def run():
from libtbx.utils import format_cpu_times
from mmtbx.rotamer import rotamer_eval
from mmtbx.rotamer import ramachandran_eval
initial_current_working_directory = os.getcwd()
rotamer_data_dir = rotamer_eval.find_rotarama_data_dir(optional=True)
if rotamer_data_dir is None:
print(' Rebuilding rotarama library skipped. Needs rotamer library.')
return
target_db = rotamer_eval.open_rotarama_dlite(
rotarama_data_dir=rotamer_data_dir)
# rebuild_pickle_files(data_dir=rotamer_data_dir,
# file_prefix="rota500-",
# target_db=target_db,
# amino_acids=rotamer_eval.aminoAcids)
rebuild_pickle_files(data_dir=rotamer_data_dir,
file_prefix="rota8000-",
target_db=target_db,
amino_acids=rotamer_eval.aminoAcids)
#
ramachandran_data_dir = rotamer_eval.find_rotarama_data_dir()
target_db = rotamer_eval.open_rotarama_dlite(
rotarama_data_dir=ramachandran_data_dir)
rebuild_pickle_files(data_dir=rotamer_data_dir,
file_prefix="rama8000-",
target_db=target_db,
amino_acids=ramachandran_eval.aminoAcids_8000)
# rebuild_pickle_files(data_dir=rotamer_data_dir,
# file_prefix="rama500-",
# target_db=target_db,
# amino_acids=ramachandran_eval.aminoAcids)
os.chdir(initial_current_working_directory)
print(format_cpu_times())
def run():
initial_current_working_directory = os.getcwd()
rotamer_data_dir = rotamer_eval.find_rotarama_data_dir(optional=True)
if rotamer_data_dir is None:
print ' Rebuilding rotarama library skipped. Needs rotamer library.'
return
target_db = rotamer_eval.open_rotarama_dlite(
rotarama_data_dir=rotamer_data_dir)
# rebuild_pickle_files(data_dir=rotamer_data_dir,
# file_prefix="rota500-",
# target_db=target_db,
# amino_acids=rotamer_eval.aminoAcids)
rebuild_pickle_files(data_dir=rotamer_data_dir,
file_prefix="rota8000-",
target_db=target_db,
amino_acids=rotamer_eval.aminoAcids)
#
ramachandran_data_dir = rotamer_eval.find_rotarama_data_dir()
target_db = rotamer_eval.open_rotarama_dlite(
rotarama_data_dir=ramachandran_data_dir)
rebuild_pickle_files(data_dir=rotamer_data_dir,
file_prefix="rama8000-",
target_db=target_db,
amino_acids=ramachandran_eval.aminoAcids_8000)
# rebuild_pickle_files(data_dir=rotamer_data_dir,
# file_prefix="rama500-",
# target_db=target_db,
# amino_acids=ramachandran_eval.aminoAcids)
os.chdir(initial_current_working_directory)
print format_cpu_times()
def __init__(self):
main_aaTables = RamachandranEval.aaTables
self.aaTables = {}
for aa,ndt_weakref in main_aaTables.items():
# convert existing weak references to strong references
self.aaTables[aa] = ndt_weakref()
rama_data_dir = find_rotarama_data_dir()
target_db = open_rotarama_dlite(rotarama_data_dir=rama_data_dir)
no_update = os.path.exists(os.path.join(rama_data_dir, "NO_UPDATE"))
for aa, aafile in aminoAcids_8000.items():
if (self.aaTables.get(aa) is not None): continue
data_file = "rama8000-"+aafile+".data"
pickle_file = "rama8000-"+aafile+".pickle"
pair_info = target_db.pair_info(
source_path=data_file,
target_path=pickle_file,
path_prefix=rama_data_dir)
if (((pair_info.needs_update) and (not no_update)) or not
os.path.exists(os.path.join(rama_data_dir, pickle_file))) :
raise Sorry(
"chem_data/rotarama_data/*.pickle files are missing or out of date.\n"
" Please run\n"
" mmtbx.rebuild_rotarama_cache\n"
" to resolve this problem.\n")
ndt = easy_pickle.load(file_name=os.path.join(
rama_data_dir, pair_info.target.path))
self.aaTables[aa] = ndt
main_aaTables[aa] = weakref.ref(ndt)
def __init__(self):
main_aaTables = RamachandranEval.aaTables
self.aaTables = {}
for aa, ndt_weakref in main_aaTables.items():
# convert existing weak references to strong references
self.aaTables[aa] = ndt_weakref()
rama_data_dir = find_rotarama_data_dir()
target_db = open_rotarama_dlite(rotarama_data_dir=rama_data_dir)
no_update = os.path.exists(os.path.join(rama_data_dir, "NO_UPDATE"))
for aa, aafile in aminoAcids_8000.items():
if (self.aaTables.get(aa) is not None): continue
data_file = "rama8000-" + aafile + ".data"
pickle_file = "rama8000-" + aafile + ".pickle"
pair_info = target_db.pair_info(source_path=data_file,
target_path=pickle_file,
path_prefix=rama_data_dir)
if (((pair_info.needs_update) and (not no_update))
or not os.path.exists(
os.path.join(rama_data_dir, pickle_file))):
raise Sorry(
"chem_data/rotarama_data/*.pickle files are missing or out of date.\n"
" Please run\n"
" mmtbx.rebuild_rotarama_cache\n"
" to resolve this problem.\n")
ndt = easy_pickle.load(
file_name=os.path.join(rama_data_dir, pair_info.target.path))
self.aaTables[aa] = ndt
main_aaTables[aa] = weakref.ref(ndt)