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)