def get_pdb_inputs(pdb_str): raw_records = flex.std_string(pdb_str.splitlines()) processed_pdb_file = rs.get_processed_pdb_object(raw_records=raw_records, rama_potential=None, log=None) xrs = processed_pdb_file.xray_structure(show_summary=False) geometry_restraints_manager = rs.get_geometry_restraints_manager( processed_pdb_file=processed_pdb_file, xray_structure=xrs ) pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy return group_args(ph=pdb_hierarchy, grm=geometry_restraints_manager, xrs=xrs)
def get_pdb_inputs(pdb_str): raw_records = flex.std_string(pdb_str.splitlines()) processed_pdb_file = rs.get_processed_pdb_object(raw_records=raw_records, rama_potential=None, log=None) xrs = processed_pdb_file.xray_structure(show_summary=False) geometry_restraints_manager = rs.get_geometry_restraints_manager( processed_pdb_file=processed_pdb_file, xray_structure=xrs) pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy return group_args(ph=pdb_hierarchy, grm=geometry_restraints_manager, xrs=xrs)
rama_potential=None, log = None) xrs = processed_pdb_file.xray_structure(show_summary = False) geometry_restraints_manager = rs.get_geometry_restraints_manager( processed_pdb_file = processed_pdb_file, xray_structure = xrs) pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy return group_args( ph = pdb_hierarchy, grm = geometry_restraints_manager, xrs = xrs) pi = get_pdb_inputs(pdb_str=pdb_str_1) restraints_manager = pi.grm import code; code.interact(local=locals()) fmodel = mmtbx.f_model.manager( f_obs = f_obs, r_free_flags = r_free_flags, xray_structure = xrs_poor) grad_calc = cartesian_dynamics.gradients_calculator_real_space_simple( restraints_manager = self.restraints_manager.geometry, target_map = self.target_map, unit_cell = self.xray_structure.unit_cell(), sites_cart = self.xray_structure.sites_cart(), wx = self.wx, wc = self.wc, update_gradient_threshold = 0) processed_pdb_file = rs.get_processed_pdb_object(raw_records=raw_records, rama_potential=None, log = None) geometry = processed_pdb_file.geometry_restraints_manager( show_energies = False, plain_pairs_radius = 5, assume_hydrogens_all_missing = not has_hd)
processed_pdb_file=processed_pdb_file, xray_structure=xrs) pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy return group_args(ph=pdb_hierarchy, grm=geometry_restraints_manager, xrs=xrs) pi = get_pdb_inputs(pdb_str=pdb_str_1) restraints_manager = pi.grm import code code.interact(local=locals()) fmodel = mmtbx.f_model.manager(f_obs=f_obs, r_free_flags=r_free_flags, xray_structure=xrs_poor) grad_calc = cartesian_dynamics.gradients_calculator_real_space_simple( restraints_manager=self.restraints_manager.geometry, target_map=self.target_map, unit_cell=self.xray_structure.unit_cell(), sites_cart=self.xray_structure.sites_cart(), wx=self.wx, wc=self.wc, update_gradient_threshold=0) processed_pdb_file = rs.get_processed_pdb_object(raw_records=raw_records, rama_potential=None, log=None) geometry = processed_pdb_file.geometry_restraints_manager( show_energies=False, plain_pairs_radius=5, assume_hydrogens_all_missing=not has_hd)