def exercise():
from mmtbx.building.alternate_conformations import density_sampling
from mmtbx.utils import fmodel_simple
from mmtbx.monomer_library import server
from iotbx import file_reader
import iotbx.pdb.hierarchy
generate_inputs()
fmodel_params = """
high_resolution = 1.2
r_free_flags_fraction = 0.1
add_sigmas = True
pdb_file = ser_frag.pdb
output {
label = F
type = *real complex
file_name = ser_frag.mtz
}
fmodel.k_sol = 0.3
fmodel.b_sol = 20
"""
open("ser_frag_fmodel.eff", "w").write(fmodel_params)
assert (easy_run.fully_buffered("phenix.fmodel ser_frag_fmodel.eff").
raise_if_errors().return_code == 0)
assert os.path.isfile("ser_frag.mtz")
mtz_in = file_reader.any_file("ser_frag.mtz")
f_obs = mtz_in.file_server.miller_arrays[0]
flags = mtz_in.file_server.miller_arrays[1]
flags = flags.customized_copy(data=(flags.data() == 1))
mon_lib_srv = server.server()
pdb_in = iotbx.pdb.hierarchy.input(file_name="ser_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()
fmodel = fmodel_simple(f_obs=f_obs,
xray_structures=[xrs],
scattering_table="n_gaussian",
r_free_flags=flags,
skip_twin_detection=True)
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)
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 = density_sampling.screen_residue(
residue=primary_conf,
prev_residue=prev_res,
next_residue=next_res,
next_next_residue=next_next_res,
sites_cart=sites_cart,
fmodel=fmodel,
mon_lib_srv=mon_lib_srv,
params=None,
backrub=True,
shear=False,
verbose=True,
out=out)
prev_res = primary_conf
if (confs is None):
continue
# TODO tweak density sampling to allow a backrubbed conformer with a
# chi1 t rotamer for Ser 99
if (i_res == 1):
assert (""" A SER 99 20.0 None t"""
in out.getvalue())
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())
confs = density_sampling.screen_residue(
residue=primary_conf,
prev_residue=prev_res,
next_residue=next_res,
next_next_residue=next_next_res,
sites_cart=sites_cart,
fmodel=fmodel,
mon_lib_srv=mon_lib_srv,
params=None,
backrub=False,
out=out)
if (i_res == 1):
print len(confs)
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("ser_frag_guided_ensemble.pdb",
"w").write(new_hierarchy.as_pdb_string())
prev_residue = next_residue = None
residue_groups = chain.residue_groups()
n_groups = len(residue_groups)
for i_res, residue_group in enumerate(residue_groups) :
if (i_res < n_groups - 1) :
next_residue = residue_groups[i_res+1].atom_groups()[0]
i_seqs = residue_group.atoms().extract_i_seq()
if (selection.select(i_seqs).all_eq(True)) :
atom_group = residue_group.only_atom_group()
if (get_class(atom_group.resname) != "common_amino_acid") :
continue
confs = density_sampling.screen_residue(
residue=atom_group,
prev_residue=prev_residue,
next_residue=next_residue,
sites_cart=sites_cart,
fmodel=fmodel,
mon_lib_srv=mon_lib_srv,
params=params,
map_file_name="map_coeffs.mtz",
out=out)
ensemble = []
for conf in confs :
conf_atoms = conf.set_atom_sites(pdb_atoms)
pdb_lines = []
for atom in conf_atoms :
pdb_lines.append(atom.format_atom_record())
ensemble.append("\n".join(pdb_lines))
ensembles.append(ensemble)
prev_residue = residue_group.atom_groups()[0]
if (len(ensembles) == 0) :
raise Sorry("No alternate conformations found.")
def run (args, out=None ):
if (out is None) : out = sys.stdout
from mmtbx.building.alternate_conformations import density_sampling
import mmtbx.maps.utils
import mmtbx.utils
from mmtbx.monomer_library import server
import iotbx.pdb.hierarchy
get_class = iotbx.pdb.common_residue_names_get_class
mon_lib_srv = server.server()
cmdline = mmtbx.utils.cmdline_load_pdb_and_data(
args=args,
master_phil=master_phil,
process_pdb_file=False,
scattering_table="n_gaussian")
params = cmdline.params
working_phil = master_phil.format(python_object=params)
master_phil.fetch_diff(source=working_phil).show(out=out)
fmodel = cmdline.fmodel
hierarchy = cmdline.pdb_hierarchy
sele_cache = hierarchy.atom_selection_cache()
assert (params.selection is not None)
selection = sele_cache.selection(params.selection)
assert (selection.count(True) > 0)
have_results = False
pdb_atoms = hierarchy.atoms()
sites_cart = pdb_atoms.extract_xyz()
ensembles = []
t1 = time.time()
for chain in hierarchy.only_model().chains() :
prev_residue = next_residue = None
residue_groups = chain.residue_groups()
n_groups = len(residue_groups)
for i_res, residue_group in enumerate(residue_groups) :
if (i_res < n_groups - 1) :
next_residue = residue_groups[i_res+1].atom_groups()[0]
i_seqs = residue_group.atoms().extract_i_seq()
if (selection.select(i_seqs).all_eq(True)) :
atom_group = residue_group.only_atom_group()
if (get_class(atom_group.resname) != "common_amino_acid") :
continue
confs = density_sampling.screen_residue(
residue=atom_group,
prev_residue=prev_residue,
next_residue=next_residue,
sites_cart=sites_cart,
fmodel=fmodel,
mon_lib_srv=mon_lib_srv,
params=params,
map_file_name="map_coeffs.mtz",
out=out)
ensemble = []
for conf in confs :
conf_atoms = conf.set_atom_sites(pdb_atoms)
pdb_lines = []
for atom in conf_atoms :
pdb_lines.append(atom.format_atom_record())
ensemble.append("\n".join(pdb_lines))
ensembles.append(ensemble)
prev_residue = residue_group.atom_groups()[0]
if (len(ensembles) == 0) :
raise Sorry("No alternate conformations found.")
t2 = time.time()
print >> out, "search time: %.1fs" % (t2-t1)
for i_ens, ensemble in enumerate(ensembles) :
ensemble_hierarchy = iotbx.pdb.hierarchy.root()
for k, model_str in enumerate(ensemble) :
input = iotbx.pdb.hierarchy.input(pdb_string=model_str)
model = input.hierarchy.only_model().detached_copy()
model.id = str(k+1)
ensemble_hierarchy.append_model(model)
f = open("ensemble_%d.pdb" % (i_ens+1), "w")
f.write(ensemble_hierarchy.as_pdb_string())
f.close()
print "wrote ensemble_%d.pdb" % (i_ens+1)
if (params.coot) :
easy_run.call("coot --pdb %s --auto map_coeffs.mtz --pdb ensemble.pdb" %
params.input.pdb.file_name[0])
def run(args, out=None):
if (out is None): out = sys.stdout
from mmtbx.building.alternate_conformations import density_sampling
import mmtbx.maps.utils
import mmtbx.utils
from mmtbx.monomer_library import server
import iotbx.pdb.hierarchy
get_class = iotbx.pdb.common_residue_names_get_class
mon_lib_srv = server.server()
cmdline = mmtbx.utils.cmdline_load_pdb_and_data(
args=args,
master_phil=master_phil,
process_pdb_file=False,
scattering_table="n_gaussian")
params = cmdline.params
working_phil = master_phil.format(python_object=params)
master_phil.fetch_diff(source=working_phil).show(out=out)
fmodel = cmdline.fmodel
hierarchy = cmdline.pdb_hierarchy
sele_cache = hierarchy.atom_selection_cache()
assert (params.selection is not None)
selection = sele_cache.selection(params.selection)
assert (selection.count(True) > 0)
have_results = False
pdb_atoms = hierarchy.atoms()
sites_cart = pdb_atoms.extract_xyz()
ensembles = []
t1 = time.time()
for chain in hierarchy.only_model().chains():
prev_residue = next_residue = None
residue_groups = chain.residue_groups()
n_groups = len(residue_groups)
for i_res, residue_group in enumerate(residue_groups):
if (i_res < n_groups - 1):
next_residue = residue_groups[i_res + 1].atom_groups()[0]
i_seqs = residue_group.atoms().extract_i_seq()
if (selection.select(i_seqs).all_eq(True)):
atom_group = residue_group.only_atom_group()
if (get_class(atom_group.resname) != "common_amino_acid"):
continue
confs = density_sampling.screen_residue(
residue=atom_group,
prev_residue=prev_residue,
next_residue=next_residue,
sites_cart=sites_cart,
fmodel=fmodel,
mon_lib_srv=mon_lib_srv,
params=params,
map_file_name="map_coeffs.mtz",
out=out)
ensemble = []
for conf in confs:
conf_atoms = conf.set_atom_sites(pdb_atoms)
pdb_lines = []
for atom in conf_atoms:
pdb_lines.append(atom.format_atom_record())
ensemble.append("\n".join(pdb_lines))
ensembles.append(ensemble)
prev_residue = residue_group.atom_groups()[0]
if (len(ensembles) == 0):
raise Sorry("No alternate conformations found.")
t2 = time.time()
print("search time: %.1fs" % (t2 - t1), file=out)
for i_ens, ensemble in enumerate(ensembles):
ensemble_hierarchy = iotbx.pdb.hierarchy.root()
for k, model_str in enumerate(ensemble):
input = iotbx.pdb.hierarchy.input(pdb_string=model_str)
model = input.hierarchy.only_model().detached_copy()
model.id = str(k + 1)
ensemble_hierarchy.append_model(model)
f = open("ensemble_%d.pdb" % (i_ens + 1), "w")
f.write(ensemble_hierarchy.as_pdb_string())
f.close()
print("wrote ensemble_%d.pdb" % (i_ens + 1))
if (params.coot):
easy_run.call(
"coot --pdb %s --auto map_coeffs.mtz --pdb ensemble.pdb" %
params.input.pdb.file_name[0])
def exercise () :
from mmtbx.building.alternate_conformations import density_sampling
from mmtbx.utils import fmodel_simple
from mmtbx.monomer_library import server
from iotbx import file_reader
import iotbx.pdb.hierarchy
generate_inputs()
fmodel_params = """
high_resolution = 1.2
r_free_flags_fraction = 0.1
add_sigmas = True
pdb_file = shear_frag.pdb
output {
label = F
type = *real complex
file_name = shear_frag.mtz
}
fmodel.k_sol = 0.3
fmodel.b_sol = 20
"""
open("shear_frag_fmodel.eff", "w").write(fmodel_params)
assert (easy_run.fully_buffered("phenix.fmodel shear_frag_fmodel.eff"
).raise_if_errors().return_code == 0)
assert os.path.isfile("shear_frag.mtz")
mtz_in = file_reader.any_file("shear_frag.mtz")
f_obs = mtz_in.file_server.miller_arrays[0]
flags = mtz_in.file_server.miller_arrays[1]
flags = flags.customized_copy(data=(flags.data()==1))
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()
fmodel = fmodel_simple(
f_obs=f_obs,
xray_structures=[xrs],
scattering_table="n_gaussian",
r_free_flags=flags,
skip_twin_detection=True)
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 = density_sampling.screen_residue(
residue=primary_conf,
prev_residue=prev_res,
next_residue=next_res,
next_next_residue=next_next_res,
sites_cart=sites_cart,
fmodel=fmodel,
mon_lib_srv=mon_lib_srv,
params=None,
backrub=True,
shear=True,
verbose=True,
out=out)
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())