def show_rigid_body_rotations_and_translations(out, prefix, frame,
euler_angle_convention,
rotations, translations):
assert euler_angle_convention in ["xyz", "zyz"]
euler_angles_as_matrix = getattr(scitbx.math.euler_angles,
euler_angle_convention + "_matrix")
print >> out, prefix_each_line_suffix(
prefix=prefix + frame,
lines_as_one_string=
" rotation (deg) translation (A) "
"\n"
" %s total xyz total "
% euler_angle_convention,
suffix=frame)
for i, r, t in zip(count(1), rotations, translations):
r = list(r)
r.reverse()
r_total = abs(
scitbx.math.r3_rotation_axis_and_angle_from_matrix(
r=euler_angles_as_matrix(*r)).angle(deg=True))
t_total = abs(matrix.col(t))
print >> out, (
prefix + frame +
" group %4d: %8.3f %8.3f %8.3f %7.2f %6.2f %6.2f %6.2f %6.2f " %
tuple([i] + r + [r_total] + list(t) + [t_total]) + frame).rstrip()
out.flush()
def show_rigid_body_rotations_and_translations(
out,
prefix,
frame,
euler_angle_convention,
rotations,
translations):
assert euler_angle_convention in ["xyz", "zyz"]
euler_angles_as_matrix = getattr(
scitbx.math.euler_angles, euler_angle_convention+"_matrix")
print >> out, prefix_each_line_suffix(
prefix=prefix+frame, lines_as_one_string=
" rotation (deg) translation (A) "
"\n"
" %s total xyz total "
% euler_angle_convention, suffix=frame)
for i,r,t in zip(count(1), rotations, translations):
r = list(r)
r.reverse()
r_total = abs(scitbx.math.r3_rotation_axis_and_angle_from_matrix(
r=euler_angles_as_matrix(*r)).angle(deg=True))
t_total = abs(matrix.col(t))
print >> out, (prefix + frame +
" group %4d: %8.3f %8.3f %8.3f %7.2f %6.2f %6.2f %6.2f %6.2f "
% tuple([i] + r + [r_total] + list(t) + [t_total])
+ frame).rstrip()
out.flush()
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. *
********************************
""")