def exercise_end_of_line(exe_name, verbose):
lines = """\
a
bc
def
ghij
klmno
""".splitlines()
open("unix.txt", "wb").write("\n".join(lines)+"\n")
open("dos.txt", "wb").write("\r\n".join(lines)+"\r\n")
open("dos2.txt", "wb").write("\r\r\n".join(lines)+"\r\n")
open("mac.txt", "wb").write("\r".join(lines)+"\r")
from libtbx import easy_run
from libtbx.utils import remove_files
import os
op = os.path
expected_outputs = [
"a \nbc \ndef \nghij\nklmn\n",
"a \nbc \ndef \nghij\nklmn\n",
"a\r \nbc\r \ndef\r\nghij\nklmn\n",
"a\rbc\n"]
for vers,expected in zip(["unix", "dos", "dos2", "mac"], expected_outputs):
remove_files(paths=["read_lines_out"])
cmd = "%s < %s.txt > read_lines_out" % (op.join(".", exe_name), vers)
if (verbose): print cmd
easy_run.fully_buffered(command=cmd).raise_if_errors_or_output()
assert op.isfile("read_lines_out")
result = open("read_lines_out", "rb").read()
assert result == expected.replace("\n", os.linesep)
def run_and_check(cmd, pdbs_file, expected_out):
abs_paths = []
for rel_path in open(op.join(dd, pdbs_file)).read().splitlines():
abs_paths.append(op.normpath(op.join(dd, rel_path)))
list_of_pdbs = "list_of_pdbs_%d" % run_serial.next()
print >> open(list_of_pdbs, "w"), "\n".join(abs_paths)
cmd = cmd % list_of_pdbs
if (valgrind):
cmd = "valgrind " + cmd
print cmd
remove_files("out")
if (not valgrind):
buffers = easy_run.fully_buffered(command=cmd).raise_if_errors()
if (expected_out is None):
return buffers.stdout_lines
else:
easy_run.call(command=cmd)
if (expected_out is None):
return None
filtered_lines = []
for line in open("out").read().splitlines():
sw = line.startswith
if (sw("pole") or sw("members") or sw("min: ") or sw("max: ")):
filtered_lines.append(line)
assert not show_diff("\n".join(filtered_lines) + "\n", expected_out)
print "OK"
def check_adp_set_b_iso(
cmd, xrsp_init, output, selection, selection_str, verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name = output)
assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance)
assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance)
assert approx_equal(xrsp.use_u_aniso,xrsp_init.use_u_aniso,tolerance)
assert approx_equal(xrsp.u_iso_not_used, xrsp_init.u_iso_not_used,tolerance)
assert approx_equal(xrsp.u_cart_not_used,xrsp_init.u_cart_not_used,tolerance)
if(selection_str is None):
assert not_approx_equal(xrsp.u_iso_used, xrsp_init.u_iso_used,tolerance)
for ucart in xrsp.u_cart:
b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart))
if b_iso > 0: assert approx_equal(b_iso, 10, 0.005)
else: assert approx_equal(b_iso, -78.956, 0.005)
else:
arg1 = xrsp.u_iso_used.select(selection.select(xrsp.use_u_iso))
arg2 = xrsp_init.u_iso_used.select(selection.select(xrsp_init.use_u_iso))
if(arg1.size() > 0): assert not_approx_equal(arg1, arg2,tolerance)
for ucart in xrsp.u_cart:
b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart))
if b_iso > 0: assert approx_equal(b_iso, 10, 0.005)
else: assert approx_equal(b_iso, -78.956, 0.005)
def check_keep_selection(cmd,
xrsp_init,
output,
selection,
selection_str,
keep_selection_str,
verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
keep_selection = xrsp_init.selection(selection_strings=keep_selection_str)
assert approx_equal(xrsp.sites_cart,
xrsp_init.sites_cart.select(keep_selection), tolerance)
assert approx_equal(xrsp.occ, xrsp_init.occ.select(keep_selection),
tolerance)
assert approx_equal(xrsp.u_iso, xrsp_init.u_iso.select(keep_selection),
tolerance)
assert approx_equal(xrsp.u_cart, xrsp_init.u_cart.select(keep_selection),
tolerance)
sct1 = xrsp_init.xray_structure.scatterers().extract_scattering_types()
assert sct1.count("C") > 0 and sct1.size() > sct1.count("C")
sct2 = xrsp.xray_structure.scatterers().extract_scattering_types()
assert sct2.count("C") == sct2.size()
assert sct1.size() > keep_selection.count(True)
assert sct1.size() > sct2.size()
def run_and_check(cmd, pdbs_file, expected_out):
abs_paths = []
for rel_path in open(op.join(dd, pdbs_file)).read().splitlines():
abs_paths.append(op.normpath(op.join(dd, rel_path)))
list_of_pdbs = "list_of_pdbs_%d" % run_serial.next()
print >> open(list_of_pdbs, "w"), "\n".join(abs_paths)
cmd = cmd % list_of_pdbs
if (valgrind):
cmd = "valgrind " + cmd
print cmd
remove_files("out")
if (not valgrind):
buffers = easy_run.fully_buffered(command=cmd).raise_if_errors()
if (expected_out is None):
return buffers.stdout_lines
else:
easy_run.call(command=cmd)
if (expected_out is None):
return None
filtered_lines = []
for line in open("out").read().splitlines():
sw = line.startswith
if (sw("pole") or sw("members") or sw("min: ") or sw("max: ")):
filtered_lines.append(line)
assert not show_diff("\n".join(filtered_lines)+"\n", expected_out)
print "OK"
def check_adp_set_b_iso(cmd,
xrsp_init,
output,
selection,
selection_str,
verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
assert approx_equal(xrsp.occ, xrsp_init.occ, tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart, tolerance)
assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso, tolerance)
assert approx_equal(xrsp.use_u_aniso, xrsp_init.use_u_aniso, tolerance)
assert approx_equal(xrsp.u_iso_not_used, xrsp_init.u_iso_not_used,
tolerance)
assert approx_equal(xrsp.u_cart_not_used, xrsp_init.u_cart_not_used,
tolerance)
if (selection_str is None):
assert not_approx_equal(xrsp.u_iso_used, xrsp_init.u_iso_used,
tolerance)
for ucart in xrsp.u_cart:
b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart))
if b_iso > 0: assert approx_equal(b_iso, 10, 0.005)
else: assert approx_equal(b_iso, -78.956, 0.005)
else:
arg1 = xrsp.u_iso_used.select(selection.select(xrsp.use_u_iso))
arg2 = xrsp_init.u_iso_used.select(
selection.select(xrsp_init.use_u_iso))
if (arg1.size() > 0): assert not_approx_equal(arg1, arg2, tolerance)
for ucart in xrsp.u_cart:
b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart))
if b_iso > 0: assert approx_equal(b_iso, 10, 0.005)
else: assert approx_equal(b_iso, -78.956, 0.005)
def exercise_end_of_line(exe_name, verbose):
lines = """\
a
bc
def
ghij
klmno
""".splitlines()
open("unix.txt", "wb").write("\n".join(lines) + "\n")
open("dos.txt", "wb").write("\r\n".join(lines) + "\r\n")
open("dos2.txt", "wb").write("\r\r\n".join(lines) + "\r\n")
open("mac.txt", "wb").write("\r".join(lines) + "\r")
from libtbx import easy_run
from libtbx.utils import remove_files
import os
op = os.path
expected_outputs = [
"a \nbc \ndef \nghij\nklmn\n", "a \nbc \ndef \nghij\nklmn\n",
"a\r \nbc\r \ndef\r\nghij\nklmn\n", "a\rbc\n"
]
for vers, expected in zip(["unix", "dos", "dos2", "mac"],
expected_outputs):
remove_files(paths=["read_lines_out"])
cmd = "%s < %s.txt > read_lines_out" % (op.join(".", exe_name), vers)
if (verbose): print cmd
easy_run.fully_buffered(command=cmd).raise_if_errors_or_output()
assert op.isfile("read_lines_out")
result = open("read_lines_out", "rb").read()
assert result == expected.replace("\n", os.linesep)
def check_all_none(cmd, xrsp_init, output, verbose, tolerance=1.e-3): remove_files(output) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance) assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance) assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance) assert approx_equal(xrsp.use_u_aniso, xrsp_init.use_u_aniso,tolerance) assert approx_equal(xrsp.u_iso, xrsp_init.u_iso,tolerance) assert approx_equal(xrsp.u_cart, xrsp_init.u_cart,tolerance)
def test_quiet(file_name, verbose):
output_file_name = "shifted.pdb"
remove_files("log")
remove_files(output_file_name)
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" output.file_name=%s shake=0.1 --quiet > log' % (
file_name, output_file_name)
run_command(command=cmd, verbose=verbose)
lines = open("log", "r").readlines()
assert len(lines) == 0
def check_all_none(cmd, xrsp_init, output, verbose, tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
assert approx_equal(xrsp.occ, xrsp_init.occ, tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart, tolerance)
assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso, tolerance)
assert approx_equal(xrsp.use_u_aniso, xrsp_init.use_u_aniso, tolerance)
assert approx_equal(xrsp.u_iso, xrsp_init.u_iso, tolerance)
assert approx_equal(xrsp.u_cart, xrsp_init.u_cart, tolerance)
def test_quiet(file_name, verbose):
output_file_name = "shifted.pdb"
remove_files("log")
remove_files(output_file_name)
assert file_name.find('"') < 0
cmd= 'phenix.pdbtools "%s" output.file_name=%s shake=0.1 --quiet > log'%(
file_name, output_file_name)
run_command(command=cmd, verbose=verbose)
lines = open("log","r").readlines()
assert len(lines) == 0
def exercise_show_number_of_removed(pdb_dir, verbose):
file_name = os.path.join(pdb_dir, "phe_h.pdb")
log = "exercise_show_number_of_removed.log"
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" remove="element H" > %s' % (file_name, log)
remove_files(log)
run_command(command=cmd, verbose=verbose)
assert os.path.isfile(log)
n_found = 0
for line in open(log).read().splitlines():
if (line == "Atoms to be kept: 13 of 24"):
n_found += 1
assert n_found == 1
def exercise_show_number_of_removed(pdb_dir, verbose):
file_name = os.path.join(pdb_dir, "phe_h.pdb")
log = "exercise_show_number_of_removed.log"
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" remove="element H" > %s' % (file_name, log)
remove_files(log)
run_command(command=cmd, verbose=verbose)
assert os.path.isfile(log)
n_found = 0
for line in open(log).read().splitlines():
if (line == "Atoms to be kept: 13 of 24"):
n_found += 1
assert n_found == 1
def check_adp_to_iso(
cmd, xrsp_init, output, selection, selection_str, verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name = output)
assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance)
assert not_approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance)
assert not_approx_equal(xrsp.use_u_aniso,xrsp_init.use_u_aniso,tolerance)
assert xrsp.u_iso_not_used.size() == 0
assert xrsp_init.u_iso_not_used.size() > 0
assert xrsp.u_cart_used.size() == 0
assert xrsp_init.u_cart_used.size() > 0
def check_sites_rt(
cmd, xrsp_init, output, selection, selection_str, verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name = output)
assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance)
assert approx_equal(xrsp.u_iso, xrsp_init.u_iso,tolerance)
assert approx_equal(xrsp.u_cart, xrsp_init.u_cart,tolerance)
if(selection_str is None):
diff = xrsp.sites_cart - xrsp_init.sites_cart
assert math.sqrt(flex.mean(diff.dot())) > 1.0
else:
diff = xrsp.sites_cart - xrsp_init.sites_cart
assert math.sqrt(flex.mean(diff.select(selection).dot())) > 1.0
assert approx_equal(
math.sqrt(flex.mean(diff.select(~selection).dot())),0.,tolerance)
def check_adp_to_iso(cmd,
xrsp_init,
output,
selection,
selection_str,
verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
assert approx_equal(xrsp.occ, xrsp_init.occ, tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart, tolerance)
assert not_approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso, tolerance)
assert not_approx_equal(xrsp.use_u_aniso, xrsp_init.use_u_aniso, tolerance)
assert xrsp.u_iso_not_used.size() == 0
assert xrsp_init.u_iso_not_used.size() > 0
assert xrsp.u_cart_used.size() == 0
assert xrsp_init.u_cart_used.size() > 0
def check_occ_randomize(
cmd, xrsp_init, output, selection,selection_str, verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name = output)
assert approx_equal(xrsp.sites_cart,xrsp_init.sites_cart,tolerance)
assert approx_equal(xrsp.u_iso, xrsp_init.u_iso,tolerance)
assert approx_equal(xrsp.u_cart, xrsp_init.u_cart,tolerance)
if(selection_str is None):
diff = flex.abs(xrsp.occ - xrsp_init.occ)
assert flex.mean(diff) > 0.0
assert flex.max(diff) > 0.0
else:
diff = flex.abs(xrsp.occ - xrsp_init.occ)
assert flex.mean(diff) > 0.0
assert flex.max(diff) > 0.0
assert approx_equal(flex.mean(diff.select(~selection)),0.,tolerance)
def check_keep_selection(
cmd, xrsp_init, output, selection, selection_str,
keep_selection_str, verbose, tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name = output)
keep_selection = xrsp_init.selection(selection_strings = keep_selection_str)
assert approx_equal(xrsp.sites_cart,
xrsp_init.sites_cart.select(keep_selection),tolerance)
assert approx_equal(xrsp.occ, xrsp_init.occ.select(keep_selection),tolerance)
assert approx_equal(
xrsp.u_iso, xrsp_init.u_iso.select(keep_selection),tolerance)
assert approx_equal(
xrsp.u_cart, xrsp_init.u_cart.select(keep_selection),tolerance)
sct1 = xrsp_init.xray_structure.scatterers().extract_scattering_types()
assert sct1.count("C") > 0 and sct1.size() > sct1.count("C")
sct2 = xrsp.xray_structure.scatterers().extract_scattering_types()
assert sct2.count("C") == sct2.size()
assert sct1.size() > keep_selection.count(True)
assert sct1.size() > sct2.size()
def check_sites_rt(cmd,
xrsp_init,
output,
selection,
selection_str,
verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
assert approx_equal(xrsp.occ, xrsp_init.occ, tolerance)
assert approx_equal(xrsp.u_iso, xrsp_init.u_iso, tolerance)
assert approx_equal(xrsp.u_cart, xrsp_init.u_cart, tolerance)
if (selection_str is None):
diff = xrsp.sites_cart - xrsp_init.sites_cart
assert math.sqrt(flex.mean(diff.dot())) > 1.0
else:
diff = xrsp.sites_cart - xrsp_init.sites_cart
assert math.sqrt(flex.mean(diff.select(selection).dot())) > 1.0
assert approx_equal(
math.sqrt(flex.mean(diff.select(~selection).dot())), 0., tolerance)
def check_occ_randomize(cmd,
xrsp_init,
output,
selection,
selection_str,
verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart, tolerance)
assert approx_equal(xrsp.u_iso, xrsp_init.u_iso, tolerance)
assert approx_equal(xrsp.u_cart, xrsp_init.u_cart, tolerance)
if (selection_str is None):
diff = flex.abs(xrsp.occ - xrsp_init.occ)
assert flex.mean(diff) > 0.0
assert flex.max(diff) > 0.0
else:
diff = flex.abs(xrsp.occ - xrsp_init.occ)
assert flex.mean(diff) > 0.0
assert flex.max(diff) > 0.0
assert approx_equal(flex.mean(diff.select(~selection)), 0., tolerance)
def build(O,
link,
file_name_cpp,
obj_name=None,
exe_name=None,
pch_name=None,
disable_warnings=False,
show_command=False,
Error=RuntimeError):
assert [obj_name, exe_name, pch_name].count(None) >= 2
if (link):
out_name = exe_name
out_suffix = O.exe_suffix
elif (pch_name is None):
out_name = obj_name
out_suffix = O.obj_suffix
else:
assert O.pch_suffix is not None
out_name = pch_name + O.pch_suffix
out_suffix = None
if (out_name is None):
assert file_name_cpp.endswith(".cpp")
out_name = file_name_cpp[:-4] + out_suffix
from libtbx.utils import remove_files
remove_files(out_name)
cmd = O.assemble_command(
link=link,
disable_warnings=disable_warnings,
file_names=[file_name_cpp],
out_name=out_name)
if (show_command):
print cmd
from libtbx import easy_run
buffers = easy_run.fully_buffered(command=cmd)
if (O.compiler != "cl" or buffers.stderr_lines != [file_name_cpp]):
buffers.raise_if_errors(Error=Error)
return out_name
def build(O,
link,
file_name_cpp,
obj_name=None,
exe_name=None,
pch_name=None,
disable_warnings=False,
show_command=False,
Error=RuntimeError):
assert [obj_name, exe_name, pch_name].count(None) >= 2
if (link):
out_name = exe_name
out_suffix = O.exe_suffix
elif (pch_name is None):
out_name = obj_name
out_suffix = O.obj_suffix
else:
assert O.pch_suffix is not None
out_name = pch_name + O.pch_suffix
out_suffix = None
if (out_name is None):
assert file_name_cpp.endswith(".cpp")
out_name = file_name_cpp[:-4] + out_suffix
from libtbx.utils import remove_files
remove_files(out_name)
cmd = O.assemble_command(link=link,
disable_warnings=disable_warnings,
file_names=[file_name_cpp],
out_name=out_name)
if (show_command):
print cmd
from libtbx import easy_run
buffers = easy_run.fully_buffered(command=cmd)
if (O.compiler != "cl" or buffers.stderr_lines != [file_name_cpp]):
buffers.raise_if_errors(Error=Error)
return out_name
def run(args):
assert len(args) == 0
tmpdir = "scitbx_rigid_body_essence"
if (not os.path.isdir(tmpdir)):
os.mkdir(tmpdir)
os.chdir(tmpdir)
scitbx_dist = libtbx.env.dist_path(module_name="scitbx")
def cp(file_name, target="."):
copy_file(os.path.join(scitbx_dist, file_name), target)
cp("matrix/__init__.py", "scitbx_matrix.py")
cp("rigid_body/essence/featherstone.py")
cp("rigid_body/essence/spatial_lib.py")
cp("rigid_body/essence/joint_lib.py")
cp("rigid_body/essence/body_lib.py")
cp("rigid_body/essence/tst_basic.py")
open("README.txt", "w").write(__doc__)
os.chdir("..")
if (os.name == "nt" or not libtbx.env.has_module(name="docutils")):
return
remove_files("scitbx_rigid_body_essence.tgz")
remove_files("scitbx_rigid_body_essence.zip")
easy_run.fully_buffered(
command="tar zcf scitbx_rigid_body_essence.tgz scitbx_rigid_body_essence")\
.raise_if_errors_or_output()
assert os.path.isfile("scitbx_rigid_body_essence.tgz")
easy_run.fully_buffered(
command="zip -r scitbx_rigid_body_essence.zip scitbx_rigid_body_essence")\
.raise_if_errors()
assert os.path.isfile("scitbx_rigid_body_essence.zip")
os.chdir("scitbx_rigid_body_essence")
easy_run.fully_buffered(
command="docutils.rst2html README.txt > README.html")\
.raise_if_errors()
remove_files("README.txt")
print >> open(".htaccess", "w").write("""\
Options Indexes
""")
def run(args):
assert len(args) == 0
tmpdir = "scitbx_rigid_body_essence"
if (not os.path.isdir(tmpdir)):
os.mkdir(tmpdir)
os.chdir(tmpdir)
scitbx_dist = libtbx.env.dist_path(module_name="scitbx")
def cp(file_name, target="."):
copy_file(os.path.join(scitbx_dist, file_name), target)
cp("matrix/__init__.py", "scitbx_matrix.py")
cp("rigid_body/essence/featherstone.py")
cp("rigid_body/essence/spatial_lib.py")
cp("rigid_body/essence/joint_lib.py")
cp("rigid_body/essence/body_lib.py")
cp("rigid_body/essence/tst_basic.py")
open("README.txt", "w").write(__doc__)
os.chdir("..")
if ( os.name == "nt"
or not libtbx.env.has_module(name="docutils")):
return
remove_files("scitbx_rigid_body_essence.tgz")
remove_files("scitbx_rigid_body_essence.zip")
easy_run.fully_buffered(
command="tar zcf scitbx_rigid_body_essence.tgz scitbx_rigid_body_essence")\
.raise_if_errors_or_output()
assert os.path.isfile("scitbx_rigid_body_essence.tgz")
easy_run.fully_buffered(
command="zip -r scitbx_rigid_body_essence.zip scitbx_rigid_body_essence")\
.raise_if_errors()
assert os.path.isfile("scitbx_rigid_body_essence.zip")
os.chdir("scitbx_rigid_body_essence")
easy_run.fully_buffered(
command="docutils.rst2html README.txt > README.html")\
.raise_if_errors()
remove_files("README.txt")
print >> open(".htaccess", "w").write("""\
Options Indexes
""")