def exercise():
tst_build_simple.prepare_inputs("tst_altconfs_cmdline")
assert os.path.isfile("tst_altconfs_cmdline_start.pdb")
assert os.path.isfile("tst_altconfs_cmdline.mtz")
args = [
"tst_altconfs_cmdline_start.pdb",
"tst_altconfs_cmdline.mtz",
"selection='chain A and resseq 3'",
"output.file_name=tst_altconfs_cmdline_out.pdb",
"expected_occupancy=0.4",
"window_size=2",
"nproc=1",
"rsr_fofc_map_target=False",
"create_dir=False",
"prefix=tst_altconfs_cmdline_out",
"--verbose",
]
build_alternate_conformations.run(args=args, out=null_out())
pdb_out = file_reader.any_file("tst_altconfs_cmdline_out.pdb")
hierarchy = pdb_out.file_object.construct_hierarchy()
validate = rotalyze.rotalyze(pdb_hierarchy=hierarchy,
data_version="8000",
outliers_only=False)
rota_out = [(r.id_str(), r.rotamer_name) for r in validate.results]
#print rota_in
assert (((' A 3 AASN', 't0') in rota_out)
and ((' A 3 BASN', 'm-40') in rota_out))
def exercise():
tst_build_simple.prepare_inputs("tst_altconfs_cmdline")
assert os.path.isfile("tst_altconfs_cmdline_start.pdb")
assert os.path.isfile("tst_altconfs_cmdline.mtz")
args = [
"tst_altconfs_cmdline_start.pdb",
"tst_altconfs_cmdline.mtz",
"selection='chain A and resseq 3'",
"output.file_name=tst_altconfs_cmdline_out.pdb",
"expected_occupancy=0.4",
"window_size=2",
"nproc=1",
"rsr_fofc_map_target=False",
"create_dir=False",
"prefix=tst_altconfs_cmdline_out",
"--verbose",
]
build_alternate_conformations.run(args=args, out=null_out())
pdb_out = file_reader.any_file("tst_altconfs_cmdline_out.pdb")
hierarchy = pdb_out.file_object.construct_hierarchy()
validate = rotalyze.rotalyze(pdb_hierarchy=hierarchy, data_version="8000", outliers_only=False)
rota_out = [(r.id_str(), r.rotamer_name) for r in validate.results]
# print rota_in
assert ((" A 3 AASN", "t0") in rota_out) and ((" A 3 BASN", "m-40") in rota_out)
def exercise_assembly (verbose=False) :
# This test subclasses the main class in sliding_window to substitute
# fake annealing results with predefined coordinate offsets. The results
# will then be processed and assembled as they were actual results.
from mmtbx.command_line import build_alternate_conformations
from mmtbx.building.alternate_conformations import sliding_window
from mmtbx.building import alternate_conformations as alt_confs
from mmtbx import building
from scitbx.array_family import flex
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/CypA_refine_3.pdb",
test=os.path.isfile)
mtz_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/3k0n.mtz",
test=os.path.isfile)
assert (not None in [pdb_file, mtz_file])
class fragment_driver (sliding_window.fragment_refinement_driver) :
def refine_window (O, window) :
processed_pdb_file = O.get_processed_pdb_file()
assert (processed_pdb_file is not None)
hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_atoms = hierarchy.atoms()
sites_cart = pdb_atoms.extract_xyz()
dxyz = [ None ] * 3
dxyz[0] = flex.vec3_double(pdb_atoms.size(), (1.0,0.2,0.3))
dxyz[1] = flex.vec3_double(pdb_atoms.size(), (-1.0,-0.1,0.0))
dxyz[2] = dxyz[1]
trials = []
if (window.residue_id_str in [" A PHE 113 ", " A SER 110 "]) :
for i in range(3) :
trials.append(alt_confs.trial_result(
sites_cart=(sites_cart + dxyz[i]).select(window.selection),
min_fofc=4.0,
mean_fofc=4.5,
rmsd=1.2,
max_dev=1.3,
cc=0.99))
elif (window.residue_id_str in [" A ASN 108 "]) :
trials.append(alt_confs.trial_result(
sites_cart=(sites_cart + dxyz[0]).select(window.selection),
min_fofc=4.0,
mean_fofc=4.5,
rmsd=1.2,
max_dev=1.3,
cc=0.99))
e = sliding_window.ensemble(window=window, sites_trials=trials)
n_keep = e.filter_trials(
sites_cart=O.sites_cart,
min_rmsd=O.params.min_rmsd,
min_dev=O.min_required_deviation)
if (n_keep > 0) :
return e
return None
class program_driver (build_alternate_conformations.build_and_refine) :
def refine (O, title=None) : pass
def rejoin (O) : return False
def build_conformers (O, stop_if_none=None) :
driver = fragment_driver(
fmodel=O.fmodel,
pdb_hierarchy=O.pdb_hierarchy,
processed_pdb_file=O.processed_pdb_file,
params=O.params.sliding_window,
mp_params=O.params,
out=O.out)
O.pdb_hierarchy = driver.assemble()
O.processed_pdb_file = None
args = [ pdb_file, mtz_file, "nproc=2", "high_resolution=2.0",
"create_dir=False", "output.prefix=tst_sliding_window" ]
out = null_out()
if (verbose) :
out = sys.stdout
hierarchy = build_alternate_conformations.run(args=args,
driver_class=program_driver,
out=out)
for residue_group in building.iter_residue_groups(hierarchy) :
n_atom_groups = len(residue_group.atom_groups())
if (n_atom_groups == 3) :
assert (106 <= residue_group.resseq_as_int() <= 115)
else :
assert (n_atom_groups == 1)
def exercise_assembly(verbose=False):
# This test subclasses the main class in sliding_window to substitute
# fake annealing results with predefined coordinate offsets. The results
# will then be processed and assembled as they were actual results.
from mmtbx.command_line import build_alternate_conformations
from mmtbx.building.alternate_conformations import sliding_window
from mmtbx.building import alternate_conformations as alt_confs
from mmtbx import building
from scitbx.array_family import flex
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/CypA_refine_3.pdb",
test=os.path.isfile)
mtz_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/reflection_files/3k0n.mtz",
test=os.path.isfile)
assert (not None in [pdb_file, mtz_file])
class fragment_driver(sliding_window.fragment_refinement_driver):
def refine_window(O, window):
processed_pdb_file = O.get_processed_pdb_file()
assert (processed_pdb_file is not None)
hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_atoms = hierarchy.atoms()
sites_cart = pdb_atoms.extract_xyz()
dxyz = [None] * 3
dxyz[0] = flex.vec3_double(pdb_atoms.size(), (1.0, 0.2, 0.3))
dxyz[1] = flex.vec3_double(pdb_atoms.size(), (-1.0, -0.1, 0.0))
dxyz[2] = dxyz[1]
trials = []
if (window.residue_id_str in [" A PHE 113 ", " A SER 110 "]):
for i in range(3):
trials.append(
alt_confs.trial_result(
sites_cart=(sites_cart + dxyz[i]).select(
window.selection),
min_fofc=4.0,
mean_fofc=4.5,
rmsd=1.2,
max_dev=1.3,
cc=0.99))
elif (window.residue_id_str in [" A ASN 108 "]):
trials.append(
alt_confs.trial_result(sites_cart=(sites_cart +
dxyz[0]).select(
window.selection),
min_fofc=4.0,
mean_fofc=4.5,
rmsd=1.2,
max_dev=1.3,
cc=0.99))
e = sliding_window.ensemble(window=window, sites_trials=trials)
n_keep = e.filter_trials(sites_cart=O.sites_cart,
min_rmsd=O.params.min_rmsd,
min_dev=O.min_required_deviation)
if (n_keep > 0):
return e
return None
class program_driver(build_alternate_conformations.build_and_refine):
def refine(O, title=None):
pass
def rejoin(O):
return False
def build_conformers(O, stop_if_none=None):
driver = fragment_driver(fmodel=O.fmodel,
pdb_hierarchy=O.pdb_hierarchy,
processed_pdb_file=O.processed_pdb_file,
params=O.params.sliding_window,
mp_params=O.params,
out=O.out)
O.pdb_hierarchy = driver.assemble()
O.processed_pdb_file = None
args = [
pdb_file, mtz_file, "nproc=2", "high_resolution=2.0",
"create_dir=False", "output.prefix=tst_sliding_window"
]
out = null_out()
if (verbose):
out = sys.stdout
hierarchy = build_alternate_conformations.run(args=args,
driver_class=program_driver,
out=out)
for residue_group in building.iter_residue_groups(hierarchy):
n_atom_groups = len(residue_group.atom_groups())
if (n_atom_groups == 3):
assert (106 <= residue_group.resseq_as_int() <= 115)
else:
assert (n_atom_groups == 1)
