Python get_processed_pdb_object Examples

Example #1

File: tst_real_space_simple.py Project: keitaroyam/cctbx_fork

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)

Example #2

File: tst_real_space_simple.py Project: hainm/cctbx_project

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)

Example #3

File: testcart.py Project: pjanowski/Pawel_PhD_Scripts

    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)

Example #4

File: testcart.py Project: handreazz/Pawel_PhD_Scripts

        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)