOM PAIRS NUMBER : %-d" % len(pair[0])
print >> out,pr+" RMSD : %-10.3f" % rms
def write_def(self, f):
special = special_wrappers.get(self.function_name, None)
if (special is not None and special[1] is not None):
print(special[1], file=f)
return
return_opaque = self.return_type in opaque_pointers
def_args = (self.function_name, self.wrapper_function_name())
self.write_no_opaque_pointers_guard_if(f=f)
self.write_version_guard_if(f=f)
if (len(self.args) == 0):
if (not return_opaque):
print(' def("%s", %s);' % def_args, file=f)
else:
print(' def("%s", %s,' % def_args, file=f)
print(" return_value_policy<return_opaque_pointer>());",
file=f)
else:
assert not return_opaque
print(' def("%s", %s, (' % def_args, file=f)
s = ""
for arg in self.args:
s += ', arg("%s")' % arg.name
s = s[2:] + "));"
for line in line_breaker(s, 73):
print(" " + line, file=f)
self.write_version_guard_endif(f=f)
self.write_no_opaque_pointers_guard_endif(f=f)
def write_def(self, f):
special = special_wrappers.get(self.function_name, None)
if (special is not None and special[1] is not None):
print >> f, special[1]
return
return_opaque = self.return_type in opaque_pointers
def_args = (self.function_name, self.wrapper_function_name())
self.write_no_opaque_pointers_guard_if(f=f)
self.write_version_guard_if(f=f)
if (len(self.args) == 0):
if (not return_opaque):
print >> f, ' def("%s", %s);' % def_args
else:
print >> f, ' def("%s", %s,' % def_args
print >> f, " return_value_policy<return_opaque_pointer>());"
else:
assert not return_opaque
print >> f, ' def("%s", %s, (' % def_args
s = ""
for arg in self.args:
s += ', arg("%s")' % arg.name
s = s[2:] + "));"
for line in line_breaker(s, 73):
print >> f, " "+line
self.write_version_guard_endif(f=f)
self.write_no_opaque_pointers_guard_endif(f=f)
def warn (self, message) :
self.__call__(message="warn", data=message, accumulate=True, cached=True)
if (self._log is not None) :
log = self._log
else :
log = sys.stdout
msg = "WARNING: %s\n" % message
print >> log, ""
for line in str_utils.line_breaker(msg, 72) :
print >> log, " " + line
def warn (self, message) :
if (not isinstance(message, (six.text_type, six.binary_type))) :
message = to_unicode(message)
self.__call__(message="warn", data=message, accumulate=True, cached=True)
if (self._log is not None) :
log = self._log
else :
log = sys.stdout
msg = "WARNING: %s\n" % message
print("", file=log)
for line in str_utils.line_breaker(msg, 72) :
print(" " + line, file=log)
def show_citation(article, out=None, max_width=79, format='default'):
if format == 'default':
output = format_citation(article)
elif format == 'iucr':
output = format_citation_iucr(article)
elif format == 'cell':
output = format_citation_cell(article)
if max_width is None or max_width < 1:
print(to_unicode(output), file=out)
else:
for line in str_utils.line_breaker(output, max_width):
print(to_unicode(line), file=out)
print(to_unicode(''), file=out)
def warn(self, message):
self.__call__(message="warn",
data=message,
accumulate=True,
cached=True)
if (self._log is not None):
log = self._log
else:
log = sys.stdout
msg = "WARNING: %s\n" % message
print >> log, ""
for line in str_utils.line_breaker(msg, 72):
print >> log, " " + line
def remark_3_tls(tlsos, selection_strings, out=None):
if (out is None): out = sys.stdout
if (len(selection_strings) == 0):
assert len(tlsos) == 1
selection_strings = [None]
else:
assert len(tlsos) == len(selection_strings)
print >> out, "REMARK 3 TLS DETAILS."
print >> out, "REMARK 3 NUMBER OF TLS GROUPS: %-6d" % len(tlsos)
print >> out, "REMARK 3 ORIGIN: CENTER OF MASS"
r3 = "REMARK 3 "
counter = 0
for tlso, selection_string in zip(tlsos, selection_strings):
if (selection_string is None):
selection_string = "all"
counter += 1
t = tlso.t
l = tlso.l
s = tlso.s
o = tlso.origin
print >> out, r3 + "TLS GROUP : %-6d" % (counter)
lines = line_breaker(selection_string, width=45)
for i_line, line in enumerate(lines):
if (i_line == 0):
print >> out, r3 + " SELECTION: %s" % line
else:
print >> out, r3 + " : %s" % line
print >> out, r3 + " ORIGIN FOR THE GROUP (A):%9.4f%9.4f%9.4f" % (
o[0], o[1], o[2])
print >> out, r3 + " T TENSOR "
print >> out, r3 + " T11:%9.4f T22:%9.4f " % (
t[0], t[1])
print >> out, r3 + " T33:%9.4f T12:%9.4f " % (
t[2], t[3])
print >> out, r3 + " T13:%9.4f T23:%9.4f " % (
t[4], t[5])
print >> out, r3 + " L TENSOR "
print >> out, r3 + " L11:%9.4f L22:%9.4f " % (
l[0], l[1])
print >> out, r3 + " L33:%9.4f L12:%9.4f " % (
l[2], l[3])
print >> out, r3 + " L13:%9.4f L23:%9.4f " % (
l[4], l[5])
print >> out, r3 + " S TENSOR "
print >> out, r3 + " S11:%9.4f S12:%9.4f S13:%9.4f " % (
s[0], s[1], s[2])
print >> out, r3 + " S21:%9.4f S22:%9.4f S23:%9.4f " % (
s[3], s[4], s[5])
print >> out, r3 + " S31:%9.4f S32:%9.4f S33:%9.4f " % (
s[6], s[7], s[8])
def format_call(self, return_directly, prefix):
s = ""
if (self.return_type != "void"):
if (return_directly):
s += "return "
else:
s += self.return_type + " result = "
s += self.function_name + "("
s += ", ".join([arg.name for arg in self.args])
s += ");"
result = []
indent = ""
for line in line_breaker(s, 70):
result.append(prefix + indent + line)
indent = " "
return result
def format_call(self, return_directly, prefix):
s = ""
if (self.return_type != "void"):
if (return_directly):
s += "return "
else:
s += self.return_type + " result = "
s += self.function_name+"("
s += ", ".join([arg.name for arg in self.args])
s += ");"
result = []
indent = ""
for line in line_breaker(s, 70):
result.append(prefix+indent+line)
indent = " "
return result
def show_anomalous_scatterer_groups(self, out = None):
if(out is None): out = sys.stdout
pr = "REMARK 3 "
print >>out,pr+"ANOMALOUS SCATTERER GROUPS DETAILS."
print >>out,pr+" NUMBER OF ANOMALOUS SCATTERER GROUPS : %-6d"%\
len(self.anomalous_scatterer_groups)
counter = 0
for group in self.anomalous_scatterer_groups:
counter += 1
print >>out,pr+" ANOMALOUS SCATTERER GROUP : %-6d"%counter
lines = line_breaker(group.selection_string, width=45)
for i_line, line in enumerate(lines):
if(i_line == 0):
print >> out, pr+" SELECTION: %s"%line
else:
print >> out, pr+" : %s"%line
print >>out,pr+" fp : %-15.4f"%group.f_prime
print >>out,pr+" fdp : %-15.4f"%group.f_double_prime
out.flush()
def show_anomalous_scatterer_groups(self, out = None):
if(out is None): out = sys.stdout
pr = "REMARK 3 "
print >>out,pr+"ANOMALOUS SCATTERER GROUPS DETAILS."
print >>out,pr+" NUMBER OF ANOMALOUS SCATTERER GROUPS : %-6d"%\
len(self.anomalous_scatterer_groups)
counter = 0
for group in self.anomalous_scatterer_groups:
counter += 1
print >>out,pr+" ANOMALOUS SCATTERER GROUP : %-6d"%counter
lines = line_breaker(group.selection_string, width=45)
for i_line, line in enumerate(lines):
if(i_line == 0):
print >> out, pr+" SELECTION: %s"%line
else:
print >> out, pr+" : %s"%line
print >>out,pr+" fp : %-15.4f"%group.f_prime
print >>out,pr+" fdp : %-15.4f"%group.f_double_prime
out.flush()
def show_torsion_ncs_groups(self, out = None):
if(out is None): out = sys.stdout
restraint_groups = self.ncs_manager.ncs_groups
torsion_counts=self.ncs_manager.get_number_of_restraints_per_group(
pdb_hierarchy=self.pdb_hierarchy)
sites_cart = self.pdb_hierarchy.atoms().extract_xyz()
self.ncs_manager.get_torsion_rmsd(sites_cart=sites_cart)
pr = "REMARK 3 "
print >>out,pr+"TORSION NCS DETAILS."
print >>out,pr+" NUMBER OF NCS GROUPS : %-6d"%len(restraint_groups)
for i_group, ncs_group in enumerate(restraint_groups):
count = 0
print >>out,pr+" NCS GROUP : %-6d"%(i_group+1)
selection_strings = ncs_group
for selection in selection_strings:
lines = line_breaker(selection, width=34)
for i_line, line in enumerate(lines):
if (i_line == 0):
print >> out, pr+" SELECTION : %s"%line
else:
print >> out, pr+" : %s"%line
count += torsion_counts[selection]
print >> out,pr+" RESTRAINED TORSIONS: %-d" % count
if self.ncs_manager.torsion_rmsd is not None:
print >> out,pr+" BELOW LIMIT RMSD : %-10.3f" % \
self.ncs_manager.torsion_rmsd
if self.ncs_manager.all_torsion_rmsd is not None:
print >> out,pr+" ALL RESTRAINT RMSD : %-10.3f" % \
self.ncs_manager.all_torsion_rmsd
if self.ncs_manager.histogram_under_limit is not None:
print >> out, pr + " Histogram of differences under limit:"
self.ncs_manager.histogram_under_limit.show(
f=out,
prefix=pr+" ",
format_cutoffs="%8.3f")
if self.ncs_manager.histogram_over_limit is not None:
print >> out, pr + " Histogram of differences over limit:"
self.ncs_manager.histogram_over_limit.show(
f=out,
prefix=pr+" ",
format_cutoffs="%8.3f")
def show_torsion_ncs_groups(self, out = None):
if(out is None): out = sys.stdout
restraint_groups = self.ncs_manager.ncs_groups
torsion_counts=self.ncs_manager.get_number_of_restraints_per_group(
pdb_hierarchy=self.pdb_hierarchy)
sites_cart = self.pdb_hierarchy.atoms().extract_xyz()
self.ncs_manager.get_torsion_rmsd(sites_cart=sites_cart)
pr = "REMARK 3 "
print >>out,pr+"TORSION NCS DETAILS."
print >>out,pr+" NUMBER OF NCS GROUPS : %-6d"%len(restraint_groups)
for i_group, ncs_group in enumerate(restraint_groups):
count = 0
print >>out,pr+" NCS GROUP : %-6d"%(i_group+1)
selection_strings = ncs_group
for selection in selection_strings:
lines = line_breaker(selection, width=34)
for i_line, line in enumerate(lines):
if (i_line == 0):
print >> out, pr+" SELECTION : %s"%line
else:
print >> out, pr+" : %s"%line
count += torsion_counts[selection]
print >> out,pr+" RESTRAINED TORSIONS: %-d" % count
if self.ncs_manager.torsion_rmsd is not None:
print >> out,pr+" BELOW LIMIT RMSD : %-10.3f" % \
self.ncs_manager.torsion_rmsd
if self.ncs_manager.all_torsion_rmsd is not None:
print >> out,pr+" ALL RESTRAINT RMSD : %-10.3f" % \
self.ncs_manager.all_torsion_rmsd
if self.ncs_manager.histogram_under_limit is not None:
print >> out, pr + " Histogram of differences under limit:"
self.ncs_manager.histogram_under_limit.show(
f=out,
prefix=pr+" ",
format_cutoffs="%8.3f")
if self.ncs_manager.histogram_over_limit is not None:
print >> out, pr + " Histogram of differences over limit:"
self.ncs_manager.histogram_over_limit.show(
f=out,
prefix=pr+" ",
format_cutoffs="%8.3f")
def remark_3_tls(tlsos, selection_strings, out = None):
if(out is None): out = sys.stdout
if (len(selection_strings) == 0):
assert len(tlsos) == 1
selection_strings = [None]
else:
assert len(tlsos) == len(selection_strings)
print >> out, "REMARK 3 TLS DETAILS."
print >> out, "REMARK 3 NUMBER OF TLS GROUPS: %-6d"%len(tlsos)
print >> out, "REMARK 3 ORIGIN: CENTER OF MASS"
r3 = "REMARK 3 "
counter = 0
for tlso, selection_string in zip(tlsos, selection_strings):
if(selection_string is None):
selection_string = "all"
counter += 1
t = tlso.t
l = tlso.l
s = tlso.s
o = tlso.origin
print >>out,r3+"TLS GROUP : %-6d"%(counter)
lines = line_breaker(selection_string, width=45)
for i_line, line in enumerate(lines):
if(i_line == 0):
print >> out, r3+" SELECTION: %s"%line
else:
print >> out, r3+" : %s"%line
print >>out,r3+" ORIGIN FOR THE GROUP (A):%9.4f%9.4f%9.4f"%(o[0],o[1],o[2])
print >>out,r3+" T TENSOR "
print >>out,r3+" T11:%9.4f T22:%9.4f "%(t[0], t[1])
print >>out,r3+" T33:%9.4f T12:%9.4f "%(t[2], t[3])
print >>out,r3+" T13:%9.4f T23:%9.4f "%(t[4], t[5])
print >>out,r3+" L TENSOR "
print >>out,r3+" L11:%9.4f L22:%9.4f "%(l[0], l[1])
print >>out,r3+" L33:%9.4f L12:%9.4f "%(l[2], l[3])
print >>out,r3+" L13:%9.4f L23:%9.4f "%(l[4], l[5])
print >>out,r3+" S TENSOR "
print >>out,r3+" S11:%9.4f S12:%9.4f S13:%9.4f "%(s[0],s[1],s[2])
print >>out,r3+" S21:%9.4f S22:%9.4f S23:%9.4f "%(s[3],s[4],s[5])
print >>out,r3+" S31:%9.4f S32:%9.4f S33:%9.4f "%(s[6],s[7],s[8])
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 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. *
********************************
""")
