def setUp(self): """Provide setup for the test on """ self.params = master_phil.extract() self.params.input.xtal_name = "FALZA-x0085" self.params.input.in_path = os.path.join( os.path.realpath("./test/resources"), self.params.input.xtal_name ) self.params.input.pdb = os.path.join(self.params.input.in_path, "refine.pdb") pdb_inp = iotbx.pdb.input(self.params.input.pdb) hier = pdb_inp.construct_hierarchy() self.sel_cache = hier.atom_selection_cache()
def setUp(self): """Provide setup for the test on """ self.params = master_phil.extract() self.params.input.xtal_name = "FALZA-x0085" self.params.input.in_path = os.path.join( os.path.realpath("./test/resources"), self.params.input.xtal_name) self.params.validate.input.base_mtz = os.path.join( self.params.input.in_path, "FALZA-x0085.free.mtz") self.params.input.mtz = os.path.join(self.params.input.in_path, "FALZA-x0085.free.mtz") self.params.input.pdb = os.path.join(self.params.input.in_path, "refine.pdb")
def setUp(self): """Provide the minimal number of parameters to test exhaustive search""" self.params = master_phil.extract() self.params.input.xtal_name = "FALZA-x0085" self.params.input.in_path = os.path.join( os.path.realpath("./test/resources"), self.params.input.xtal_name) self.params.validate.input.base_mtz = os.path.join( self.params.input.in_path, "FALZA-x0085.free.mtz") self.params.input.mtz = os.path.join(self.params.input.in_path, "FALZA-x0085.free.mtz") self.params.input.pdb = os.path.join(self.params.input.in_path, "refine.pdb") self.params.output.out_dir = os.path.realpath("./test/output") self.params.output.log_dir = os.path.realpath( os.path.join("./test/output", "logs")) self.params.exhaustive.options.step = 0.05
def setUp(self): self.params = master_phil.extract()
from exhaustive.utils.phil import master_phil from exhaustive.utils.phil import prepare_validate_phil from exhaustive.plotting.plot import plot_2d_occ_b_validation params = master_phil.extract() plot_2d_occ_b_validation( start_occ=0.05, end_occ=1, step=0.1, set_b=40.0, dataset_prefix='FALZA-x0085', out_dir="/dls/science/groups/i04-1/elliot-dev/Work/exhaustive_search/test/output/per_res", params=params, )