def exercise () :
from mmtbx.building.alternate_conformations import conformer_generation
from mmtbx.monomer_library import server
import iotbx.pdb.hierarchy
generate_inputs()
params = master_phil().extract()
mon_lib_srv = server.server()
pdb_in = iotbx.pdb.hierarchy.input(file_name="shear_frag_single.pdb")
hierarchy = pdb_in.hierarchy
pdb_atoms = hierarchy.atoms()
pdb_atoms.reset_i_seq()
sites_cart = pdb_atoms.extract_xyz()
xrs = pdb_in.input.xray_structure_simple()
models = []
prev_res = next_res = next_next_res = None
for chain in hierarchy.only_model().chains() :
residue_groups = chain.residue_groups()
n_rg = len(residue_groups) # should be 4
for i_res, residue_group in enumerate(residue_groups) :
sites_orig = sites_cart.deep_copy()
next_res = next_next_res = None
if (i_res < (n_rg - 1)) :
next_res = residue_groups[i_res+1].atom_groups()[0]
if (i_res < (n_rg - 2)) :
next_next_res = residue_groups[i_res+2].atom_groups()[0]
atom_groups = residue_group.atom_groups()
primary_conf = atom_groups[0]
out = StringIO()
confs = []
for conf in conformer_generation.generate_single_residue_confs(
atom_group=primary_conf,
sites_cart=sites_cart.deep_copy(),
mon_lib_srv=mon_lib_srv,
params=params.torsion_search,
prev_residue=prev_res,
next_residue=next_res,
next_next_residue=next_next_res,
backrub=False,
shear=True) :
conf.show_summary(out=out)
confs.append(conf)
prev_res = primary_conf
if (confs is None) :
continue
if (i_res == 1) :
assert (""" A ILE 7 None 4.0 mt""")
for conf in confs :
sites_new = sites_cart.set_selected(conf.sites_selection,
conf.sites_selected())
pdb_atoms.set_xyz(sites_new)
models.append(hierarchy.only_model().detached_copy())
new_hierarchy = iotbx.pdb.hierarchy.root()
for i_model, conf in enumerate(models) :
conf.id = str(i_model + 1)
new_hierarchy.append_model(conf)
open("shear_frag_naive_ensemble.pdb", "w").write(
new_hierarchy.as_pdb_string())
def screen_residue(residue,
prev_residue,
next_residue,
next_next_residue,
sites_cart,
fmodel,
mon_lib_srv,
params,
fofc_map=None,
two_fofc_map=None,
map_file_name=None,
backrub=False,
shear=False,
verbose=False,
out=None):
from mmtbx.building.alternate_conformations import conformer_generation
if (out is None):
out = sys.stdout
if (params is None):
params = master_phil().extract()
xrs = fmodel.xray_structure
occ_start = xrs.scatterers().extract_occupancies()
i_seqs = residue.atoms().extract_i_seq()
assert (not i_seqs.all_eq(0))
if (params.set_partial_occupancy is not None):
occ = occ_start.deep_copy()
occ.set_selected(i_seqs, params.set_partial_occupancy)
xrs.set_occupancies(occ)
fmodel.update_xray_structure(xrs, update_f_calc=True)
if (fofc_map is None) or (params.set_partial_occupancy is not None):
two_fofc_coeffs = fmodel.map_coefficients(map_type="2mFo-DFc")
fofc_coeffs = fmodel.map_coefficients(map_type="mFo-DFc")
two_fofc_fft = two_fofc_coeffs.fft_map(resolution_factor=1 / 4.)
fofc_fft = fofc_coeffs.fft_map(resolution_factor=1 / 4.)
two_fofc_map = two_fofc_fft.apply_sigma_scaling().real_map_unpadded()
fofc_map = fofc_fft.apply_sigma_scaling().real_map_unpadded()
if (map_file_name is not None):
import iotbx.map_tools
iotbx.map_tools.write_map_coeffs(two_fofc_coeffs, fofc_coeffs,
map_file_name)
unit_cell = xrs.unit_cell()
sites_start = sites_cart.deep_copy()
good_confs = []
n_confs = 0
t_start = time.time()
for conf in conformer_generation.generate_single_residue_confs(
atom_group=residue,
sites_cart=sites_cart.deep_copy(),
mon_lib_srv=mon_lib_srv,
params=params.torsion_search,
prev_residue=prev_residue,
next_residue=next_residue,
next_next_residue=next_next_residue,
backrub=backrub,
shear=shear):
n_confs += 1
# basically a very crude rigid-body grid search
translations = []
for sites_new, translation in translation_search(
sites=conf.sites_selected(),
translation=params.translation,
translation_sampling=params.translation_sampling):
conf_trans = conf.translate_sites(
sites_new=sites_new,
translation=translation).update_rmsd(sites_start)
good_maps = score_density(self=conf_trans,
two_fofc_map=two_fofc_map,
fofc_map=fofc_map,
unit_cell=unit_cell,
params=params.sidechain_scoring)
translations.append(conf_trans)
if (good_maps): #and (conf_trans.rmsd > params.rmsd_min):
translations.append(conf_trans)
if (len(translations) > 0):
cmp_fn = lambda a, b: cmp(b.mean_fofc, a.mean_fofc)
translations.sort(key=cmp_to_key(cmp_fn))
good_confs.append(translations[0])
if (n_confs > 1) and (len(good_confs) != 0):
for conf in good_confs:
conf.show_summary(out=out)
xrs.set_occupancies(occ_start)
t_end = time.time()
if (verbose):
print("time to sample residue: %.2fs" % (t_end - t_start), file=out)
return good_confs
def screen_residue(
residue,
prev_residue,
next_residue,
next_next_residue,
sites_cart,
fmodel,
mon_lib_srv,
params,
fofc_map=None,
two_fofc_map=None,
map_file_name=None,
backrub=False,
shear=False,
verbose=False,
out=None,
):
from mmtbx.building.alternate_conformations import conformer_generation
if out is None:
out = sys.stdout
if params is None:
params = master_phil().extract()
xrs = fmodel.xray_structure
occ_start = xrs.scatterers().extract_occupancies()
i_seqs = residue.atoms().extract_i_seq()
assert not i_seqs.all_eq(0)
if params.set_partial_occupancy is not None:
occ = occ_start.deep_copy()
occ.set_selected(i_seqs, params.set_partial_occupancy)
xrs.set_occupancies(occ)
fmodel.update_xray_structure(xrs, update_f_calc=True)
if (fofc_map is None) or (params.set_partial_occupancy is not None):
two_fofc_coeffs = fmodel.map_coefficients(map_type="2mFo-DFc")
fofc_coeffs = fmodel.map_coefficients(map_type="mFo-DFc")
two_fofc_fft = two_fofc_coeffs.fft_map(resolution_factor=1 / 4.0)
fofc_fft = fofc_coeffs.fft_map(resolution_factor=1 / 4.0)
two_fofc_map = two_fofc_fft.apply_sigma_scaling().real_map_unpadded()
fofc_map = fofc_fft.apply_sigma_scaling().real_map_unpadded()
if map_file_name is not None:
import iotbx.map_tools
iotbx.map_tools.write_map_coeffs(two_fofc_coeffs, fofc_coeffs, map_file_name)
unit_cell = xrs.unit_cell()
sites_start = sites_cart.deep_copy()
good_confs = []
n_confs = 0
t_start = time.time()
for conf in conformer_generation.generate_single_residue_confs(
atom_group=residue,
sites_cart=sites_cart.deep_copy(),
mon_lib_srv=mon_lib_srv,
params=params.torsion_search,
prev_residue=prev_residue,
next_residue=next_residue,
next_next_residue=next_next_residue,
backrub=backrub,
shear=shear,
):
n_confs += 1
# basically a very crude rigid-body grid search
translations = []
for sites_new, translation in translation_search(
sites=conf.sites_selected(),
translation=params.translation,
translation_sampling=params.translation_sampling,
):
conf_trans = conf.translate_sites(sites_new=sites_new, translation=translation).update_rmsd(sites_start)
good_maps = score_density(
self=conf_trans,
two_fofc_map=two_fofc_map,
fofc_map=fofc_map,
unit_cell=unit_cell,
params=params.sidechain_scoring,
)
translations.append(conf_trans)
if good_maps: # and (conf_trans.rmsd > params.rmsd_min) :
translations.append(conf_trans)
if len(translations) > 0:
translations.sort(lambda a, b: cmp(b.mean_fofc, a.mean_fofc))
good_confs.append(translations[0])
if (n_confs > 1) and (len(good_confs) != 0):
for conf in good_confs:
conf.show_summary(out=out)
xrs.set_occupancies(occ_start)
t_end = time.time()
if verbose:
print >> out, "time to sample residue: %.2fs" % (t_end - t_start)
return good_confs
