def test_rs_mapper(dials_regression, tmpdir):
tmpdir.chdir()
result = procrunner.run_process([
'dials.rs_mapper',
os.path.join(dials_regression, "centroid_test_data", "datablock.json"),
'map_file="junk.ccp4"',
])
assert result['exitcode'] == 0
assert result['stderr'] == ''
assert os.path.exists('junk.ccp4')
# load results
from iotbx import ccp4_map
from scitbx.array_family import flex
m = ccp4_map.map_reader(file_name="junk.ccp4")
assert len(m.data) == 7189057
assert m.header_min == -1.0
assert flex.min(m.data) == -1.0
assert m.header_max == 2052.75
assert flex.max(m.data) == 2052.75
assert m.header_mean == pytest.approx(0.018606403842568398, abs=1e-6)
assert flex.mean(m.data) == pytest.approx(0.018606403842568398, abs=1e-6)
def test_rs_mapper(dials_data, tmpdir):
result = procrunner.run(
[
"dials.rs_mapper",
dials_data("centroid_test_data").join("datablock.json").strpath,
'map_file="junk.ccp4"',
],
working_directory=tmpdir.strpath,
)
assert not result.returncode and not result.stderr
assert tmpdir.join("junk.ccp4").check()
# load results
from iotbx import ccp4_map
from scitbx.array_family import flex
m = ccp4_map.map_reader(file_name=tmpdir.join("junk.ccp4").strpath)
assert len(m.data) == 7189057
assert m.header_min == 0.0
assert flex.min(m.data) == 0.0
assert m.header_max == 2052.75
assert flex.max(m.data) == 2052.75
assert m.header_mean == pytest.approx(0.018905939534306526, abs=1e-6)
assert flex.mean(m.data) == pytest.approx(0.018905939534306526, abs=1e-6)
def test1():
dials_regression = libtbx.env.find_in_repositories(
relative_path="dials_regression",
test=os.path.isdir)
data_dir = os.path.join(dials_regression, "centroid_test_data")
datablock_path = os.path.join(data_dir, "datablock.json")
# work in a temporary directory
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory(suffix="tst_rs_mapper")
os.chdir(tmp_dir)
cmd = 'dials.rs_mapper ' + datablock_path + ' map_file="junk.ccp4"'
result = easy_run.fully_buffered(command=cmd).raise_if_errors()
# load results
from iotbx import ccp4_map
from scitbx.array_family import flex
m = ccp4_map.map_reader(file_name="junk.ccp4")
assert len(m.data) == 7189057
assert approx_equal(m.header_min, -1.0)
assert approx_equal(flex.min(m.data), -1.0)
assert approx_equal(m.header_max, 2052.75)
assert approx_equal(flex.max(m.data), 2052.75)
assert approx_equal(m.header_mean, 0.018606403842568398)
assert approx_equal(flex.mean(m.data), 0.018606403842568398)
print "OK"
return
def test1():
dials_regression = libtbx.env.find_in_repositories(
relative_path="dials_regression", test=os.path.isdir)
data_dir = os.path.join(dials_regression, "centroid_test_data")
datablock_path = os.path.join(data_dir, "datablock.json")
# work in a temporary directory
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory(suffix="tst_rs_mapper")
os.chdir(tmp_dir)
cmd = 'dials.rs_mapper ' + datablock_path + ' map_file="junk.ccp4"'
result = easy_run.fully_buffered(command=cmd).raise_if_errors()
# load results
from iotbx import ccp4_map
from scitbx.array_family import flex
m = ccp4_map.map_reader(file_name="junk.ccp4")
assert len(m.data) == 7189057
assert approx_equal(m.header_min, -1.0)
assert approx_equal(flex.min(m.data), -1.0)
assert approx_equal(m.header_max, 2052.75)
assert approx_equal(flex.max(m.data), 2052.75)
assert approx_equal(m.header_mean, 0.018606403842568398)
assert approx_equal(flex.mean(m.data), 0.018606403842568398)
print "OK"
return
def test_masked(dials_data, tmp_path):
procrunner.run(
[
"dials.import",
dials_data("thaumatin_eiger_screen", pathlib=True) /
"Therm_6_1_master.h5",
],
working_directory=tmp_path,
)
result = procrunner.run(
["dials.rs_mapper", "imported.expt", "map_file=junk.ccp4"],
working_directory=tmp_path,
)
assert not result.returncode and not result.stderr
assert (tmp_path / "junk.ccp4").is_file()
# load results
m = ccp4_map.map_reader(file_name=str(tmp_path / "junk.ccp4"))
assert m.header_max == pytest.approx(6330.33350)
def ccp4_to_npy(map_name, save_name = None):
"""
Convert a ccp4 map to numpy format and optionally save to given path.
Inputs:
-------
map_name: path to .CCP4 map file
save_name: path to output numpy file, optional
Output:
-------
f_as_npy: converted CCP4 map volume as numpy array
"""
f = ccp4_map.map_reader(file_name = map_name)
shape = f.data.focus()
f_as_npy = np.array(f.data).reshape(shape)
if save_name is not None:
np.save(save_name, f_as_npy)
return f_as_npy
def test_masked(dials_data, tmpdir):
procrunner.run(
[
"dials.import",
dials_data("thaumatin_eiger_screen").join(
"Therm_6_1_master.h5").strpath,
],
working_directory=tmpdir.strpath,
)
result = procrunner.run(
["dials.rs_mapper", "imported.expt", "map_file=junk.ccp4"],
working_directory=tmpdir.strpath,
)
assert not result.returncode and not result.stderr
assert tmpdir.join("junk.ccp4").check()
# load results
from iotbx import ccp4_map
m = ccp4_map.map_reader(file_name=tmpdir.join("junk.ccp4").strpath)
assert m.header_max == pytest.approx(6330.33350)
def test_rs_mapper(dials_data, tmp_path):
result = procrunner.run(
[
"dials.rs_mapper",
dials_data("centroid_test_data", pathlib=True) /
"imported_experiments.json",
'map_file="junk.ccp4"',
],
working_directory=tmp_path,
)
assert not result.returncode and not result.stderr
assert (tmp_path / "junk.ccp4").is_file()
# load results
m = ccp4_map.map_reader(file_name=str(tmp_path / "junk.ccp4"))
assert len(m.data) == 7189057
assert m.header_min == 0.0
assert flex.min(m.data) == 0.0
assert m.header_max == 2052.75
assert flex.max(m.data) == 2052.75
assert m.header_mean == pytest.approx(0.018924040719866753, abs=1e-6)
assert flex.mean(m.data) == pytest.approx(0.01892407052218914, abs=1e-6)
def run(args, prefix="tst_00", validated=False):
user_input_pdb = ''
user_input_map = ''
# very simple parsing of model and map
for i, arg in enumerate(args):
if arg.endswith('.cif') or arg.endswith('.ent') or arg.endswith('.pdb'): # EMD-3981 has 6exv.ent instead of .pdb
user_input_pdb = arg
if arg.find('=')==-1:
args[i]='model=%s' % arg
elif arg.endswith('.ccp4') or arg.endswith('.map'):
user_input_map = arg
if arg.find('=')==-1:
args[i]='map=%s' % arg
argument_interpreter = libtbx.phil.command_line.argument_interpreter(
master_phil=master_phil,
home_scope="cryo_fit2",
)
user_input_pdb = clean_pdb_for_phenix(user_input_pdb)
pdbs = []
maps = []
phils = []
phil_args = []
for arg in args:
if os.path.isfile(arg) :
if iotbx.pdb.is_pdb_file(arg):
pdbs.append(arg)
elif arg.endswith('.ccp4') or arg.endswith('.map'): # not the smartest
maps.append(arg)
else:
try :
file_phil = phil.parse(file_name=arg)
except RuntimeError :
pass
else :
phils.append(file_phil)
else :
phil_args.append(arg)
phils.append(argument_interpreter.process(arg))
working_phil = master_phil.fetch(sources=phils)
working_phil.show()
working_params = working_phil.extract()
if (not validated):
validate_params(working_params)
# Compute a target map
from iotbx import ccp4_map
ccp4_map = ccp4_map.map_reader(user_input_map)
print('Map read from %s' %(user_input_map))
target_map_data = ccp4_map.map_data()
# initial atomic model that we want to fit to an EM-map
pdb_inp = iotbx.pdb.input(file_name=user_input_pdb)
model = mmtbx.model.manager(model_input = pdb_inp)
# Initialize states accumulator
states = mmtbx.utils.states(
pdb_hierarchy = model.get_hierarchy(),
xray_structure = model.get_xray_structure())
states.add(sites_cart = model.get_xray_structure().sites_cart())
#
params = sa.master_params().extract()
params.start_temperature=2000
params.final_temperature=0
params.cool_rate = 100
params.number_of_steps = 1000
params.update_grads_shift = 0.
params.interleave_minimization=False #Pavel will fix the error that occur when params.interleave_minimization=True
print('CC: %s' %(calculate_cc(map_data=target_map_data, model=model, resolution=3.)))
#STOP()
result = sa.run(
params = params,
xray_structure = model.get_xray_structure(),
restraints_manager = model.get_restraints_manager(),
target_map = target_map_data,
real_space = True,
wx = 100, # wx=5 broke helix conformation of tst_00_poor.pdb, wx=100 kept helix well
wc = 1,
states_collector = states)
states.write(file_name = "all_states.pdb")
model.set_xray_structure(result.xray_structure)
with open("refined.pdb", "w") as f:
f.write(model.model_as_pdb())