def run(args,
out=None,
driver_class=None,
require_single_conformer_starting_model=False):
import mmtbx.utils
if (out is None): out = sys.stdout
usage_string = """phenix.alternator model.pdb data.mtz [selection=...] [options]"""
cmdline = mmtbx.command_line.load_model_and_data(args=args,
master_phil=master_phil(),
process_pdb_file=True,
usage_string=usage_string,
out=out,
create_log_buffer=True)
params = cmdline.params
if (params.output.output_dir is not None):
os.chdir(params.output.output_dir)
dir_name = os.getcwd()
if (params.output.create_dir):
dir_name = create_run_directory(
"alt_confs",
default_directory_number=params.output.directory_number)
os.chdir(dir_name)
log = cmdline.start_log_file("%s.log" % params.output.prefix)
print >> log, "Output will be in %s" % dir_name
#working_phil = master_phil.format(python_object=params)
#make_sub_header("Final input parameters", out=log)
#master_phil.fetch_diff(source=working_phil).show(out=log)
if (driver_class is None):
driver_class = build_and_refine
multi_conf_selection = alternate_conformations.multi_conformer_selection(
pdb_hierarchy=cmdline.pdb_hierarchy)
if ((len(multi_conf_selection) != 0)
and require_single_conformer_starting_model):
atoms = cmdline.pdb_hierarchy.select(multi_conf_selection).atoms()
print >> log, "First %d atoms with alternate conformations:" % min(
10, len(atoms))
for atom in atoms[0:10]:
print >> log, atom.format_atom_record()
raise Sorry(
"Existing alternate conformations detected - this program " +
"can only be run on a single-conformer model at present.")
driver = driver_class(params=params.alt_confs,
fmodel=cmdline.fmodel,
pdb_hierarchy=cmdline.pdb_hierarchy,
processed_pdb_file=cmdline.processed_pdb_file,
geometry_restraints_manager=cmdline.geometry,
cif_objects=[o for (f, o) in cmdline.cif_objects],
cif_files=params.input.monomers.file_name,
debug=params.output.debug,
verbose=params.output.verbose,
out=log)
output_file_base = os.path.join(os.getcwd(), params.output.prefix)
driver.write_pdb_file(output_file_base + ".pdb",
remove_hd=params.output.remove_hydrogens)
driver.write_map_file(output_file_base + ".mtz")
# TODO final result object
return driver.pdb_hierarchy
def run (args, out=None, driver_class=None,
require_single_conformer_starting_model=False) :
import mmtbx.utils
if (out is None) : out = sys.stdout
usage_string = """phenix.alternator model.pdb data.mtz [selection=...] [options]"""
cmdline = mmtbx.command_line.load_model_and_data(
args=args,
master_phil=master_phil(),
process_pdb_file=True,
usage_string=usage_string,
out=out,
create_log_buffer=True)
params = cmdline.params
if (params.output.output_dir is not None) :
os.chdir(params.output.output_dir)
dir_name = os.getcwd()
if (params.output.create_dir) :
dir_name = create_run_directory("alt_confs",
default_directory_number=params.output.directory_number)
os.chdir(dir_name)
log = cmdline.start_log_file("%s.log" % params.output.prefix)
print >> log, "Output will be in %s" % dir_name
#working_phil = master_phil.format(python_object=params)
#make_sub_header("Final input parameters", out=log)
#master_phil.fetch_diff(source=working_phil).show(out=log)
if (driver_class is None) :
driver_class = build_and_refine
multi_conf_selection = alternate_conformations.multi_conformer_selection(
pdb_hierarchy=cmdline.pdb_hierarchy)
if ((len(multi_conf_selection) != 0) and
require_single_conformer_starting_model) :
atoms = cmdline.pdb_hierarchy.select(multi_conf_selection).atoms()
print >> log, "First %d atoms with alternate conformations:" % min(10,
len(atoms))
for atom in atoms[0:10] :
print >> log, atom.format_atom_record()
raise Sorry("Existing alternate conformations detected - this program "+
"can only be run on a single-conformer model at present.")
driver = driver_class(
params=params.alt_confs,
fmodel=cmdline.fmodel,
pdb_hierarchy=cmdline.pdb_hierarchy,
processed_pdb_file=cmdline.processed_pdb_file,
geometry_restraints_manager=cmdline.geometry,
cif_objects=[ o for (f,o) in cmdline.cif_objects ],
cif_files=params.input.monomers.file_name,
debug=params.output.debug,
verbose=params.output.verbose,
out=log)
output_file_base = os.path.join(os.getcwd(), params.output.prefix)
driver.write_pdb_file(output_file_base + ".pdb",
remove_hd=params.output.remove_hydrogens)
driver.write_map_file(output_file_base + ".mtz")
# TODO final result object
return driver.pdb_hierarchy
def exercise_dir_utils():
dirs = ["tst_utils_1", "tst_utils_2", "tst_utils_45"]
for dir_name in dirs :
if (os.path.isdir(dir_name)) : os.rmdir(dir_name)
dir_name = utils.create_run_directory("tst_utils")
assert (os.path.basename(dir_name) == "tst_utils_1")
dir_name = utils.create_run_directory("tst_utils")
assert (os.path.basename(dir_name) == "tst_utils_2")
dir_name = utils.create_run_directory("tst_utils", 45)
assert (os.path.basename(dir_name) == "tst_utils_45")
for dir_name in dirs :
os.rmdir(dir_name)
file_name = "/cctbx/%s/%s/XXXX.pdb" % (random.random(), random.random())
try :
utils.check_if_output_directory_exists(file_name)
except utils.Sorry :
pass
else :
raise Exception_expected
dir_name = os.getcwd()
utils.check_if_output_directory_exists(dir_name=dir_name)
dir_created = False
if (not os.path.exists("Dropbox")):
os.mkdir("Dropbox")
dir_created = True
dir_name = os.path.join(os.getcwd(), "Dropbox")
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
utils.check_if_output_directory_exists(dir_name=dir_name)
assert len(w) == 1
assert "Dropbox directory" in str(w[-1].message)
if (dir_created):
os.rmdir("Dropbox")
host_info = utils.host_and_user()
assert not utils.allow_delete_directory(host_info.homedir)
target_dir = os.path.join(host_info.homedir, "Downloads")
assert not utils.allow_delete_directory(target_dir)
target_dir = os.path.join(host_info.homedir, "data", "lysozyme")
assert utils.allow_delete_directory(target_dir)
def exercise_dir_utils () :
dirs = ["tst_utils_1", "tst_utils_2", "tst_utils_45"]
for dir_name in dirs :
if (os.path.isdir(dir_name)) : os.rmdir(dir_name)
dir_name = utils.create_run_directory("tst_utils")
assert (os.path.basename(dir_name) == "tst_utils_1")
dir_name = utils.create_run_directory("tst_utils")
assert (os.path.basename(dir_name) == "tst_utils_2")
dir_name = utils.create_run_directory("tst_utils", 45)
assert (os.path.basename(dir_name) == "tst_utils_45")
for dir_name in dirs :
os.rmdir(dir_name)
file_name = "/cctbx/%s/%s/XXXX.pdb" % (random.random(), random.random())
try :
utils.check_if_output_directory_exists(file_name)
except utils.Sorry :
pass
else :
raise Exception_expected
dir_name = os.getcwd()
utils.check_if_output_directory_exists(dir_name=dir_name)
dir_created = False
if (not os.path.exists("Dropbox")) :
os.mkdir("Dropbox")
dir_created = True
dir_name = os.path.join(os.getcwd(), "Dropbox")
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
utils.check_if_output_directory_exists(dir_name=dir_name)
assert len(w) == 1
assert "Dropbox directory" in str(w[-1].message)
if (dir_created) :
os.rmdir("Dropbox")
host_info = utils.host_and_user()
assert not utils.allow_delete_directory(host_info.homedir)
target_dir = os.path.join(host_info.homedir, "Downloads")
assert not utils.allow_delete_directory(target_dir)
target_dir = os.path.join(host_info.homedir, "data", "lysozyme")
assert utils.allow_delete_directory(target_dir)