def exercise_1():
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = server.server(),
ener_lib = server.ener_lib(),
raw_records = flex.std_string(pdb_str_1.splitlines()),
strict_conflict_handling = True,
force_symmetry = True,
log = None)
grm = processed_pdb_file.geometry_restraints_manager()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
sites_cart = pdb_hierarchy.atoms().extract_xyz()
# c-beta restraints are added by default!!!
assert len(grm.get_c_beta_torsion_proxies()) == 4
#test global selection and removing c-beta restraints
tst_boolsel = pdb_hierarchy.atom_selection_cache().selection("resname TYR")
tst_iselection = tst_boolsel.iselection()
#test global selection
grm2 = grm.select(iselection=tst_iselection)
assert len(grm2.get_c_beta_torsion_proxies()) == 2
grm2 = grm.select(selection=tst_boolsel)
assert len(grm2.get_c_beta_torsion_proxies()) == 2
#remove a selection
grm.remove_c_beta_torsion_restraints_in_place(selection=tst_iselection)
assert len(grm.get_c_beta_torsion_proxies()) == 2
#add a selection
grm.remove_c_beta_torsion_restraints_in_place()
assert len(grm.get_c_beta_torsion_proxies()) == 0
c_beta_torsion_proxies = c_beta.get_c_beta_torsion_proxies(
pdb_hierarchy,
selection=tst_iselection,
sigma=2.5)
assert len(c_beta_torsion_proxies) == 2
def run():
pdb_file_name = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/adp_restraints.pdb",
test=os.path.isfile)
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=monomer_library.server.server(),
ener_lib=monomer_library.server.ener_lib(),
file_name=pdb_file_name)
xray_structure = processed_pdb_file.xray_structure()
grm = processed_pdb_file.geometry_restraints_manager(
plain_pairs_radius=5.0)
grm.pair_proxies(sites_cart=xray_structure.sites_cart())
class parameters:
sphere_radius = 1.6
distance_power = 0.0
average_power = 0.0
min_u_sum = 1.e-6
sel = flex.bool(xray_structure.scatterers().size(), True)
xray_structure.scatterers().flags_set_grad_u_iso(sel.iselection())
for use_hd in [True, False]:
energies_adp = cctbx.adp_restraints.energies_iso(
geometry_restraints_manager=grm,
xray_structure=xray_structure,
use_hd=use_hd,
use_u_local_only=False,
parameters=parameters)
u_iso_restraints = grm.harmonic_restraints(
variables=xray_structure.extract_u_iso_or_u_equiv(),
type_indices=None,
type_weights=1.0)
assert approx_equal(u_iso_restraints.residual_sum,
energies_adp.residual_sum)
assert approx_equal(u_iso_restraints.gradients, energies_adp.gradients)
def test_solvent_model():
# correct values
p = pdb.input(source_info='string',lines=test_pdb)
sr = p.xray_structure_simple().scattering_type_registry()
# test values
p1 = pdb.input(source_info='string',lines=test_pdb)
mls = server.server()
el = server.ener_lib()
ip = pdb_interpretation.process(mon_lib_srv=mls,ener_lib=el,pdb_inp=p1)
sg = structure_generator()
sg.add_species(p,1)
sm = solvent_model()
sm.interpreted_pdb = ip
sm.xyz = sg.species[0].xyz
new_sr = sm.add_bulk_solvent(sr)
assert(new_sr.sum_of_scattering_factors_at_diffraction_angle_0() <
sr.sum_of_scattering_factors_at_diffraction_angle_0())
sm.bulk_solvent_scale = 0.0
new_sr = sm.add_bulk_solvent(sr)
assert(approx_equal(sr.sum_of_scattering_factors_at_diffraction_angle_0(),
new_sr.sum_of_scattering_factors_at_diffraction_angle_0()))
sm.boundary_layer_scale = 0.0
new_sr = sm.add_boundary_layer_solvent(new_sr)
assert(approx_equal(sr.sum_of_scattering_factors_at_diffraction_angle_0(),
new_sr.sum_of_scattering_factors_at_diffraction_angle_0()))
sm.boundary_layer_scale = 0.6
new_sr = sm.add_boundary_layer_solvent(new_sr)
assert(new_sr.sum_of_scattering_factors_at_diffraction_angle_0() >
sr.sum_of_scattering_factors_at_diffraction_angle_0())
def exercise_1():
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = server.server(),
ener_lib = server.ener_lib(),
raw_records = flex.std_string(pdb_str_1.splitlines()),
strict_conflict_handling = True,
force_symmetry = True,
log = None)
grm = processed_pdb_file.geometry_restraints_manager()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
sites_cart = pdb_hierarchy.atoms().extract_xyz()
# c-beta restraints are added by default!!!
assert len(grm.get_c_beta_torsion_proxies()) == 4
#test global selection and removing c-beta restraints
tst_boolsel = pdb_hierarchy.atom_selection_cache().selection("resname TYR")
tst_iselection = tst_boolsel.iselection()
#test global selection
grm2 = grm.select(iselection=tst_iselection)
assert len(grm2.get_c_beta_torsion_proxies()) == 2
grm2 = grm.select(selection=tst_boolsel)
assert len(grm2.get_c_beta_torsion_proxies()) == 2
#remove a selection
grm.remove_c_beta_torsion_restraints_in_place(selection=tst_iselection)
assert len(grm.get_c_beta_torsion_proxies()) == 2
#add a selection
grm.remove_c_beta_torsion_restraints_in_place()
assert len(grm.get_c_beta_torsion_proxies()) == 0
c_beta_torsion_proxies = c_beta.get_c_beta_torsion_proxies(
pdb_hierarchy,
selection=tst_iselection,
sigma=2.5)
assert len(c_beta_torsion_proxies) == 2
def run (args, out=sys.stdout, quiet=False) :
from mmtbx.monomer_library import pdb_interpretation
from mmtbx.monomer_library import server
import iotbx.pdb
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=get_master_phil(),
pdb_file_def="model",
usage_string=usage_string)
params = cmdline.work.extract()
if (params.model is None) :
raise Usage(usage_string)
pdb_in = iotbx.pdb.input(source_info=params.model, file_name=params.model)
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
pdb_inp=pdb_in,
substitute_non_crystallographic_unit_cell_if_necessary=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
geometry = processed_pdb_file.geometry_restraints_manager()
result = rna_validation(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry,
params=params,
outliers_only=params.outliers_only)
result.show(out=out)
return result
def run():
pdb_file_name = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/adp_restraints.pdb", test=os.path.isfile)
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = monomer_library.server.server(),
ener_lib = monomer_library.server.ener_lib(),
file_name = pdb_file_name)
xray_structure = processed_pdb_file.xray_structure()
grm = processed_pdb_file.geometry_restraints_manager(
plain_pairs_radius = 5.0)
grm.pair_proxies(sites_cart=xray_structure.sites_cart())
class parameters:
sphere_radius = 1.6
distance_power = 0.0
average_power = 0.0
min_u_sum = 1.e-6
sel = flex.bool(xray_structure.scatterers().size(), True)
xray_structure.scatterers().flags_set_grad_u_iso(sel.iselection())
for use_hd in [True, False]:
energies_adp = cctbx.adp_restraints.energies_iso(
geometry_restraints_manager=grm,
xray_structure=xray_structure,
use_hd = use_hd,
use_u_local_only = False,
parameters=parameters)
u_iso_restraints = grm.harmonic_restraints(
variables = xray_structure.extract_u_iso_or_u_equiv(),
type_indices = None,
type_weights = 1.0)
assert approx_equal(u_iso_restraints.residual_sum, energies_adp.residual_sum)
assert approx_equal(u_iso_restraints.gradients, energies_adp.gradients)
def run(pdb_file, cif_file):
from mmtbx.monomer_library import server
import iotbx
from mmtbx.monomer_library import pdb_interpretation
pdb_inp = iotbx.pdb.input(file_name=pdb_file)
pdb_hierarchy = pdb_inp.construct_hierarchy()
raw_lines = pdb_hierarchy.as_pdb_string(
crystal_symmetry=pdb_inp.crystal_symmetry())
f=file(cif_file, "rb")
ligand_cif = f.read()
f.close()
cif_object = iotbx.cif.model.cif()
iotbx.cif.reader(input_string=ligand_cif,
cif_object=cif_object,
strict=False)
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
for srv in [mon_lib_srv, ener_lib]:
srv.process_cif_object(cif_object=cif_object,
file_name="LIGAND")
processed_pdb = pdb_interpretation.process(
mon_lib_srv,
ener_lib,
raw_records=raw_lines)
geometry_restraints_manager = processed_pdb.geometry_restraints_manager()
def run(args, out=sys.stdout, quiet=False):
from mmtbx.monomer_library import pdb_interpretation
from mmtbx.monomer_library import server
import iotbx.pdb
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=get_master_phil(),
pdb_file_def="model",
usage_string=usage_string)
params = cmdline.work.extract()
if (params.model is None):
raise Usage(usage_string)
pdb_in = iotbx.pdb.input(source_info=params.model, file_name=params.model)
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
pdb_inp=pdb_in,
substitute_non_crystallographic_unit_cell_if_necessary=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
geometry = processed_pdb_file.geometry_restraints_manager()
result = rna_validation(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry,
params=params,
outliers_only=params.outliers_only)
result.show(out=out)
return result
def run(args, command_name=libtbx.env.dispatcher_name):
parser = argparse.ArgumentParser(
prog=command_name,
usage='%s pdb_file "atom_selection" [...]' % command_name)
parser.add_argument("file_name",
nargs=1,
help="File name of the model file")
parser.add_argument(
"inselections",
help="Atom selection strings",
nargs='+',
)
parser.add_argument("--write-pdb-file",
action="store",
help="write selected atoms to new PDB file",
default=None)
parser.add_argument(
"--cryst1-replacement-buffer-layer",
action="store",
type=float,
help="replace CRYST1 with pseudo unit cell covering the selected"
" atoms plus a surrounding buffer layer",
default=None)
co = parser.parse_args(args)
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb_file = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=co.file_name[0],
log=sys.stdout)
print
acp = processed_pdb_file.all_chain_proxies
selection_cache = acp.pdb_hierarchy.atom_selection_cache()
atoms = acp.pdb_atoms
all_bsel = flex.bool(atoms.size(), False)
for selection_string in co.inselections:
print selection_string
isel = acp.iselection(string=selection_string, cache=selection_cache)
all_bsel.set_selected(isel, True)
if (not co.write_pdb_file):
print " %d atom%s selected" % plural_s(isel.size())
for atom in atoms.select(isel):
print " %s" % atom.format_atom_record()
print
if (co.write_pdb_file):
print "Writing file:", show_string(co.write_pdb_file)
sel_hierarchy = acp.pdb_hierarchy.select(all_bsel)
if (co.cryst1_replacement_buffer_layer is None):
crystal_symmetry = acp.special_position_settings
else:
import cctbx.crystal
crystal_symmetry = cctbx.crystal.non_crystallographic_symmetry(
sites_cart=sel_hierarchy.atoms().extract_xyz(),
buffer_layer=co.cryst1_replacement_buffer_layer)
write_whole_pdb_file(file_name=co.write_pdb_file,
processed_pdb_file=processed_pdb_file,
pdb_hierarchy=sel_hierarchy,
crystal_symmetry=crystal_symmetry)
print
def exercise_1(mon_lib_srv, ener_lib):
f = open("1.pdb", "w")
f.write(pdb_str_1)
f.close()
log = cStringIO.StringIO()
dihedral_proxies = utils.get_complete_dihedral_proxies(
raw_records=pdb_str_1)
assert len(dihedral_proxies) == 54, \
"Expected 54, got %d" % len(dihedral_proxies)
# default run (1 residue is out of NCS)
params = pdb_interpretation.master_params.extract()
params.ncs_search.enabled=True
ppf = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
raw_records=flex.split_lines(pdb_str_1))
ncs_manager = torsion_ncs.torsion_ncs(
processed_pdb_file=ppf,
ncs_obj=ppf.ncs_obj,
log=log)
nprox = ncs_manager.get_n_proxies()
assert nprox == 28, "got %d instead of 28" % nprox
# supply full NCS
cuspars = iotbx.phil.parse("""
ncs_search.enabled=True
ncs_group {
reference = (chain A )
selection = (chain B )
}
""")
params = pdb_interpretation.master_params
p = params.fetch(cuspars).extract()
ppf = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=p,
raw_records=flex.split_lines(pdb_str_1))
ncs_manager = torsion_ncs.torsion_ncs(
processed_pdb_file=ppf,
ncs_obj=ppf.ncs_obj,
log=log)
nprox = ncs_manager.get_n_proxies()
assert nprox == 40, "got %d instead of 40" % nprox
def exercise_ramachandran_selections(mon_lib_srv, ener_lib):
# Just check overall rama proxies
file_name = libtbx.env.find_in_repositories(
# relative_path="phenix_regression/pdb/3mku.pdb",
relative_path="phenix_regression/pdb/fab_a_cut.pdb",
test=os.path.isfile)
if (file_name is None) :
print "Skipping test."
return
params = pdb_interpretation.master_params.fetch().extract()
params.peptide_link.ramachandran_restraints = True
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
file_name=file_name,
log=StringIO())
grm = processed_pdb_file.geometry_restraints_manager()
# print grm.ramachandran_manager.get_n_proxies() # 47 is wrong here
# simple selection
params = pdb_interpretation.master_params.fetch().extract()
params.peptide_link.ramachandran_restraints = True
params.peptide_link.rama_selection = "chain A and resid 1:7"
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
file_name=file_name,
log=StringIO())
grm = processed_pdb_file.geometry_restraints_manager()
nprox = grm.ramachandran_manager.get_n_proxies()
assert nprox == 5, ""+\
"Want to get 5 rama proxies, got %d" % nprox
# 7 residues: there are insertion codes
params = pdb_interpretation.master_params.fetch().extract()
params.peptide_link.ramachandran_restraints = True
params.peptide_link.rama_selection = "chain A and resid 27:28"
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
file_name=file_name,
log=StringIO())
grm = processed_pdb_file.geometry_restraints_manager()
def exercise_lbfgs_simple (mon_lib_srv, ener_lib, verbose=False) :
# three peptides:
# 1 = poly-ALA, favored
# 2 = poly-ALA, outlier
# 3 = poly-TRP, outlier
#
# Note that the ramalyze score for the first actually gets slightly worse,
# but it's still good and we're starting from an excellent score anyway.
#
# residuals = [0.00024512, 307.616444, 294.913714]
residuals = [0.00168766995882, 186.24718562, 177.259069807]
for i, peptide in enumerate([pdb1, pdb2, pdb3]) :
pdb_in = iotbx.pdb.input(source_info="peptide",
lines=flex.split_lines(peptide))
params = pdb_interpretation.master_params.extract()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
log = StringIO()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
atoms = pdb_hierarchy.atoms()
sites_cart_1 = atoms.extract_xyz().deep_copy()
gradients_fd = flex.vec3_double(sites_cart_1.size(), (0,0,0))
gradients_an = flex.vec3_double(sites_cart_1.size(), (0,0,0))
params = ramachandran.master_phil.fetch().extract()
rama_manager = ramachandran.ramachandran_manager(
pdb_hierarchy, None, params, log)
assert rama_manager.get_n_proxies() == 1
residual_an = rama_manager.target_and_gradients(
unit_cell=None,
sites_cart=sites_cart_1,
gradient_array=gradients_an)
# print "comparing", residual_an
assert approx_equal(residual_an, residuals[i], eps=0.00001)
if verbose :
print ""
for i, peptide in enumerate([pdb1, pdb2, pdb3]) :
pdb_in = iotbx.pdb.input(source_info="peptide",
lines=flex.split_lines(peptide))
o = benchmark_structure(pdb_in, mon_lib_srv, ener_lib, verbose)
phi0, psi0 = o.r0.results[0].phi, o.r0.results[0].psi
phi1, psi1 = o.r1.results[0].phi, o.r1.results[0].psi
phi2, psi2 = o.r2.results[0].phi, o.r2.results[0].psi
r0 = o.r0.results[0].score
r1 = o.r1.results[0].score
r2 = o.r2.results[0].score
if verbose :
print "peptide %d" % (i+1)
print " before: rmsd_bonds=%-6.4f rmsd_angles=%-6.3f" % (o.b0,o.a0)
print " phi=%-6.1f psi=%-6.1f score=%-.2f" % (phi0, psi0, r0)
print " simple: rmsd_bonds=%-6.4f rmsd_angles=%-6.3f" % (o.b1,o.a1)
print " phi=%-6.1f psi=%-6.1f score=%-.2f" % (phi1, psi1, r1)
print " + Rama: rmsd_bonds=%-6.4f rmsd_angles=%-6.3f" % (o.b2,o.a2)
print " phi=%-6.1f psi=%-6.1f score=%-.2f" % (phi2, psi2, r2)
print ""
def exercise_3():
pdb_raw = """\
ATOM 1 CA GLY A 1 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 2 CA GLY A 2 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 3 CA GLY A 3 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 4 CA GLY A 4 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 5 CA GLY A 5 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 6 CA GLY A 6 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 7 CA GLY A 7 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 8 CA GLY A 8 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 9 CA GLY A 9 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 10 CA GLY A 10 -0.227 9.888 -15.197 1.00 54.04 C
HETATM 11 N SEP A 11 -2.112 0.368 -0.991 1.00 20.00 A N
HETATM 12 CA SEP A 11 -0.692 0.284 -0.951 1.00 20.00 A C
HETATM 13 CB SEP A 11 -0.234 0.166 0.485 1.00 20.00 A C
HETATM 14 OG SEP A 11 1.130 -0.184 0.515 1.00 20.00 A O
HETATM 15 C SEP A 11 -0.237 -0.930 -1.727 1.00 20.00 A C
HETATM 16 O SEP A 11 -0.767 -2.051 -1.509 1.00 20.00 A O
HETATM 18 P SEP A 11 1.922 -0.008 1.871 1.00 20.00 A P
HETATM 19 O1P SEP A 11 2.139 1.462 2.140 1.00 20.00 A O
HETATM 20 O2P SEP A 11 3.259 -0.703 1.767 1.00 20.00 A O-1
HETATM 21 O3P SEP A 11 1.127 -0.614 3.002 1.00 20.00 A O-1
END"""
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
xrs = pdb_in.input.xray_structure_simple()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs),
crystal_symmetry=xrs,
log=null_out())
pdb_in.hierarchy.atoms().reset_i_seq()
ligand_sel = pdb_in.hierarchy.atom_selection_cache().selection(
"resname SEP")
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ligand_selection=ligand_sel,
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
assert (mstats.n_protein == 10)
assert ("Ligands:" in out.getvalue())
assert approx_equal(mstats.macromolecules.b_mean, 54.04)
# now with just the raw selection string
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ligand_selection="resname SEP",
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
assert (mstats.n_protein == 10)
assert ("Ligands:" in out.getvalue())
def run(args, residue_type, expected_results):
verbose = "--verbose" in args
debug = "--debug" in args
pdb_files = libtbx.env.find_in_repositories(
relative_path="phenix_regression/%s_pdb_files" % residue_type,
test=os.path.isdir)
if (pdb_files is None):
print "Skipping tst_%s_interpretation: input files not available" \
% residue_type
return
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
for file_name in os.listdir(pdb_files):
if (file_name[-4:] not in [".ent", ".pdb"]): continue
if (verbose):
log = sys.stdout
else:
log = null_out()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=os.path.join(pdb_files, file_name),
log=log)
for mm in processed_pdb_file.all_chain_proxies.all_monomer_mappings:
residue_name = mm.residue_name
if (mm.classification == "RNA"):
for c in ["2", "3"]:
expected_mod = "%rna" + c + "p_pur"
if (mm.residue_name.find(expected_mod) > 0):
residue_name = mm.residue_name.replace(
expected_mod, "")
break
expected_mod = "%rna" + c + "p_pyr"
if (mm.residue_name.find(expected_mod) > 0):
residue_name = mm.residue_name.replace(
expected_mod, "")
break
assert len(mm.duplicate_atoms) == 0
assert len(mm.ignored_atoms) == 0
assert not mm.is_unusual
unexpected_names = [atom.name for atom in mm.unexpected_atoms]
result = [
residue_name,
len(mm.expected_atoms), unexpected_names, mm.classification,
mm.is_terminus, mm.incomplete_info
]
key = file_name[:-4]
if (debug):
print '"%s":' % key
print " ", str(result) + ","
print " ", str(expected_results[key]) + ","
if (expected_results is not None):
assert result == expected_results[key], "%s not %s" % (
result,
expected_results[key],
)
print "OK"
def run(args, residue_type, expected_results):
verbose = "--verbose" in args
debug = "--debug" in args
pdb_files = libtbx.env.find_in_repositories(
relative_path="phenix_regression/%s_pdb_files" % residue_type,
test=os.path.isdir)
if (pdb_files is None):
print "Skipping tst_%s_interpretation: input files not available" \
% residue_type
return
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
for file_name in os.listdir(pdb_files):
if (file_name[-4:] not in [".ent", ".pdb"]): continue
if (verbose):
log = sys.stdout
else:
log = null_out()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=os.path.join(pdb_files, file_name),
log=log)
for mm in processed_pdb_file.all_chain_proxies.all_monomer_mappings:
residue_name = mm.residue_name
if (mm.classification == "RNA"):
for c in ["2", "3"]:
expected_mod = "%rna"+c+"p_pur"
if (mm.residue_name.find(expected_mod) > 0):
residue_name = mm.residue_name.replace(expected_mod, "")
break
expected_mod = "%rna"+c+"p_pyr"
if (mm.residue_name.find(expected_mod) > 0):
residue_name = mm.residue_name.replace(expected_mod, "")
break
assert len(mm.duplicate_atoms) == 0
assert len(mm.ignored_atoms) == 0
assert not mm.is_unusual
unexpected_names = [atom.name for atom in mm.unexpected_atoms]
result = [
residue_name,
len(mm.expected_atoms),
unexpected_names,
mm.classification,
mm.is_terminus,
mm.incomplete_info]
key = file_name[:-4]
if (debug):
print '"%s":' % key
print " ", str(result)+","
print " ", str(expected_results[key])+","
if (expected_results is not None):
assert result == expected_results[key], "%s not %s" % (
result,
expected_results[key],
)
print "OK"
def exercise_3 () :
pdb_raw = """\
ATOM 1 CA GLY A 1 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 2 CA GLY A 2 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 3 CA GLY A 3 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 4 CA GLY A 4 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 5 CA GLY A 5 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 6 CA GLY A 6 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 7 CA GLY A 7 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 8 CA GLY A 8 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 9 CA GLY A 9 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 10 CA GLY A 10 -0.227 9.888 -15.197 1.00 54.04 C
HETATM 11 N SEP A 11 -2.112 0.368 -0.991 1.00 20.00 A N
HETATM 12 CA SEP A 11 -0.692 0.284 -0.951 1.00 20.00 A C
HETATM 13 CB SEP A 11 -0.234 0.166 0.485 1.00 20.00 A C
HETATM 14 OG SEP A 11 1.130 -0.184 0.515 1.00 20.00 A O
HETATM 15 C SEP A 11 -0.237 -0.930 -1.727 1.00 20.00 A C
HETATM 16 O SEP A 11 -0.767 -2.051 -1.509 1.00 20.00 A O
HETATM 18 P SEP A 11 1.922 -0.008 1.871 1.00 20.00 A P
HETATM 19 O1P SEP A 11 2.139 1.462 2.140 1.00 20.00 A O
HETATM 20 O2P SEP A 11 3.259 -0.703 1.767 1.00 20.00 A O-1
HETATM 21 O3P SEP A 11 1.127 -0.614 3.002 1.00 20.00 A O-1
END"""
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
xrs = pdb_in.input.xray_structure_simple()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs),
crystal_symmetry=xrs,
log=null_out())
pdb_in.hierarchy.atoms().reset_i_seq()
ligand_sel = pdb_in.hierarchy.atom_selection_cache().selection("resname SEP")
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ligand_selection=ligand_sel,
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
assert (mstats.n_protein == 10)
assert ("Ligands:" in out.getvalue())
assert approx_equal(mstats.macromolecules.b_mean, 54.04)
# now with just the raw selection string
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ligand_selection="resname SEP",
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
assert (mstats.n_protein == 10)
assert ("Ligands:" in out.getvalue())
def benchmark_structure (pdb_in, mon_lib_srv, ener_lib, verbose=False, w=1.0) :
params = pdb_interpretation.master_params.extract()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
log = StringIO()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
r0 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
atoms = pdb_hierarchy.atoms()
sites_cart_1 = atoms.extract_xyz().deep_copy()
sites_cart_2 = sites_cart_1.deep_copy()
grm = processed_pdb_file.geometry_restraints_manager()
assert (grm is not None)
e = grm.energies_sites(sites_cart=sites_cart_1)
b0 = e.bond_deviations()[-1]
a0 = e.angle_deviations()[-1]
flags = cctbx.geometry_restraints.flags.flags(default=True)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_1,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a1 = lbfgs.rmsd_angles
b1 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_1)
r1 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
rama_params = ramachandran.master_phil.fetch().extract()
rama_manager = ramachandran.ramachandran_manager(
pdb_hierarchy, None, rama_params, log)
grm.set_ramachandran_restraints(rama_manager)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_2,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a2 = lbfgs.rmsd_angles
b2 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_2)
r2 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
return group_args(
a0=a0,
a1=a1,
a2=a2,
b0=b0,
b1=b1,
b2=b2,
r0=r0,
r1=r1,
r2=r2)
def exercise_ramachandran_selections(mon_lib_srv, ener_lib):
# Just check overall rama proxies
file_name = libtbx.env.find_in_repositories(
# relative_path="phenix_regression/pdb/3mku.pdb",
relative_path="phenix_regression/pdb/fab_a_cut.pdb",
test=os.path.isfile)
if (file_name is None):
print "Skipping test."
return
params = pdb_interpretation.master_params.fetch().extract()
params.peptide_link.ramachandran_restraints = True
processed_pdb_file = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
file_name=file_name,
log=StringIO())
grm = processed_pdb_file.geometry_restraints_manager()
# print grm.ramachandran_manager.get_n_proxies() # 47 is wrong here
# simple selection
params = pdb_interpretation.master_params.fetch().extract()
params.peptide_link.ramachandran_restraints = True
params.peptide_link.rama_selection = "chain A and resid 1:7"
processed_pdb_file = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
file_name=file_name,
log=StringIO())
grm = processed_pdb_file.geometry_restraints_manager()
nprox = grm.ramachandran_manager.get_n_proxies()
assert nprox == 5, ""+\
"Want to get 5 rama proxies, got %d" % nprox
# 7 residues: there are insertion codes
params = pdb_interpretation.master_params.fetch().extract()
params.peptide_link.ramachandran_restraints = True
params.peptide_link.rama_selection = "chain A and resid 27:28"
processed_pdb_file = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
file_name=file_name,
log=StringIO())
grm = processed_pdb_file.geometry_restraints_manager()
def exercise_1(mon_lib_srv, ener_lib):
f = open("1.pdb", "w")
f.write(pdb_str_1)
f.close()
log = cStringIO.StringIO()
dihedral_proxies = utils.get_complete_dihedral_proxies(
raw_records=pdb_str_1)
assert len(dihedral_proxies) == 54, \
"Expected 54, got %d" % len(dihedral_proxies)
# default run (1 residue is out of NCS)
params = pdb_interpretation.master_params.extract()
params.ncs_search.enabled = True
ppf = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
raw_records=flex.split_lines(pdb_str_1))
ncs_manager = torsion_ncs.torsion_ncs(processed_pdb_file=ppf,
ncs_obj=ppf.ncs_obj,
log=log)
nprox = ncs_manager.get_n_proxies()
assert nprox == 28, "got %d instead of 28" % nprox
# supply full NCS
cuspars = iotbx.phil.parse("""
ncs_search.enabled=True
ncs_group {
reference = (chain A )
selection = (chain B )
}
""")
params = pdb_interpretation.master_params
p = params.fetch(cuspars).extract()
ppf = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=p,
raw_records=flex.split_lines(pdb_str_1))
ncs_manager = torsion_ncs.torsion_ncs(processed_pdb_file=ppf,
ncs_obj=ppf.ncs_obj,
log=log)
nprox = ncs_manager.get_n_proxies()
assert nprox == 40, "got %d instead of 40" % nprox
def get_rna_pucker_ref(self, test_pucker=False):
flags = geometry_restraints.flags.flags(default=True)
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
self.bond_dict = {}
self.angle_dict = {}
self.processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=None,
raw_records=self.sample_bases)
self.geometry = self.processed_pdb_file.geometry_restraints_manager()
#confirm puckers are correct
if test_pucker:
r = rna_validate()
r.pucker_evaluate(hierarchy=self.processed_pdb_file.
all_chain_proxies.pdb_hierarchy)
assert not r.pucker_states[0].is_2p
assert r.pucker_states[1].is_2p
i_seq_name_hash = utils.build_name_hash(
pdb_hierarchy=self.processed_pdb_file.all_chain_proxies.
pdb_hierarchy)
pair_proxies = self.geometry.pair_proxies(
flags=flags,
sites_cart=self.processed_pdb_file.all_chain_proxies.sites_cart)
bond_proxies = pair_proxies.bond_proxies
for bond in bond_proxies.simple:
atom1 = i_seq_name_hash[bond.i_seqs[0]][0:4]
atom2 = i_seq_name_hash[bond.i_seqs[1]][0:4]
if (atom1.strip() not in self.rna_backbone_atoms
and atom2.strip() not in self.rna_backbone_atoms):
continue
key = atom1 + atom2
sigma = (1 / bond.weight)**(.5)
try:
self.bond_dict[key].append((bond.distance_ideal, sigma))
except Exception:
self.bond_dict[key] = []
self.bond_dict[key].append((bond.distance_ideal, sigma))
for angle in self.geometry.angle_proxies:
atom1 = i_seq_name_hash[angle.i_seqs[0]][0:4]
atom2 = i_seq_name_hash[angle.i_seqs[1]][0:4]
atom3 = i_seq_name_hash[angle.i_seqs[2]][0:4]
if (atom1.strip() not in self.rna_backbone_atoms
and atom2.strip() not in self.rna_backbone_atoms
and atom3.strip() not in self.rna_backbone_atoms):
continue
key = atom1 + atom2 + atom3
sigma = (1 / angle.weight)**(.5)
try:
self.angle_dict[key].append((angle.angle_ideal, sigma))
except Exception:
self.angle_dict[key] = []
self.angle_dict[key].append((angle.angle_ideal, sigma))
def benchmark_structure(pdb_in, mon_lib_srv, ener_lib, verbose=False, w=1.0):
params = pdb_interpretation.master_params.extract()
processed_pdb_file = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
log = StringIO()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
r0 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
atoms = pdb_hierarchy.atoms()
sites_cart_1 = atoms.extract_xyz().deep_copy()
sites_cart_2 = sites_cart_1.deep_copy()
grm = processed_pdb_file.geometry_restraints_manager()
assert (grm is not None)
e = grm.energies_sites(sites_cart=sites_cart_1)
b0 = e.bond_deviations()[-1]
a0 = e.angle_deviations()[-1]
flags = cctbx.geometry_restraints.flags.flags(default=True)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_1,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a1 = lbfgs.rmsd_angles
b1 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_1)
r1 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
rama_params = ramachandran.master_phil.fetch().extract()
rama_manager = ramachandran.ramachandran_manager(pdb_hierarchy, None,
rama_params, log)
grm.set_ramachandran_restraints(rama_manager)
lbfgs = geometry_minimization.lbfgs(
sites_cart=sites_cart_2,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
geometry_restraints_flags=flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
a2 = lbfgs.rmsd_angles
b2 = lbfgs.rmsd_bonds
atoms.set_xyz(sites_cart_2)
r2 = ramalyze(pdb_hierarchy=pdb_hierarchy, outliers_only=False)
return group_args(a0=a0,
a1=a1,
a2=a2,
b0=b0,
b1=b1,
b2=b2,
r0=r0,
r1=r1,
r2=r2)
def get_rna_pucker_ref(self, test_pucker=False):
flags = geometry_restraints.flags.flags(default=True)
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
self.bond_dict = {}
self.angle_dict = {}
self.processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=None,
raw_records=self.sample_bases)
self.geometry = self.processed_pdb_file.geometry_restraints_manager()
#confirm puckers are correct
if test_pucker:
r = rna_validate()
r.pucker_evaluate(
hierarchy=self.processed_pdb_file.all_chain_proxies.pdb_hierarchy)
assert not r.pucker_states[0].is_2p
assert r.pucker_states[1].is_2p
i_seq_name_hash = utils.build_name_hash(
pdb_hierarchy=self.processed_pdb_file.all_chain_proxies.pdb_hierarchy)
pair_proxies = self.geometry.pair_proxies(
flags=flags,
sites_cart=self.processed_pdb_file.all_chain_proxies.sites_cart)
bond_proxies = pair_proxies.bond_proxies
for bond in bond_proxies.simple:
atom1 = i_seq_name_hash[bond.i_seqs[0]][0:4]
atom2 = i_seq_name_hash[bond.i_seqs[1]][0:4]
if (atom1.strip() not in self.rna_backbone_atoms and
atom2.strip() not in self.rna_backbone_atoms):
continue
key = atom1+atom2
sigma = (1/bond.weight)**(.5)
try:
self.bond_dict[key].append((bond.distance_ideal, sigma))
except Exception:
self.bond_dict[key] = []
self.bond_dict[key].append((bond.distance_ideal, sigma))
for angle in self.geometry.angle_proxies:
atom1 = i_seq_name_hash[angle.i_seqs[0]][0:4]
atom2 = i_seq_name_hash[angle.i_seqs[1]][0:4]
atom3 = i_seq_name_hash[angle.i_seqs[2]][0:4]
if (atom1.strip() not in self.rna_backbone_atoms and
atom2.strip() not in self.rna_backbone_atoms and
atom3.strip() not in self.rna_backbone_atoms):
continue
key = atom1+atom2+atom3
sigma = (1/angle.weight)**(.5)
try:
self.angle_dict[key].append((angle.angle_ideal, sigma))
except Exception:
self.angle_dict[key] = []
self.angle_dict[key].append((angle.angle_ideal, sigma))
def read_dummy_type(file_name=None, pdb_inp=None):
assert ((file_name is not None) or (pdb_inp is not None))
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
if (pdb_inp is None):
tmp_obj = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv, ener_lib=ener_lib,
file_name=file_name).all_chain_proxies
else:
tmp_obj = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
pdb_inp=pdb_inp).all_chain_proxies
ats = tmp_obj.nonbonded_energy_type_registry.symbols
els = tmp_obj.scattering_type_registry.symbols
for i in range(ats.size()):
if ats[i] == "":
ats[i] = els[i]
return ats
def reprocess_pdb (pdb_hierarchy, crystal_symmetry, cif_objects, out) :
from mmtbx.monomer_library import pdb_interpretation
from mmtbx.monomer_library import server
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
for cif_object in cif_objects :
for srv in [mon_lib_srv, ener_lib]:
srv.process_cif_object(cif_object=cif_object)
return pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_hierarchy.as_pdb_string(crystal_symmetry=crystal_symmetry),
crystal_symmetry=crystal_symmetry,
log=out)
def reprocess_pdb(pdb_hierarchy, crystal_symmetry, cif_objects, out):
from mmtbx.monomer_library import pdb_interpretation
from mmtbx.monomer_library import server
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
for cif_object in cif_objects:
for srv in [mon_lib_srv, ener_lib]:
srv.process_cif_object(cif_object=cif_object)
return pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_hierarchy.as_pdb_string(
crystal_symmetry=crystal_symmetry),
crystal_symmetry=crystal_symmetry,
log=out)
def exercise_1(mon_lib_srv, ener_lib):
pdb_in = simple_pdb()
params = pdb_interpretation.master_params.extract()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
grm = processed_pdb_file.geometry_restraints_manager()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
sites_cart = pdb_hierarchy.atoms().extract_xyz()
proxies = reference.add_coordinate_restraints(sites_cart=sites_cart)
assert proxies.size() == 29, "expected 29, got %d" % proxies.size()
import boost.python
ext = boost.python.import_ext("mmtbx_reference_coordinate_ext")
grads = flex.vec3_double(sites_cart.size(), (0.0,0.0,0.0))
residual = ext.reference_coordinate_residual_sum(
sites_cart=sites_cart,
proxies=proxies,
gradient_array=grads)
assert approx_equal(residual, 0.0)
#test selection
ca_selection = pdb_hierarchy.get_peptide_c_alpha_selection()
ca_sites_cart = sites_cart.select(ca_selection)
proxies = reference.add_coordinate_restraints(
sites_cart=ca_sites_cart,
selection=ca_selection)
assert proxies.size() == 3, "expected 3, got %d" % proxies.size()
tst_iselection = flex.size_t()
for atom in pdb_hierarchy.atoms():
if atom.name == " CA " or atom.name == " N ":
tst_iselection.append(atom.i_seq)
tst_sites_cart = sites_cart.select(tst_iselection)
proxies = reference.add_coordinate_restraints(
sites_cart=tst_sites_cart,
selection=tst_iselection)
assert proxies.size() == 6, "expected 6, got %d" % proxies.size()
#test remove
selection = flex.bool([False]*29)
proxies = proxies.proxy_remove(selection=selection)
assert proxies.size() == 6, "expected 6, got %d" % proxies.size()
proxies = proxies.proxy_remove(selection=ca_selection)
assert proxies.size() == 3, "expected 3, got %d" % proxies.size()
selection = flex.bool([True]*29)
proxies = proxies.proxy_remove(selection=selection)
assert proxies.size() == 0, "expected 0, got %d" % proxies.size()
def get_pdb_inputs(pdb_str):
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=server.server(),
ener_lib=server.ener_lib(),
raw_records=flex.std_string(pdb_str.splitlines()),
strict_conflict_handling=True,
force_symmetry=True,
log=None)
xrs = processed_pdb_file.xray_structure(show_summary=False)
geometry_restraints_manager = geometry_minimization.\
get_geometry_restraints_manager(processed_pdb_file, 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):
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = server.server(),
ener_lib = server.ener_lib(),
raw_records = flex.std_string(pdb_str.splitlines()),
strict_conflict_handling = True,
force_symmetry = True,
log = None)
xrs = processed_pdb_file.xray_structure(show_summary = False)
geometry_restraints_manager = geometry_minimization.\
get_geometry_restraints_manager(processed_pdb_file, 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_complete_dihedral_proxies(
pdb_hierarchy=None,
file_name=None,
raw_records=None,
mon_lib_srv=None,
ener_lib=None,
crystal_symmetry=None,
log=None):
#
# This function is called only for reference files, that were not processed
# yet. For the main file only get_dihedrals_and_phi_psi below is called.
#
assert [pdb_hierarchy,
file_name,
raw_records].count(None) == 2
from mmtbx.monomer_library import server, pdb_interpretation
import cStringIO
if log is None:
log = sys.stdout
if mon_lib_srv is None:
mon_lib_srv = server.server()
if ener_lib is None:
ener_lib = server.ener_lib()
if pdb_hierarchy is not None:
raw_records = pdb_hierarchy.as_pdb_string()
if raw_records is not None:
if (isinstance(raw_records, str)):
raw_records = flex.split_lines(raw_records)
work_params = pdb_interpretation.master_params.extract()
work_params.c_beta_restraints=False
work_params.automatic_linking.link_none=True
work_params.clash_guard.nonbonded_distance_threshold = None
processed_pdb_file_local = \
pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=work_params,
file_name=file_name,
raw_records=raw_records,
strict_conflict_handling=False,
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
log=cStringIO.StringIO(),
substitute_non_crystallographic_unit_cell_if_necessary=True)
return get_dihedrals_and_phi_psi(processed_pdb_file_local)
def exercise_1(mon_lib_srv, ener_lib):
pdb_in = simple_pdb()
params = pdb_interpretation.master_params.extract()
processed_pdb_file = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
grm = processed_pdb_file.geometry_restraints_manager()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
sites_cart = pdb_hierarchy.atoms().extract_xyz()
proxies = reference.add_coordinate_restraints(sites_cart=sites_cart)
assert proxies.size() == 29, "expected 29, got %d" % proxies.size()
import boost.python
ext = boost.python.import_ext("mmtbx_reference_coordinate_ext")
grads = flex.vec3_double(sites_cart.size(), (0.0, 0.0, 0.0))
residual = ext.reference_coordinate_residual_sum(sites_cart=sites_cart,
proxies=proxies,
gradient_array=grads)
assert approx_equal(residual, 0.0)
#test selection
ca_selection = pdb_hierarchy.get_peptide_c_alpha_selection()
ca_sites_cart = sites_cart.select(ca_selection)
proxies = reference.add_coordinate_restraints(sites_cart=ca_sites_cart,
selection=ca_selection)
assert proxies.size() == 3, "expected 3, got %d" % proxies.size()
tst_iselection = flex.size_t()
for atom in pdb_hierarchy.atoms():
if atom.name == " CA " or atom.name == " N ":
tst_iselection.append(atom.i_seq)
tst_sites_cart = sites_cart.select(tst_iselection)
proxies = reference.add_coordinate_restraints(sites_cart=tst_sites_cart,
selection=tst_iselection)
assert proxies.size() == 6, "expected 6, got %d" % proxies.size()
#test remove
selection = flex.bool([False] * 29)
proxies = proxies.proxy_remove(selection=selection)
assert proxies.size() == 6, "expected 6, got %d" % proxies.size()
proxies = proxies.proxy_remove(selection=ca_selection)
assert proxies.size() == 3, "expected 3, got %d" % proxies.size()
selection = flex.bool([True] * 29)
proxies = proxies.proxy_remove(selection=selection)
assert proxies.size() == 0, "expected 0, got %d" % proxies.size()
def __init__(self, pdb_file_name=None, raw_records=None):
# assert count(pdb_file_name, raw_records)==1
if pdb_file_name:
self.pdb_inp = iotbx.pdb.input(file_name=pdb_file_name)
else:
self.pdb_inp = iotbx.pdb.input(lines=raw_records,
source_info='raw_records')
self.hierarchy = self.pdb_inp.construct_hierarchy()
self.mon_lib_srv = server.server()
self.ener_lib = server.ener_lib()
self.processed_pdb = pdb_interpretation.process(
self.mon_lib_srv,
self.ener_lib,
file_name=pdb_file_name,
raw_records=raw_records)
self.geometry_restraints_manager = self.processed_pdb.geometry_restraints_manager(
)
self.atom_elements = {}
def get_mstats(pdb_raw):
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
xrs = pdb_in.input.xray_structure_simple()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs),
crystal_symmetry=xrs,
log=null_out())
pdb_in.hierarchy.atoms().reset_i_seq()
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ignore_hd=True)
return mstats
def get_complete_dihedral_proxies(pdb_hierarchy=None,
file_name=None,
raw_records=None,
mon_lib_srv=None,
ener_lib=None,
crystal_symmetry=None,
log=None):
#
# This function is called only for reference files, that were not processed
# yet. For the main file only get_dihedrals_and_phi_psi below is called.
# Still used for reference model torsion restraints
#
assert [pdb_hierarchy, file_name, raw_records].count(None) == 2
from mmtbx.monomer_library import server, pdb_interpretation
import cStringIO
if log is None:
log = sys.stdout
if mon_lib_srv is None:
mon_lib_srv = server.server()
if ener_lib is None:
ener_lib = server.ener_lib()
if pdb_hierarchy is not None:
raw_records = pdb_hierarchy.as_pdb_string()
if raw_records is not None:
if (isinstance(raw_records, str)):
raw_records = flex.split_lines(raw_records)
work_params = pdb_interpretation.master_params.extract()
work_params.c_beta_restraints = False
work_params.automatic_linking.link_none = True
work_params.clash_guard.nonbonded_distance_threshold = None
processed_pdb_file_local = \
pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=work_params,
file_name=file_name,
raw_records=raw_records,
strict_conflict_handling=False,
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
log=cStringIO.StringIO(),
substitute_non_crystallographic_unit_cell_if_necessary=True)
return get_dihedrals_and_phi_psi(processed_pdb_file_local)
def get_geometry_restraints_manager(pdb_filename,
#pdb_inp,
#pdb_hierarchy,
):
t0 = time.time()
from mmtbx.monomer_library import server
from mmtbx.monomer_library import pdb_interpretation
#lines = pdb_hierarchy.as_pdb_string(
# crystal_symmetry=pdb_inp.crystal_symmetry(),
# )
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb = pdb_interpretation.process(
mon_lib_srv,
ener_lib,
#raw_records=lines,
file_name=pdb_filename,
)
geometry_restraints_manager = processed_pdb.geometry_restraints_manager()
print 'time', time.time() - t0
return geometry_restraints_manager
def get_geometry_restraints_manager(pdb_filename,
#pdb_inp,
#pdb_hierarchy,
):
t0=time.time()
from mmtbx.monomer_library import server
from mmtbx.monomer_library import pdb_interpretation
#lines = pdb_hierarchy.as_pdb_string(
# crystal_symmetry=pdb_inp.crystal_symmetry(),
# )
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb = pdb_interpretation.process(
mon_lib_srv,
ener_lib,
#raw_records=lines,
file_name=pdb_filename,
)
geometry_restraints_manager = processed_pdb.geometry_restraints_manager()
print 'time',time.time()-t0
return geometry_restraints_manager
def exercise_other(mon_lib_srv, ener_lib):
file_name = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/3mku.pdb", test=os.path.isfile)
if (file_name is None):
print "Skipping test."
return
params = pdb_interpretation.master_params.fetch().extract()
params.peptide_link.ramachandran_restraints = True
processed_pdb_file = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
params2 = ramachandran.refine_opt_params.fetch().extract()
params2.exclude_secondary_structure = True
ramachandran.process_refinement_settings(
params=params2,
pdb_hierarchy=pdb_hierarchy,
secondary_structure_manager=ss_mgr,
d_min=2.9,
log=StringIO())
def run_validation(self) :
# get required elements to run:
# - pdb_hierarchy and geometry
pdb_in = iotbx.pdb.input(file_name=self.pdb_file)
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
pdb_inp=pdb_in,
substitute_non_crystallographic_unit_cell_if_necessary=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
geometry = processed_pdb_file.geometry_restraints_manager()
# - params
import mmtbx.command_line.rna_validate
params = mmtbx.command_line.rna_validate.get_master_phil().extract()
# run rna_validation
self.result = rna_validation(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry,
params=params,
outliers_only=False)
def __init__(self,
pdb_hierarchy,
geometry_restraints_manager=None,
params=None,
outliers_only=True):
if (geometry_restraints_manager is None):
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
pdb_inp=pdb_hierarchy.as_pdb_input(),
substitute_non_crystallographic_unit_cell_if_necessary=True)
geometry_restraints_manager = \
processed_pdb_file.geometry_restraints_manager()
pdb_hierarchy = \
processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_atoms = pdb_hierarchy.atoms()
self.bonds = rna_bonds(
pdb_hierarchy=pdb_hierarchy,
pdb_atoms=pdb_atoms,
geometry_restraints_manager=geometry_restraints_manager,
outliers_only=outliers_only)
self.angles = rna_angles(
pdb_hierarchy=pdb_hierarchy,
pdb_atoms=pdb_atoms,
geometry_restraints_manager=geometry_restraints_manager,
outliers_only=outliers_only)
self.puckers = rna_puckers(pdb_hierarchy=pdb_hierarchy,
params=getattr(params,
"rna_sugar_pucker_analysis",
None),
outliers_only=outliers_only)
self.suites = rna_suites(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry_restraints_manager,
outliers_only=outliers_only)
def exercise_2 () :
pdb_raw = """\
ATOM 6407 N GLY A 388 -0.783 9.368 -16.436 1.00 51.96 N
ATOM 6408 CA GLY A 388 -0.227 9.888 -15.197 1.00 54.04 C
ATOM 6409 C GLY A 388 -0.637 11.320 -14.897 1.00 55.86 C
ATOM 6410 O GLY A 388 -1.728 11.738 -15.347 1.00 56.70 O
ATOM 6411 OXT GLY A 388 0.129 12.024 -14.203 1.00 56.98 O
ATOM 6412 D GLY A 388 -0.460 9.727 -17.309 1.00 51.44 D
ATOM 6413 HA2 GLY A 388 -0.561 9.258 -14.385 1.00 54.07 H
ATOM 6414 HA3 GLY A 388 0.843 9.835 -15.243 1.00 54.13 H
TER 6415 GLY A 388
HETATM 6416 D D8U A 401 -12.236 -13.695 -42.992 1.00 15.23 D
HETATM 6417 O DOD A1001 -4.151 -5.107 -38.592 1.00 13.40 O
HETATM 6418 D1 DOD A1001 -4.760 -5.026 -39.326 1.00 15.45 D
HETATM 6419 D2 DOD A1001 -4.625 -4.741 -37.845 1.00 14.81 D
"""
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
xrs = pdb_in.input.xray_structure_simple()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs),
crystal_symmetry=xrs,
log=null_out())
pdb_in.hierarchy.atoms().reset_i_seq()
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
assert ("Ligands:" in out.getvalue())
assert ("B_iso: mean = 15.2 max = 15.2 min = 15.2" in out.getvalue())
def exercise_other (mon_lib_srv, ener_lib) :
file_name = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/3mku.pdb",
test=os.path.isfile)
if (file_name is None) :
print "Skipping test."
return
params = pdb_interpretation.master_params.fetch().extract()
params.peptide_link.ramachandran_restraints = True
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
params2 = ramachandran.refine_opt_params.fetch().extract()
params2.exclude_secondary_structure = True
ramachandran.process_refinement_settings(
params=params2,
pdb_hierarchy=pdb_hierarchy,
secondary_structure_manager=ss_mgr,
d_min=2.9,
log=StringIO())
def __init__(self,
pdb_hierarchy,
geometry_restraints_manager,
params,
outliers_only=True):
if (geometry_restraints_manager is None) :
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
pdb_inp=pdb_hierarchy.as_pdb_input(),
substitute_non_crystallographic_unit_cell_if_necessary=True)
geometry_restraints_manager = \
processed_pdb_file.geometry_restraints_manager()
pdb_hierarchy = \
processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_atoms = pdb_hierarchy.atoms()
self.bonds = rna_bonds(
pdb_hierarchy=pdb_hierarchy,
pdb_atoms=pdb_atoms,
geometry_restraints_manager=geometry_restraints_manager,
outliers_only=outliers_only)
self.angles = rna_angles(
pdb_hierarchy=pdb_hierarchy,
pdb_atoms=pdb_atoms,
geometry_restraints_manager=geometry_restraints_manager,
outliers_only=outliers_only)
self.puckers = rna_puckers(
pdb_hierarchy=pdb_hierarchy,
params=getattr(params, "rna_sugar_pucker_analysis", None),
outliers_only=outliers_only)
self.suites = rna_suites(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry_restraints_manager,
outliers_only=outliers_only)
def exercise_3(mon_lib_srv, ener_lib):
#test torsion restraints
for use_reference in ['True', 'False', 'top_out', 'None']:
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
raw_records = flex.std_string(pdb_str_2.splitlines()),
strict_conflict_handling = True,
force_symmetry = True,
log = None)
grm = processed_pdb_file.geometry_restraints_manager()
xrs2 = processed_pdb_file.xray_structure(show_summary = False)
awl2 = processed_pdb_file.all_chain_proxies.pdb_hierarchy.atoms_with_labels()
pdb2 = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_inp3 = iotbx.pdb.input(source_info=None, lines=pdb_str_3)
xrs3 = pdb_inp3.xray_structure_simple()
ph3 = pdb_inp3.construct_hierarchy()
ph3.atoms().reset_i_seq()
awl3 = ph3.atoms_with_labels()
sites_cart_reference = flex.vec3_double()
selection = flex.size_t()
min_selection = flex.size_t()
reference_names = ["N", "CA", "CB", "CG", "CD", "NE", "CZ", "NH1", "NH2"]
minimize_names = ["CG", "CD", "NE", "CZ", "NH1", "NH2"]
for a2,a3 in zip(tuple(awl2), tuple(awl3)):
assert a2.resname == a3.resname
assert a2.name == a3.name
assert a2.i_seq == a3.i_seq
if(a2.resname == "ARG" and a2.name.strip() in reference_names):
selection.append(a2.i_seq)
sites_cart_reference.append(a3.xyz)
if a2.name.strip() in minimize_names:
min_selection.append(a2.i_seq)
assert selection.size() == len(reference_names)
selection_bool = flex.bool(xrs2.scatterers().size(), min_selection)
if(use_reference == 'True'):
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pdb2,
sites_cart = sites_cart_reference,
selection = selection,
sigma = 2.5)
elif(use_reference == 'top_out'):
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pdb2,
sites_cart = sites_cart_reference,
selection = selection,
sigma = 2.5,
limit = 180.0,
top_out_potential=True)
elif(use_reference == 'None'):
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pdb2,
sites_cart = sites_cart_reference,
selection = selection,
sigma = 2.5)
grm.remove_chi_torsion_restraints_in_place(
selection = selection)
d1 = flex.mean(flex.sqrt((xrs2.sites_cart().select(min_selection) -
xrs3.sites_cart().select(min_selection)).dot()))
print "distance start (use_reference: %s): %6.4f"%(str(use_reference), d1)
assert d1>4.0
assert approx_equal(
flex.max(flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())), 0)
from cctbx import geometry_restraints
import mmtbx.refinement.geometry_minimization
import scitbx.lbfgs
grf = geometry_restraints.flags.flags(default=True)
grf.nonbonded = False
sites_cart = xrs2.sites_cart()
minimized = mmtbx.refinement.geometry_minimization.lbfgs(
sites_cart = sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager = grm,
sites_cart_selection = flex.bool(sites_cart.size(), min_selection),
geometry_restraints_flags = grf,
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=5000))
xrs2.set_sites_cart(sites_cart = sites_cart)
d2 = flex.mean(flex.sqrt((xrs2.sites_cart().select(min_selection) -
xrs3.sites_cart().select(min_selection)).dot()))
print "distance final (use_reference: %s): %6.4f"%(str(use_reference), d2)
if(use_reference in ['True', 'top_out']): assert d2<0.02, d2
else: assert d2>4.0, d2
assert approx_equal(
flex.max(flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())), 0)
#test torsion manipulation
grm.remove_chi_torsion_restraints_in_place()
grm.remove_chi_torsion_restraints_in_place()
sites_cart_reference = []
selections_reference = []
for model in pdb2.models():
for chain in model.chains():
for residue in chain.residues():
sites_cart_reference.append(residue.atoms().extract_xyz())
selections_reference.append(residue.atoms().extract_i_seq())
#one residue at a time (effectively chi angles only)
for sites_cart, selection in zip(sites_cart_reference, selections_reference):
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pdb2,
sites_cart = sites_cart,
selection = selection)
assert grm.get_n_chi_torsion_proixes() == 6
grm.remove_chi_torsion_restraints_in_place()
#all sites at once, chi angles only
sites_cart = xrs2.sites_cart()
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pdb2,
sites_cart = sites_cart,
selection = None,
chi_angles_only = True)
assert grm.get_n_chi_torsion_proixes() == 6
#all sites at once, all torsions
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pdb2,
sites_cart = sites_cart,
selection = None,
chi_angles_only = False)
# grm.get_chi_torsion_proxies().show_sorted(
# by_value='residual',
# sites_cart=sites_cart,
# site_labels=[atom.id_str() for atom in pdb2.atoms()])
assert grm.get_n_chi_torsion_proixes() == 12, grm.get_n_chi_torsion_proixes()
def run(args, command_name=libtbx.env.dispatcher_name):
if (len(args) == 0): args = ["--help"]
command_line = (option_parser(
usage='%s pdb_file "atom_selection" [...]' % command_name).option(
None,
"--write_pdb_file",
action="store",
type="string",
default=None,
help="write selected atoms to new PDB file",
metavar="FILE"
).option(
None,
"--cryst1_replacement_buffer_layer",
action="store",
type="float",
default=None,
help="replace CRYST1 with pseudo unit cell covering the selected"
" atoms plus a surrounding buffer layer",
metavar="WIDTH")).process(args=args, min_nargs=2)
co = command_line.options
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=command_line.args[0],
log=sys.stdout)
print
acp = processed_pdb_file.all_chain_proxies
hierarchy = acp.pdb_hierarchy
asc = hierarchy.atom_selection_cache()
sel = asc.selection(string="chain 'A' and resid 1 through 8 and icode ' '")
h1 = hierarchy.select(sel) # keep original hierarchy too
print h1.as_pdb_string()
selection_cache = acp.pdb_hierarchy.atom_selection_cache()
atoms = acp.pdb_atoms
all_bsel = flex.bool(atoms.size(), False)
for selection_string in command_line.args[1:]:
print selection_string
isel = acp.iselection(string=selection_string, cache=selection_cache)
all_bsel.set_selected(isel, True)
if (not co.write_pdb_file):
print " %d atom%s selected" % plural_s(isel.size())
for atom in atoms.select(isel):
print " %s" % atom.format_atom_record()
print
if (co.write_pdb_file):
print "Writing file:", show_string(co.write_pdb_file)
sel_hierarchy = acp.pdb_hierarchy.select(all_bsel)
if (co.cryst1_replacement_buffer_layer is None):
crystal_symmetry = acp.special_position_settings
else:
import cctbx.crystal
crystal_symmetry = cctbx.crystal.non_crystallographic_symmetry(
sites_cart=sel_hierarchy.atoms().extract_xyz(),
buffer_layer=co.cryst1_replacement_buffer_layer)
write_whole_pdb_file(file_name=co.write_pdb_file,
processed_pdb_file=processed_pdb_file,
pdb_hierarchy=sel_hierarchy,
crystal_symmetry=crystal_symmetry)
print
def exercise_2(mon_lib_srv, ener_lib):
for use_reference in [True, False, None]:
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
raw_records = flex.std_string(pdb_str_2.splitlines()),
strict_conflict_handling = True,
force_symmetry = True,
log = None)
grm = processed_pdb_file.geometry_restraints_manager()
xrs2 = processed_pdb_file.xray_structure(show_summary = False)
awl2 = processed_pdb_file.all_chain_proxies.pdb_hierarchy.atoms_with_labels()
pdb_inp3 = iotbx.pdb.input(source_info=None, lines=pdb_str_3)
xrs3 = pdb_inp3.xray_structure_simple()
ph3 = pdb_inp3.construct_hierarchy()
ph3.atoms().reset_i_seq()
awl3 = ph3.atoms_with_labels()
sites_cart_reference = flex.vec3_double()
selection = flex.size_t()
reference_names = ["CG", "CD", "NE", "CZ", "NH1", "NH2"]
for a2,a3 in zip(tuple(awl2), tuple(awl3)):
assert a2.resname == a3.resname
assert a2.name == a3.name
assert a2.i_seq == a3.i_seq
if(a2.resname == "ARG" and a2.name.strip() in reference_names):
selection.append(a2.i_seq)
sites_cart_reference.append(a3.xyz)
assert selection.size() == len(reference_names)
selection_bool = flex.bool(xrs2.scatterers().size(), selection)
if(use_reference):
grm.adopt_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = sites_cart_reference,
selection = selection,
sigma = 0.01))
elif(use_reference is None):
grm.adopt_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = sites_cart_reference,
selection = selection,
sigma = 0.01))
grm.remove_reference_coordinate_restraints_in_place(
selection = selection)
d1 = flex.mean(flex.sqrt((xrs2.sites_cart().select(selection) -
xrs3.sites_cart().select(selection)).dot()))
print "distance start (use_reference: %s): %6.4f"%(str(use_reference), d1)
assert d1>4.0
assert approx_equal(
flex.max(flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())), 0)
from cctbx import geometry_restraints
import mmtbx.refinement.geometry_minimization
import scitbx.lbfgs
grf = geometry_restraints.flags.flags(default=True)
sites_cart = xrs2.sites_cart()
minimized = mmtbx.refinement.geometry_minimization.lbfgs(
sites_cart = sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager = grm,
sites_cart_selection = flex.bool(sites_cart.size(), selection),
geometry_restraints_flags = grf,
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=5000))
xrs2.set_sites_cart(sites_cart = sites_cart)
d2 = flex.mean(flex.sqrt((xrs2.sites_cart().select(selection) -
xrs3.sites_cart().select(selection)).dot()))
print "distance final (use_reference: %s): %6.4f"%(str(use_reference), d2)
if(use_reference): assert d2<0.005, "failed: %f<0.05" % d2
else: assert d2>4.0, d2
assert approx_equal(
flex.max(flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())), 0)
def morph_models (params, out=None, debug=False) :
assert len(params.morph.pdb_file) > 1
assert (len(params.morph.frames) == (len(params.morph.pdb_file) - 1))
if (out is None) : out = sys.stdout
from mmtbx.monomer_library import pdb_interpretation, server
from iotbx import file_reader
pdb_hierarchies = []
for pdb_file in params.morph.pdb_file :
pdb_in = file_reader.any_file(pdb_file, force_type="pdb")
pdb_in.check_file_type("pdb")
hierarchy = pdb_in.file_object.hierarchy
pdb_hierarchies.append(hierarchy)
new_pdb = homogenize_structures(
pdb_hierarchies=pdb_hierarchies,
delete_waters=params.morph.delete_waters,
debug=debug)
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
for cif_file in params.morph.cif_file :
print "Loading CIF file %s" % cif_file
cif_object = server.read_cif(file_name=cif_file)
mon_lib_serv.process_cif_object(cif_object=cif_object, file_name=cif_file)
ener_lib.process_cif_object(cif_object=cif_object, file_name=cif_file)
if (params.morph.minimization.interpolate_dihedrals) :
params.pdb_interpretation.peptide_link.discard_psi_phi = False
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params.pdb_interpretation,
pdb_inp=new_pdb[0],
substitute_non_crystallographic_unit_cell_if_necessary=True)
all_chain_proxies = processed_pdb_file.all_chain_proxies
static_coords = [ all_chain_proxies.pdb_hierarchy.atoms().extract_xyz() ]
for pdb_inp in new_pdb[1:] :
sites = pdb_inp.atoms().extract_xyz()
static_coords.append(sites)
if (params.morph.fitting.align_atoms is not None) :
print >> out, "Superposing on initial structure..."
selection_cache = all_chain_proxies.pdb_hierarchy.atom_selection_cache()
selection = selection_cache.selection(params.morph.fitting.align_atoms)
if (selection.count(True) == 0) :
raise Sorry("No atoms in alignment selection!")
i_ref = params.morph.fitting.reference_structure
sites_fixed = static_coords[i_ref]
j = 0
while (j < len(static_coords)) :
if (j != i_ref) :
sites_moving = static_coords[j]
assert (len(sites_moving) == len(sites_fixed) > 0)
if (params.morph.fitting.sieve_fit) :
from scitbx.math import superpose
lsq_fit = superpose.sieve_fit(
sites_fixed=sites_fixed,
sites_moving=sites_moving,
selection=selection)
sites_moving_new = lsq_fit.r.elems * sites_moving + lsq_fit.t.elems
else :
sites_moving_new = fit_sites(
sites_fixed=sites_fixed,
sites_moving=sites_moving,
selection=selection)
assert (sites_moving_new.size() == sites_moving.size())
static_coords[j] = sites_moving_new
j += 1
print >> out, "Ready to morph"
morphs = []
restraints_manager = processed_pdb_file.geometry_restraints_manager()
for i in range(len(params.morph.pdb_file) - 1) :
morph = adiabatic_mapping(
pdb_hierarchy=all_chain_proxies.pdb_hierarchy,
restraints_manager=restraints_manager,
start_coords = static_coords[i],
end_coords = static_coords[i+1],
params = params.morph.minimization,
nsteps = params.morph.frames[i],
out=out)
morphs.append(morph)
serial = 1
if (params.morph.output_directory is not None) :
output_base = os.path.join(params.morph.output_directory,
params.morph.output_prefix)
else :
output_base = params.morph.output_prefix
for i, morph in enumerate(morphs) :
serial = morph.write_pdb_files(
output_base=output_base,
serial=serial,
serial_format=params.morph.serial_format,
pause=params.morph.pause,
pause_at_end=(i == (len(morphs) - 1)),
log=out)
f = open("%s.pml" % output_base, "w")
for i in range(1, serial) :
format_base = "%s_%s" % (output_base, params.morph.serial_format)
print >> f, "load %s.pdb, morph" % (format_base % i)
f.close()
print >> out, "PyMOL script is %s.pml" % output_base
def exercise_3(mon_lib_srv, ener_lib):
#test torsion restraints
for use_reference in ['True', 'False', 'top_out', 'None']:
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=flex.std_string(pdb_str_2.splitlines()),
strict_conflict_handling=True,
force_symmetry=True,
log=None)
grm = processed_pdb_file.geometry_restraints_manager()
xrs2 = processed_pdb_file.xray_structure(show_summary=False)
awl2 = processed_pdb_file.all_chain_proxies.pdb_hierarchy.atoms_with_labels(
)
pdb2 = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_inp3 = iotbx.pdb.input(source_info=None, lines=pdb_str_3)
xrs3 = pdb_inp3.xray_structure_simple()
ph3 = pdb_inp3.construct_hierarchy()
ph3.atoms().reset_i_seq()
awl3 = ph3.atoms_with_labels()
sites_cart_reference = flex.vec3_double()
selection = flex.size_t()
min_selection = flex.size_t()
reference_names = [
"N", "CA", "CB", "CG", "CD", "NE", "CZ", "NH1", "NH2"
]
minimize_names = ["CG", "CD", "NE", "CZ", "NH1", "NH2"]
for a2, a3 in zip(tuple(awl2), tuple(awl3)):
assert a2.resname == a3.resname
assert a2.name == a3.name
assert a2.i_seq == a3.i_seq
if (a2.resname == "ARG" and a2.name.strip() in reference_names):
selection.append(a2.i_seq)
sites_cart_reference.append(a3.xyz)
if a2.name.strip() in minimize_names:
min_selection.append(a2.i_seq)
assert selection.size() == len(reference_names)
selection_bool = flex.bool(xrs2.scatterers().size(), min_selection)
if (use_reference == 'True'):
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy=pdb2,
sites_cart=sites_cart_reference,
selection=selection,
sigma=2.5)
elif (use_reference == 'top_out'):
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy=pdb2,
sites_cart=sites_cart_reference,
selection=selection,
sigma=2.5,
limit=180.0,
top_out_potential=True)
elif (use_reference == 'None'):
grm.add_chi_torsion_restraints_in_place(
pdb_hierarchy=pdb2,
sites_cart=sites_cart_reference,
selection=selection,
sigma=2.5)
grm.remove_chi_torsion_restraints_in_place(selection=selection)
d1 = flex.mean(
flex.sqrt((xrs2.sites_cart().select(min_selection) -
xrs3.sites_cart().select(min_selection)).dot()))
print "distance start (use_reference: %s): %6.4f" % (
str(use_reference), d1)
assert d1 > 4.0
assert approx_equal(
flex.max(
flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())),
0)
from cctbx import geometry_restraints
import mmtbx.refinement.geometry_minimization
import scitbx.lbfgs
grf = geometry_restraints.flags.flags(default=True)
grf.nonbonded = False
sites_cart = xrs2.sites_cart()
minimized = mmtbx.refinement.geometry_minimization.lbfgs(
sites_cart=sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
sites_cart_selection=flex.bool(sites_cart.size(), min_selection),
geometry_restraints_flags=grf,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=5000))
xrs2.set_sites_cart(sites_cart=sites_cart)
d2 = flex.mean(
flex.sqrt((xrs2.sites_cart().select(min_selection) -
xrs3.sites_cart().select(min_selection)).dot()))
print "distance final (use_reference: %s): %6.4f" % (
str(use_reference), d2)
if (use_reference in ['True', 'top_out']): assert d2 < 0.02, d2
else: assert d2 > 4.0, d2
assert approx_equal(
flex.max(
flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())),
0)
#test torsion manipulation
grm.remove_chi_torsion_restraints_in_place()
grm.remove_chi_torsion_restraints_in_place()
sites_cart_reference = []
selections_reference = []
for model in pdb2.models():
for chain in model.chains():
for residue in chain.residues():
sites_cart_reference.append(residue.atoms().extract_xyz())
selections_reference.append(residue.atoms().extract_i_seq())
#one residue at a time (effectively chi angles only)
for sites_cart, selection in zip(sites_cart_reference,
selections_reference):
grm.add_chi_torsion_restraints_in_place(pdb_hierarchy=pdb2,
sites_cart=sites_cart,
selection=selection)
assert grm.get_n_chi_torsion_proixes() == 6
grm.remove_chi_torsion_restraints_in_place()
#all sites at once, chi angles only
sites_cart = xrs2.sites_cart()
grm.add_chi_torsion_restraints_in_place(pdb_hierarchy=pdb2,
sites_cart=sites_cart,
selection=None,
chi_angles_only=True)
assert grm.get_n_chi_torsion_proixes() == 6
#all sites at once, all torsions
grm.add_chi_torsion_restraints_in_place(pdb_hierarchy=pdb2,
sites_cart=sites_cart,
selection=None,
chi_angles_only=False)
# grm.get_chi_torsion_proxies().show_sorted(
# by_value='residual',
# sites_cart=sites_cart,
# site_labels=[atom.id_str() for atom in pdb2.atoms()])
assert grm.get_n_chi_torsion_proixes(
) == 12, grm.get_n_chi_torsion_proixes()
def exercise_acs(mon_lib_srv, ener_lib):
ac_pdb1 = """\
CRYST1 72.072 33.173 34.033 90.00 90.00 90.00 P 1
SCALE1 0.013875 0.000000 0.000000 0.00000
SCALE2 0.000000 0.030145 0.000000 0.00000
SCALE3 0.000000 0.000000 0.029383 0.00000
ATOM 519 N HIS B 1 5.000 8.515 18.112 1.00 20.00 N
ATOM 520 CA HIS B 1 5.999 8.713 17.074 1.00 20.00 C
ATOM 521 C HIS B 1 7.157 9.627 17.517 1.00 20.00 C
ATOM 522 O HIS B 1 8.302 9.165 17.614 1.00 20.00 O
ATOM 523 CB AHIS B 1 5.315 9.226 15.797 0.50 20.00 C
ATOM 523 CB BHIS B 1 5.315 9.226 15.797 0.50 20.00 C
ATOM 524 HA HIS B 1 6.434 7.742 16.835 1.00 20.00 H
ATOM 525 N TRP B 2 6.845 10.900 17.805 1.00 20.00 N
ATOM 526 CA TRP B 2 7.853 11.954 18.083 1.00 20.00 C
ATOM 527 C TRP B 2 8.071 12.262 19.565 1.00 20.00 C
ATOM 528 O TRP B 2 8.355 13.406 19.941 1.00 20.00 O
ATOM 529 CB TRP B 2 7.516 13.257 17.336 1.00 20.00 C
ATOM 530 HA TRP B 2 8.809 11.606 17.692 1.00 20.00 H
ATOM 531 H ATRP B 2 5.886 11.243 17.855 0.50 20.00 H
ATOM 532 D BTRP B 2 5.886 11.243 17.855 0.50 20.00 D
ATOM 533 N GLU B 3 7.910 11.239 20.396 1.00 20.00 N
ATOM 534 CA GLU B 3 8.310 11.284 21.798 1.00 20.00 C
ATOM 535 C GLU B 3 9.344 10.190 21.979 1.00 20.00 C
ATOM 536 O GLU B 3 10.197 10.267 22.867 1.00 20.00 O
ATOM 537 CB GLU B 3 7.115 11.041 22.731 1.00 20.00 C
ATOM 538 HA GLU B 3 8.761 12.248 22.034 1.00 20.00 H
ATOM 539 H AGLU B 3 7.474 10.360 20.122 0.50 20.00 H
ATOM 540 D BGLU B 3 7.474 10.360 20.122 0.50 20.00 D """
ac_pdb2 = """\
CRYST1 72.072 33.173 34.033 90.00 90.00 90.00 P 1
SCALE1 0.013875 0.000000 0.000000 0.00000
SCALE2 0.000000 0.030145 0.000000 0.00000
SCALE3 0.000000 0.000000 0.029383 0.00000
ATOM 519 N HIS B 1 5.000 8.515 18.112 1.00 20.00 N
ATOM 520 CA HIS B 1 5.999 8.713 17.074 1.00 20.00 C
ATOM 521 C HIS B 1 7.157 9.627 17.517 1.00 20.00 C
ATOM 522 O HIS B 1 8.302 9.165 17.614 1.00 20.00 O
ATOM 523 CB HIS B 1 5.315 9.226 15.797 1.00 20.00 C
ATOM 524 HA HIS B 1 6.434 7.742 16.835 1.00 20.00 H
ATOM 525 N TRP B 2 6.845 10.900 17.805 1.00 20.00 N
ATOM 526 CA ATRP B 2 7.853 11.954 18.083 0.50 20.00 C
ATOM 556 CA BTRP B 2 7.453 11.454 18.083 0.50 20.00 C
ATOM 527 C TRP B 2 8.071 12.262 19.565 1.00 20.00 C
ATOM 528 O TRP B 2 8.355 13.406 19.941 1.00 20.00 O
ATOM 529 CB TRP B 2 7.516 13.257 17.336 1.00 20.00 C
ATOM 530 HA TRP B 2 8.809 11.606 17.692 1.00 20.00 H
ATOM 531 H ATRP B 2 5.886 11.243 17.855 0.50 20.00 H
ATOM 532 D BTRP B 2 5.886 11.243 17.855 0.50 20.00 D
ATOM 533 N GLU B 3 7.910 11.239 20.396 1.00 20.00 N
ATOM 534 CA GLU B 3 8.310 11.284 21.798 1.00 20.00 C
ATOM 535 C GLU B 3 9.344 10.190 21.979 1.00 20.00 C
ATOM 536 O GLU B 3 10.197 10.267 22.867 1.00 20.00 O
ATOM 537 CB GLU B 3 7.115 11.041 22.731 1.00 20.00 C
ATOM 538 HA GLU B 3 8.761 12.248 22.034 1.00 20.00 H
ATOM 539 H AGLU B 3 7.474 10.360 20.122 0.50 20.00 H
ATOM 540 D BGLU B 3 7.474 10.360 20.122 0.50 20.00 D """
no_ac_pdb = """\
CRYST1 72.072 33.173 34.033 90.00 90.00 90.00 P 1
SCALE1 0.013875 0.000000 0.000000 0.00000
SCALE2 0.000000 0.030145 0.000000 0.00000
SCALE3 0.000000 0.000000 0.029383 0.00000
ATOM 519 N HIS B 1 5.000 8.515 18.112 1.00 20.00 N
ATOM 520 CA HIS B 1 5.999 8.713 17.074 1.00 20.00 C
ATOM 521 C HIS B 1 7.157 9.627 17.517 1.00 20.00 C
ATOM 522 O HIS B 1 8.302 9.165 17.614 1.00 20.00 O
ATOM 523 CB HIS B 1 5.315 9.226 15.797 1.00 20.00 C
ATOM 525 N TRP B 2 6.845 10.900 17.805 1.00 20.00 N
ATOM 556 CA TRP B 2 7.453 11.454 18.083 0.50 20.00 C
ATOM 527 C TRP B 2 8.071 12.262 19.565 1.00 20.00 C
ATOM 528 O TRP B 2 8.355 13.406 19.941 1.00 20.00 O
ATOM 529 CB TRP B 2 7.516 13.257 17.336 1.00 20.00 C
ATOM 533 N GLU B 3 7.910 11.239 20.396 1.00 20.00 N
ATOM 534 CA GLU B 3 8.310 11.284 21.798 1.00 20.00 C
ATOM 535 C GLU B 3 9.344 10.190 21.979 1.00 20.00 C
ATOM 536 O GLU B 3 10.197 10.267 22.867 1.00 20.00 O
ATOM 537 CB GLU B 3 7.115 11.041 22.731 1.00 20.00 C
"""
for correct_nprox, pdb_str in [
(1, ac_pdb1),
(2, ac_pdb2),
(1, no_ac_pdb),
]:
params = pdb_interpretation.master_params.fetch().extract()
params.peptide_link.ramachandran_restraints = True
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
raw_records=pdb_str.split("\n"),
log=StringIO())
grm = processed_pdb_file.geometry_restraints_manager()
nprox = grm.ramachandran_manager.get_n_proxies()
assert nprox == correct_nprox, ""+\
"Want to get %d rama proxies, got %d" % (correct_nprox, nprox)
def run(args, command_name=libtbx.env.dispatcher_name):
if (len(args) == 0): args = ["--help"]
command_line = (option_parser(
usage='%s pdb_file "atom_selection" [...]' % command_name)
.option(None, "--write_pdb_file",
action="store",
type="string",
default=None,
help="write selected atoms to new PDB file",
metavar="FILE")
.option(None, "--cryst1_replacement_buffer_layer",
action="store",
type="float",
default=None,
help="replace CRYST1 with pseudo unit cell covering the selected"
" atoms plus a surrounding buffer layer",
metavar="WIDTH")
).process(args=args, min_nargs=2)
co = command_line.options
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=command_line.args[0],
log=sys.stdout)
print
acp = processed_pdb_file.all_chain_proxies
hierarchy=acp.pdb_hierarchy
asc=hierarchy.atom_selection_cache()
sel=asc.selection(string = "chain 'A' and resid 1 through 8 and icode ' '")
h1=hierarchy.select(sel) # keep original hierarchy too
print h1.as_pdb_string()
selection_cache = acp.pdb_hierarchy.atom_selection_cache()
atoms = acp.pdb_atoms
all_bsel = flex.bool(atoms.size(), False)
for selection_string in command_line.args[1:]:
print selection_string
isel = acp.iselection(string=selection_string, cache=selection_cache)
all_bsel.set_selected(isel, True)
if (not co.write_pdb_file):
print " %d atom%s selected" % plural_s(isel.size())
for atom in atoms.select(isel):
print " %s" % atom.format_atom_record()
print
if (co.write_pdb_file):
print "Writing file:", show_string(co.write_pdb_file)
sel_hierarchy = acp.pdb_hierarchy.select(all_bsel)
if (co.cryst1_replacement_buffer_layer is None):
crystal_symmetry = acp.special_position_settings
else:
import cctbx.crystal
crystal_symmetry = cctbx.crystal.non_crystallographic_symmetry(
sites_cart=sel_hierarchy.atoms().extract_xyz(),
buffer_layer=co.cryst1_replacement_buffer_layer)
write_whole_pdb_file(
file_name=co.write_pdb_file,
processed_pdb_file=processed_pdb_file,
pdb_hierarchy=sel_hierarchy,
crystal_symmetry=crystal_symmetry)
print
def run(args, pdb_interpretation_params=None):
if (len(args) == 0 or "--help" in args or "--h" in args or "-h" in args):
raise Usage(usage())
pdbID = None
master_phil = get_master_phil()
import iotbx.utils
input_objects = iotbx.utils.process_command_line_inputs(
args=args,
master_phil=master_phil,
input_types=("pdb", "cif"))
auto_cdl=True
for po in input_objects["phil"]:
if po.as_str().find(".cdl")>-1:
auto_cdl=False
break
work_phil = master_phil.fetch(sources=input_objects["phil"])
work_params = work_phil.extract()
if auto_cdl:
work_params.kinemage.pdb_interpretation.restraints_library.cdl = Auto
if work_params.kinemage.pdb == None:
assert len(input_objects["pdb"]) == 1
file_obj = input_objects["pdb"][0]
file_name = file_obj.file_name
else:
file_name = work_params.kinemage.pdb
if file_name and os.path.exists(file_name):
pdb_io = pdb.input(file_name)
pdbID = os.path.basename(pdb_io.source_info().split(' ')[1]).split('.')[0]
else :
raise Sorry("PDB file does not exist")
assert pdb_io is not None
cif_file = None
cif_object = None
if len(work_params.kinemage.cif) == 0:
if len(input_objects["cif"]) > 0:
cif_file = []
for cif in input_objects["cif"]:
cif_file.append(cif.file_name)
else:
cif_file = work_params.kinemage.cif
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
if cif_file != None:
for cif in cif_file:
try:
cif_object = monomer_library.server.read_cif(file_name=cif)
except Exception:
raise Sorry("Unknown file format: %s" % show_string(cif))
if cif_object != None:
for srv in [mon_lib_srv, ener_lib]:
srv.process_cif_object(cif_object=cif_object)
if pdb_interpretation_params is None:
#pdb_int_work_params = pdb_interpretation.master_params.extract()
pdb_int_work_params = work_params.kinemage.pdb_interpretation
else:
pdb_int_work_params = pdb_interpretation_params
pdb_int_work_params.clash_guard.nonbonded_distance_threshold = None
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
pdb_inp=pdb_io,
params=pdb_int_work_params,
substitute_non_crystallographic_unit_cell_if_necessary=True)
if work_params.kinemage.out_file is not None:
outfile = work_params.kinemage.out_file
else :
outfile = pdbID+'.kin'
outfile = make_multikin(f=outfile,
processed_pdb_file=processed_pdb_file,
pdbID=pdbID,
keep_hydrogens=work_params.kinemage.keep_hydrogens)
return outfile
def run(file_name):
print "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
processed = monomer_library.pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
file_name = file_name,
keep_monomer_mappings = True,
log = sys.stdout).all_chain_proxies
total_missing = 0.0
still_missing = 0.0
still_missing_h = []
atom_number = 0
file_name_ = os.path.basename(file_name)+"_h"
file = open(file_name_,"w")
for monomer_mapping in processed.all_monomer_mappings:
atom_number = write_atoms(monomer_mapping,
atom_number,
file)
bond_list = monomer_mapping.monomer.bond_list
angle_list = monomer_mapping.monomer.angle_list
missing_h = monomer_mapping.missing_hydrogen_atoms.keys()
residue_name = monomer_mapping.monomer.chem_comp.three_letter_code
print
print "Residue name: ",
print monomer_mapping.residue_name, monomer_mapping.monomer.chem_comp.three_letter_code
print "Missing hydrogen atoms: ", missing_h
print
total_missing += len(missing_h)
unknown_h = []
n_missed = len(missing_h)-1
while n_missed > 0:
n_missed -= 1
h = missing_h[0]
for bl in bond_list:
if(h == bl.atom_id_1 or h == bl.atom_id_2):
for atom in (bl.atom_id_1,bl.atom_id_2):
if(h != atom): target_atom_name = atom
for atom_name,atom in monomer_mapping.expected_atoms.items():
if(atom_name == target_atom_name):
target_site = atom.xyz
bond_dist = bl.value_dist
format="missing %4s: bond: %4s %4s bond distance = %5.3f"
print format % (h, bl.atom_id_1, bl.atom_id_2, bl.value_dist)
angles = []
for al in angle_list:
if(h == al.atom_id_1 or h == al.atom_id_2 or h == al.atom_id_3):
format=" %4s: angle: %4s %4s %4s = %5.3f"
print format % (h, al.atom_id_1,al.atom_id_2,al.atom_id_3,al.value_angle)
angles.append([al.value_angle,al.atom_id_1,al.atom_id_2,al.atom_id_3])
bonded_to_target_site = []
#for bl in bond_list:
# if(target_atom_name in (bl.atom_id_1,bl.atom_id_2)):
# for atom in (bl.atom_id_1,bl.atom_id_2):
# if(atom != target_atom_name):
# bonded_to_target_site.append(atom)
#print "target_site, bonded_to_target_site ", target_atom_name, bonded_to_target_site
### ring hydrogens: TYR,PHE,HIS,TRP
if(residue_name in ["PHE","TYR","HIS","TRP","ARG"]):
ring_h = {
"HE1":{"PHE":["CE1","CD1","CZ"],
"TYR":["CE1","CD1","CZ"],
"HIS":["CE1","ND1","NE2"],
"TRP":["NE1","CD1","CE2"]},
"HE2":{"PHE":["CE2","CD2","CZ"],
"TYR":["CE2","CD2","CZ"],
"HIS":["NE2","CE1","CD2"]},
"HE3":{"TRP":["CE3","CZ3","CD2"]},
"HD1":{"PHE":["CD1","CE1","CG"],
"TYR":["CD1","CE1","CG"],
"HIS":["ND1","CG","CE1"],
"TRP":["CD1","CG","NE1"]},
"HD2":{"PHE":["CD2","CE2","CG"],
"TYR":["CD2","CE2","CG"],
"HIS":["CD2","NE2","CG"]},
"HH2":{"TRP":["CH2","CZ2","CZ3"]},
"HZ" :{"PHE":["CZ","CE1","CE2"]},
"HZ2":{"TRP":["CZ2","CE2","CH2"]},
"HZ3":{"TRP":["CZ3","CH2","CE3"]},
"HE" :{"ARG":["NE","CZ","CD"]}
}
if(h in ring_h.keys()):
if(residue_name in ring_h[h].keys()):
targets = ring_h[h][residue_name]
print "Building:", h, " ..."
site_0 = None
site_1 = None
site_2 = None
for atom_name,atom in monomer_mapping.expected_atoms.items():
if(atom_name == targets[0]):
site_0 = atom.xyz
if(atom_name == targets[1]):
site_1 = atom.xyz
if(atom_name == targets[2]):
site_2 = atom.xyz
alpha = angles[0][0]
beta = angles[1][0]
assert site_0 is not None and site_1 is not None and site_2 is not None
xyz = add_ring_h(site_0,site_1,site_2,bond_dist,alpha,beta)
atom_number = write_atoms(monomer_mapping,
atom_number,
file,
new_atom_name = h,
new_atom_coordinates = xyz)
missing_h.remove(h)
### CA hydrogen(s): HA or/and HA1 or/and HA2
if(h == "HA" or h == "HA1" or h == "HA2"):
build_one = False
build_two = False
if("HA" in missing_h):
build_one = True
if("HA1" in missing_h and "HA2" in missing_h):
build_two = True
if(("HA1" in missing_h or "HA2" in missing_h) and build_two == False):
build_one = True
assert build_one == True and build_two == False or \
build_one == False and build_two == True
if(build_two == True):
print "Building: HA1 and HA2"
site_0 = None
site_1 = None
site_2 = None
for atom_name,atom in monomer_mapping.expected_atoms.items():
if(atom_name == "CA"):
site_0 = atom.xyz
if(atom_name == "C"):
site_1 = atom.xyz
if(atom_name == "N"):
site_2 = atom.xyz
if(site_0 is not None and site_1 is not None and site_2 is not None):
for angle in angles:
if("C" in angle and "CA" in angle): alpha = angle[0]
if("N" in angle and "CA" in angle): beta = angle[0]
xyz = add_ca_ha1_and_ha2(site_0,site_1,site_2,bond_dist,alpha,beta)
atom_number = write_atoms(monomer_mapping,
atom_number,
file,
new_atom_name = "HA1",
new_atom_coordinates = xyz[0])
atom_number = write_atoms(monomer_mapping,
atom_number,
file,
new_atom_name = "HA2",
new_atom_coordinates = xyz[1])
missing_h.remove("HA1")
missing_h.remove("HA2")
if(build_one == True):
print "Building: ", h
site_0 = None
site_1 = None
site_2 = None
site_3 = None
for atom_name,atom in monomer_mapping.expected_atoms.items():
if(atom_name == "CA"):
site_0 = atom.xyz
if(atom_name == "C"):
site_1 = atom.xyz
if(atom_name == "N"):
site_2 = atom.xyz
if(atom_name == "CB" or atom_name == "HA1" or atom_name == "HA2"):
site_3 = atom.xyz
cb_or_ha1_or_ha2 = atom_name
if(site_0 is not None and site_1 is not None and site_2 is not None):
for angle in angles:
if("C" in angle and "CA" in angle): alpha = angle[0]
if("N" in angle and "CA" in angle): beta = angle[0]
if("CA" in angle and cb_or_ha1_or_ha2 in angle): gamma = angle[0]
xyz = add_ca_ha1_or_ha2(site_0,site_1,site_2,site_3,bond_dist,alpha,beta,gamma)
atom_number = write_atoms(monomer_mapping,
atom_number,
file,
new_atom_name = h,
new_atom_coordinates = xyz)
missing_h.remove(h)
### CB hydrogen(s): HB1 or/and HB2 and similar
cb_like_h = {
"HB1":[["CB","CA","CG","HB2"],["CB","CA","OG","HB2"],["CB","CA","SG","HB2"]],
"HB2":[["CB","CA","CG","HB1"],["CB","CA","OG","HB1"],["CB","CA","SG","HB1"]],
"HG1":[["CG","CB","CD","HG2"],],
"HG2":[["CG","CB","CD","HG1"],],
"HD1":[["CD","CG","NE","HD2"],["CD","CG","CE","HD2"]],
"HD2":[["CD","CG","NE","HD1"],["CD","CG","CE","HD1"]],
"HE1":[["CE","CD","NZ","HE2"],],
"HE2":[["CE","CD","NZ","HE1"],],
"HG" :[["CG","CB","CD1","CD2"],],
"HB" :[["CB","CG2","CA","CG1"],["CB","CG2","CA","OG1"]]
}
if(h in cb_like_h.keys()):
if(h in missing_h):
targets_ = cb_like_h[h]
for targets in targets_:
build_one = False
build_two = False
if(h in missing_h and targets[3] in missing_h):
build_two = True
if((h in missing_h or targets[3] in missing_h) and build_two == False):
build_one = True
if(build_one == True and build_two == False or \
build_one == False and build_two == True):
if(build_two == True):
print "Building: ", h," and ",targets[3]
site_0 = None
site_1 = None
site_2 = None
for atom_name,atom in monomer_mapping.expected_atoms.items():
if(atom_name == targets[0]):
site_0 = atom.xyz
if(atom_name == targets[1]):
site_1 = atom.xyz
if(atom_name == targets[2]):
site_2 = atom.xyz
if(site_0 is not None and site_1 is not None and site_2 is not None):
for angle in angles:
if(targets[1] in angle and targets[0] in angle): alpha = angle[0]
if(targets[0] in angle and targets[2] in angle): beta = angle[0]
xyz = add_ca_ha1_and_ha2(site_0,site_1,site_2,bond_dist,alpha,beta)
atom_number = write_atoms(monomer_mapping,
atom_number,
file,
new_atom_name = h,
new_atom_coordinates = xyz[0])
atom_number = write_atoms(monomer_mapping,
atom_number,
file,
new_atom_name = targets[3],
new_atom_coordinates = xyz[1])
missing_h.remove(h)
missing_h.remove(targets[3])
if(build_one == True):
print "Building: ", h
site_0 = None
site_1 = None
site_2 = None
site_3 = None
alpha = None
beta = None
gamma = None
for atom_name,atom in monomer_mapping.expected_atoms.items():
if(atom_name == targets[0]):
site_0 = atom.xyz
if(atom_name == targets[1]):
site_1 = atom.xyz
if(atom_name == targets[2]):
site_2 = atom.xyz
if(atom_name == h or atom_name == targets[3]):
site_3 = atom.xyz
cb_or_ha1_or_ha2 = atom_name
if(site_0 is not None and site_1 is not None and site_2 is not None and site_3 is not None):
for angle in angles:
if(targets[1] in angle and targets[0] in angle): alpha = angle[0]
if(targets[0] in angle and targets[2] in angle): beta = angle[0]
if(targets[0] in angle and cb_or_ha1_or_ha2 in angle): gamma = angle[0]
if(alpha is not None and beta is not None and gamma is not None):
xyz = add_ca_ha1_or_ha2(site_0,site_1,site_2,site_3,bond_dist,alpha,beta,gamma)
atom_number = write_atoms(monomer_mapping,
atom_number,
file,
new_atom_name = h,
new_atom_coordinates = xyz)
missing_h.remove(h)
### HT1,HT2,HT3 like hydrogens; rotational optimization is necessary
hhh_like_h = {
"HB1" :[["CB","CA","HB2","HB3"],],
"HB2" :[["CB","CA","HB1","HB3"],],
"HB3" :[["CB","CA","HB1","HB2"],],
"HD11":[["CD1","CG","HD12","HD13"],["CD1","CG1","HD12","HD13"]],
"HD12":[["CD1","CG","HD11","HD13"],["CD1","CG1","HD11","HD13"]],
"HD13":[["CD1","CG","HD11","HD12"],["CD1","CG1","HD11","HD12"]],
"HD21":[["CD2","CG","HD22","HD23"],],
"HD22":[["CD2","CG","HD21","HD23"],],
"HD23":[["CD2","CG","HD21","HD22"],],
"HG21":[["CG2","CB","HG22","HG23"],],
"HG22":[["CG2","CB","HG21","HG23"],],
"HG23":[["CG2","CB","HG21","HG22"],],
"HG11":[["CG1","CB","HG12","HG13"],],
"HG12":[["CG1","CB","HG11","HG13"],],
"HG13":[["CG1","CB","HG11","HG12"],],
"HZ1" :[["NZ","CE","HZ2","HZ3"],],
"HZ2" :[["NZ","CE","HZ1","HZ3"],],
"HZ3" :[["NZ","CE","HZ1","HZ2"],]
}
hhh_residues = ["ALA","LEU","ILE","VAL","THR","LYS"]
if(h in hhh_like_h.keys() and residue_name in hhh_residues and h in missing_h):
targets = hhh_like_h[h]
for target in targets:
site_0 = None
site_1 = None
for atom_name,atom in monomer_mapping.expected_atoms.items():
if(atom_name == target[0]):
site_0 = atom.xyz
if(atom_name == target[1]):
site_1 = atom.xyz
alpha = angles[0][0]
beta = angles[2][0]
if(site_0 is not None and site_1 is not None):
print "Building:", h, " ..."
xyz = add_hhh(site_0,site_1,bond_dist,alpha,beta)
for atom_name, coordinates in zip((h,target[2],target[3]),(xyz[0],xyz[1][0],xyz[1][1])):
atom_number = write_atoms(monomer_mapping,
atom_number,
file,
new_atom_name = atom_name,
new_atom_coordinates = coordinates)
if(h in missing_h): missing_h.remove(h)
if(target[2] in missing_h): missing_h.remove(target[2])
if(target[3] in missing_h): missing_h.remove(target[3])
### add ARG-like NH's:
arg_like_h = {
"HH11":[["NH1","CZ","NH2","HH12",2],],
"HH12":[["NH1","CZ","NH2","HH11",2],],
"HH21":[["NH2","CZ","NH1","HH22",2],],
"HH22":[["NH2","CZ","NH1","HH21",2],],
"HG" :[["OG","CB","CA","HG",1],["SG","CB","CA","HG",1]] ,
"HH" :[["OH","CZ","CE1","HH",1],]
}
residue_names = ["ARG","SER","TYR","CYS"]
if(h in arg_like_h.keys() and residue_name in residue_names):
targets = arg_like_h[h]
for target in targets:
site_0 = None
site_1 = None
site_2 = None
for atom_name,atom in monomer_mapping.expected_atoms.items():
if(atom_name == target[0]):
site_0 = atom.xyz
if(atom_name == target[1]):
site_1 = atom.xyz
if(atom_name == target[2]):
site_2 = atom.xyz
alpha = angles[0][0]
if(site_0 is not None and site_1 is not None and site_2 is not None):
print "Building:", h, " ..."
xyz = add_arg_like_h(site_0,site_1,site_2,bond_dist,alpha,flag = target[4])
if(target[4] == 1):
atom_number = write_atoms(monomer_mapping,
atom_number,
file,
new_atom_name = h,
new_atom_coordinates = xyz)
if(target[4] == 2):
atom_number = write_atoms(monomer_mapping,
atom_number,
file,
new_atom_name = h,
new_atom_coordinates = xyz[0])
atom_number = write_atoms(monomer_mapping,
atom_number,
file,
new_atom_name = target[3],
new_atom_coordinates = xyz[1])
if(h in missing_h): missing_h.remove(h)
if(target[3] in missing_h): missing_h.remove(target[3])
### UNKNOWN H:
if(h in missing_h):
print "Unknown hydrogen type: ", h
missing_h.remove(h)
unknown_h.append(h)
n_missed = len(missing_h)
print
print "Still missing: ", residue_name,unknown_h
still_missing_h.append((residue_name,unknown_h))
still_missing += len(unknown_h)
print "Build ", int(total_missing - still_missing),
print " from ", int(total_missing), " % = ",
print (total_missing - still_missing)*100./total_missing
print
for item in still_missing_h:
print item
file.close()
file = open(file_name_,"r")
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
file_name = file_name_,
strict_conflict_handling = False,
crystal_symmetry = processed.pdb_inp.crystal_symmetry(),
force_symmetry = True,
log = sys.stdout)
file.close()
assert processed_pdb_file.xray_structure() is not None
assert processed_pdb_file.geometry_restraints_manager() is not None
xray_structure = processed_pdb_file.xray_structure()
geometry_restraints_manager = processed_pdb_file.geometry_restraints_manager()
regularize_model(xray_structure = xray_structure,
geometry_restraints_manager = geometry_restraints_manager,
max_iterations = 50000)
processed_pdb_file.all_chain_proxies.pdb_atoms.set_xyz(
new_xyz=xray_structure.sites_cart())
processed_pdb_file.all_chain_proxies.pdb_hierarchy.write_pdb_file(
file_name="out.pdb")
def exercise_1 () :
pdb_raw = """\
ATOM 1134 N LYS A 82 5.933 36.285 21.572 1.00 70.94 N
ATOM 1135 CA LYS A 82 6.564 37.423 20.931 1.00 76.69 C
ATOM 1136 C LYS A 82 5.553 38.547 20.756 1.00 78.75 C
ATOM 1137 O LYS A 82 5.325 39.038 19.654 1.00 86.47 O
ATOM 1138 CB LYS A 82 7.179 37.024 19.583 1.00 82.32 C
ATOM 1139 CG LYS A 82 8.190 38.035 19.048 0.00 70.34 C
ATOM 1140 CD LYS A 82 9.429 38.129 19.944 0.00 67.69 C
ATOM 1141 CE LYS A 82 9.983 39.545 20.014 0.00 64.44 C
ATOM 1142 NZ LYS A 82 10.933 39.832 18.908 0.00 61.45 N
ATOM 1143 H LYS A 82 5.139 36.115 21.291 1.00 85.12 H
ATOM 1144 HA LYS A 82 7.279 37.749 21.501 1.00 92.03 H
ATOM 1145 HB2 LYS A 82 6.469 36.939 18.928 1.00 98.78 H
ATOM 1146 HB3 LYS A 82 7.636 36.175 19.687 1.00 98.78 H
ATOM 1147 HG2 LYS A 82 8.476 37.762 18.163 0.00 84.41 H
ATOM 1148 HG3 LYS A 82 7.775 38.912 19.011 0.00 84.41 H
ATOM 1149 HD2 LYS A 82 9.193 37.853 20.843 0.00 81.23 H
ATOM 1150 HD3 LYS A 82 10.122 37.551 19.589 0.00 81.23 H
ATOM 1151 HE2 LYS A 82 9.249 40.177 19.952 0.00 77.33 H
ATOM 1152 HE3 LYS A 82 10.453 39.662 20.854 0.00 77.33 H
ATOM 1153 HZ1 LYS A 82 11.237 40.666 18.977 0.00 73.75 H
ATOM 1154 HZ2 LYS A 82 10.523 39.738 18.123 0.00 73.75 H
ATOM 1155 HZ3 LYS A 82 11.621 39.269 18.944 0.00 73.75 H
ATOM 1156 N LYS A 83 4.936 38.927 21.866 1.00 75.79 N
ATOM 1157 CA LYS A 83 4.177 40.172 21.966 1.00 82.80 C
ATOM 1158 C LYS A 83 4.081 40.508 23.460 1.00 86.23 C
ATOM 1159 O LYS A 83 2.978 40.521 24.017 1.00 79.81 O
ATOM 1160 CB LYS A 83 2.790 40.044 21.332 1.00 79.16 C
ATOM 1161 CG LYS A 83 2.038 41.342 21.175 0.00 70.42 C
ATOM 1162 CD LYS A 83 2.072 41.803 19.735 0.00 66.90 C
ATOM 1163 CE LYS A 83 1.295 43.089 19.552 0.00 62.46 C
ATOM 1164 NZ LYS A 83 1.004 43.350 18.118 0.00 60.73 N
ATOM 1165 H LYS A 83 4.940 38.470 22.594 1.00 90.95 H
ATOM 1166 HA LYS A 83 4.658 40.885 21.518 1.00 99.36 H
ATOM 1167 HB2 LYS A 83 2.251 39.459 21.887 1.00 95.00 H
ATOM 1168 HB3 LYS A 83 2.890 39.655 20.449 1.00 95.00 H
ATOM 1169 HG2 LYS A 83 1.113 41.213 21.435 0.00 84.51 H
ATOM 1170 HG3 LYS A 83 2.453 42.024 21.726 0.00 84.51 H
ATOM 1171 HD2 LYS A 83 2.992 41.962 19.471 0.00 80.28 H
ATOM 1172 HD3 LYS A 83 1.672 41.123 19.171 0.00 80.28 H
ATOM 1173 HE2 LYS A 83 0.452 43.024 20.027 0.00 74.95 H
ATOM 1174 HE3 LYS A 83 1.818 43.830 19.896 0.00 74.95 H
ATOM 1175 HZ1 LYS A 83 0.521 42.683 17.780 0.00 72.87 H
ATOM 1176 HZ2 LYS A 83 1.764 43.417 17.661 0.00 72.87 H
ATOM 1177 HZ3 LYS A 83 0.548 44.109 18.034 0.00 72.87 H
ATOM 3630 N ASN A 242 -5.454 -3.027 1.145 0.00 67.69 N
ATOM 3631 CA ASN A 242 -4.759 -2.535 -0.037 0.00 65.44 C
ATOM 3632 C ASN A 242 -5.734 -2.397 -1.208 0.00 63.57 C
ATOM 3633 O ASN A 242 -6.425 -3.357 -1.552 0.00 63.94 O
ATOM 3634 CB ASN A 242 -3.626 -3.503 -0.392 0.00 63.13 C
ATOM 3635 CG ASN A 242 -2.802 -3.044 -1.576 0.00 63.58 C
ATOM 3636 OD1 ASN A 242 -2.524 -1.862 -1.731 0.00 65.52 O
ATOM 3637 ND2 ASN A 242 -2.399 -3.988 -2.416 0.00 62.17 N
ATOM 3638 H ASN A 242 -5.562 -3.880 1.129 0.00 81.22 H
ATOM 3639 HA ASN A 242 -4.375 -1.665 0.151 0.00 78.53 H
ATOM 3640 HB2 ASN A 242 -3.032 -3.587 0.370 0.00 75.76 H
ATOM 3641 HB3 ASN A 242 -4.007 -4.368 -0.611 0.00 75.76 H
ATOM 3642 HD21 ASN A 242 -1.929 -3.779 -3.104 0.00 74.60 H
ATOM 3643 HD22 ASN A 242 -2.609 -4.810 -2.272 0.00 74.60 H
ATOM 2 CA ALYS A 32 10.574 8.177 11.768 0.40 71.49 C
ATOM 3 CB ALYS A 32 9.197 8.686 12.246 0.40 74.71 C
ATOM 2 CA BLYS A 32 10.574 8.177 11.768 0.40 71.49 C
ATOM 3 CB BLYS A 32 9.197 8.686 12.246 0.40 74.71 C
ATOM 5 CA AVAL A 33 11.708 5.617 14.332 0.50 71.42 C
ATOM 6 CB AVAL A 33 11.101 4.227 14.591 0.50 71.47 C
ATOM 5 CA BVAL A 33 11.708 5.617 14.332 0.40 71.42 C
ATOM 6 CB BVAL A 33 11.101 4.227 14.591 0.40 71.47 C
TER
ATOM 1 N GLU X 18 -13.959 12.159 -6.598 1.00260.08 N
ATOM 2 CA GLU X 18 -13.297 13.465 -6.628 1.00269.83 C
ATOM 3 C GLU X 18 -11.946 13.282 -7.309 1.00269.18 C
ATOM 4 CB GLU X 18 -13.128 14.035 -5.210 1.00261.96 C
ATOM 5 CG GLU X 18 -14.455 14.401 -4.522 1.00263.56 C
ATOM 6 CD GLU X 18 -14.291 15.239 -3.242 1.00264.89 C
ATOM 7 OE1 GLU X 18 -14.172 14.646 -2.143 1.00264.24 O
ATOM 8 OE2 GLU X 18 -14.309 16.498 -3.306 1.00264.37 O1-
HETATM 614 S SO4 B 101 14.994 20.601 10.862 0.00 7.02 S
HETATM 615 O1 SO4 B 101 14.234 20.194 12.077 0.00 7.69 O
HETATM 616 O2 SO4 B 101 14.048 21.062 9.850 0.00 9.28 O
HETATM 617 O3 SO4 B 101 15.905 21.686 11.261 0.00 8.01 O
HETATM 618 O4 SO4 B 101 15.772 19.454 10.371 0.00 8.18 O
TER
HETATM 122 O HOH S 1 5.334 8.357 8.032 1.00 0.00 O
HETATM 123 O HOH S 2 5.396 15.243 10.734 1.00202.95 O
HETATM 124 O HOH S 3 -25.334 18.357 18.032 0.00 20.00 O
"""
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
xrs = pdb_in.input.xray_structure_simple()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs),
crystal_symmetry=xrs,
log=null_out())
pdb_in.hierarchy.atoms().reset_i_seq()
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
#print out.getvalue()
assert not show_diff(out.getvalue(), """\
Overall:
Number of atoms = 50 (anisotropic = 0)
B_iso: mean = 96.0 max = 269.8 min = 0.0
Occupancy: mean = 0.47 max = 1.00 min = 0.00
warning: 22 atoms with zero occupancy
67 total B-factor or occupancy problem(s) detected
Atoms or residues with zero occupancy:
LYS A 82 CG occ=0.00
LYS A 82 CD occ=0.00
LYS A 82 CE occ=0.00
LYS A 82 NZ occ=0.00
LYS A 83 CG occ=0.00
LYS A 83 CD occ=0.00
LYS A 83 CE occ=0.00
LYS A 83 NZ occ=0.00
ASN A 242 (all) occ=0.00
SO4 B 101 (all) occ=0.00
HOH S 3 O occ=0.00
Macromolecules:
Number of atoms = 42 (anisotropic = 0)
B_iso: mean = 108.0 max = 269.8 min = 60.7
Occupancy: mean = 0.51 max = 1.00 min = 0.00
warning: 16 atoms with zero occupancy
57 total B-factor or occupancy problem(s) detected
Ligands:
Number of atoms = 5 (anisotropic = 0)
B_iso: mean = 8.0 max = 9.3 min = 7.0
Occupancy: mean = 0.00 max = 0.00 min = 0.00
warning: 5 atoms with zero occupancy
6 total B-factor or occupancy problem(s) detected
Waters:
Number of atoms = 3 (anisotropic = 0)
B_iso: mean = 74.3 max = 202.9 min = 0.0
Occupancy: mean = 0.67 max = 1.00 min = 0.00
warning: 1 atoms with zero occupancy
4 total B-factor or occupancy problem(s) detected
(Hydrogen atoms not included in overall counts.)
""")
assert (len(mstats.all.bad_adps) == 1)
assert (mstats.all.n_zero_b == 1)
mstats2 = loads(dumps(mstats))
out1 = StringIO()
out2 = StringIO()
mstats.show(out=out1)
mstats2.show(out=out2)
assert (out1.getvalue() == out2.getvalue())
# now with ignore_hd=False
mstats3 = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ignore_hd=False)
out2 = StringIO()
mstats3.show(out=out2)
assert (out2.getvalue() != out.getvalue())
assert (""" LYS A 83 HZ3 occ=0.00""" in out2.getvalue())
outliers = mstats3.all.as_gui_table_data(include_zoom=True)
assert (len(outliers) == 84)
# test with all_chain_proxies undefined
mstats4 = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=None,
ignore_hd=False)
outliers = mstats4.all.as_gui_table_data(include_zoom=True)
assert (len(outliers) == 84)
import iotbx
import time
from iotbx import pdb
from mmtbx import *
from mmtbx.monomer_library import server
from mmtbx.monomer_library import pdb_interpretation
from mmtbx.conformation_dependent_library import generate_protein_fragments
hierarchy = pdb_inp.construct_hierarchy()
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
processed_pdb = pdb_interpretation.process(self.mon_lib_srv,
self.ener_lib,
file_name=pdb_file_name,
raw_records=raw_records)
geometry_restraints_manager = processed_pdb.geometry_restraints_manager()
# generate five ca
def generate_ca(self):
t0 = time.time()
self.hierarchy.reset_atom_i_seqs()
self.hierarchy.reset_i_seq_if_necessary()
for five in generate_protein_fragments(self.hierarchy,
self.geometry_restraints_manager,
length=5):
rc = []
for atom in five.atoms():
if atom.name == ' CA ':
rc.append(atom)
if len(rc) == 5:
def run(args):
"""
I suggest adding here:
cctbx_project/mmtbx/validation/regression/tst_mp_geo.py
test cases with just .pdb, without arguments, etc.
"""
master_phil = get_master_phil()
import iotbx.phil
input_objects = iotbx.phil.process_command_line_with_files(
args=args, master_phil=master_phil, pdb_file_def="mp_geo.pdb")
work_params = input_objects.work.extract()
assert len(work_params.mp_geo.pdb) == 1, "Need a model file to run"
file_name = work_params.mp_geo.pdb[0]
out_file = None
if work_params.mp_geo.out_file != None:
out_file = work_params.mp_geo.out_file
do_bonds_and_angles = work_params.mp_geo.bonds_and_angles
do_kinemage = work_params.mp_geo.kinemage
do_rna_backbone = work_params.mp_geo.rna_backbone
outliers_only = work_params.mp_geo.outliers_only
use_cdl = work_params.mp_geo.cdl
log = StringIO()
basename = os.path.basename(file_name)
if out_file == None:
import sys
out = sys.stdout
else:
if do_bonds_and_angles:
out = file(out_file, 'w')
elif do_kinemage:
out = file(out_file, 'a')
elif do_rna_backbone:
out = file(out_file, 'w')
restraints_loading_flags = {}
restraints_loading_flags["use_neutron_distances"] = False
from mmtbx.validation import utils
params = pdb_interpretation.master_params.extract()
params.restraints_library.cdl = use_cdl
params.clash_guard.nonbonded_distance_threshold = None
processed_pdb_file = pdb_interpretation.process(
params=params,
mon_lib_srv=server.server(),
ener_lib=server.ener_lib(),
file_name=file_name,
strict_conflict_handling=True,
restraints_loading_flags=restraints_loading_flags,
force_symmetry=True,
substitute_non_crystallographic_unit_cell_if_necessary=True,
log=log)
grm = processed_pdb_file.geometry_restraints_manager()
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=processed_pdb_file.all_chain_proxies.pdb_hierarchy)
if do_bonds_and_angles or do_kinemage:
rc = get_bond_and_angle_outliers(
pdb_hierarchy=processed_pdb_file.all_chain_proxies.pdb_hierarchy,
xray_structure=processed_pdb_file.xray_structure(),
geometry_restraints_manager=grm,
use_segids=use_segids,
outliers_only=outliers_only)
#get chain types
chain_types = {}
for chain in processed_pdb_file.all_chain_proxies.\
pdb_hierarchy.models()[0].chains():
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
main_conf = chain.conformers()[0]
if chain_types.get(chain_id) not in ["NA", "PROTEIN"]:
if (main_conf.is_na()):
chain_types[chain_id] = "NA"
elif (main_conf.is_protein()):
chain_types[chain_id] = "PROTEIN"
else:
chain_types[chain_id] = "UNK"
outliers = []
#bonds
#for result in rc.bonds.results:
for result in sorted(
rc.bonds.results,
key=lambda x:
(x.atoms_info[0].resseq, get_altloc(atoms_info=x.atoms_info),
get_atoms_str(atoms_info=x.atoms_info))):
atom_info = result.atoms_info[0]
# label:chain:number:ins:alt:type:measure:value:sigmas:class
atoms_str = get_atoms_str(atoms_info=result.atoms_info)
altloc = get_altloc(atoms_info=result.atoms_info)
chain_id = atom_info.chain_id
outliers.append([
chain_id, atom_info.resseq, atom_info.icode, altloc,
atom_info.resname, atoms_str, result.model, result.score,
chain_types[atom_info.chain_id]
])
#angles
#for result in rc.angles.results:
for result in sorted(
rc.angles.results,
key=lambda x:
(x.atoms_info[0].resseq, get_altloc(atoms_info=x.atoms_info),
get_atoms_str(atoms_info=x.atoms_info))):
atom_info = result.atoms_info[0]
# label:chain:number:ins:alt:type:measure:value:sigmas:class
atoms_str = get_atoms_str(atoms_info=result.atoms_info)
altloc = get_altloc(atoms_info=result.atoms_info)
chain_id = atom_info.chain_id
outliers.append([
chain_id, atom_info.resseq, atom_info.icode, altloc,
atom_info.resname, atoms_str, result.model, result.score,
chain_types[atom_info.chain_id]
])
if do_bonds_and_angles:
for outlier in outliers:
print >> out, "%s:%2s:%s:%s:%s:%s:%s:%.3f:%.3f:%s" % (
basename, outlier[0], outlier[1], outlier[2], outlier[3],
outlier[4], outlier[5], outlier[6], outlier[7], outlier[8])
elif do_kinemage:
print >> out, rc.bonds.kinemage_header
for result in rc.bonds.results:
print >> out, result.as_kinemage()
print >> out, rc.angles.kinemage_header
for result in rc.angles.results:
print >> out, result.as_kinemage()
out.close()
elif do_rna_backbone:
from mmtbx.validation import utils
rna_bb = utils.get_rna_backbone_dihedrals(processed_pdb_file)
print >> out, rna_bb
if out_file is not None:
out.close()
def run(args):
master_phil = get_master_phil()
import iotbx.utils
input_objects = iotbx.utils.process_command_line_inputs(
args=args,
master_phil=master_phil,
input_types=("pdb",))
work_phil = master_phil.fetch(sources=input_objects["phil"])
work_params = work_phil.extract()
file_name = work_params.mp_geo.pdb
out_file = None
if work_params.mp_geo.out_file != None:
out_file = work_params.mp_geo.out_file
do_bonds_and_angles = work_params.mp_geo.bonds_and_angles
do_kinemage = work_params.mp_geo.kinemage
do_rna_backbone = work_params.mp_geo.rna_backbone
outliers_only = work_params.mp_geo.outliers_only
use_cdl = work_params.mp_geo.cdl
log = StringIO()
basename = os.path.basename(file_name)
if do_bonds_and_angles:
out = file(out_file, 'w')
elif do_kinemage:
out = file(out_file, 'a')
elif do_rna_backbone:
if out_file == None:
import sys
out = sys.stdout
else:
out = file(out_file, 'w')
restraints_loading_flags = {}
restraints_loading_flags["use_neutron_distances"]=False
from mmtbx.validation import utils
params = pdb_interpretation.master_params.extract()
params.restraints_library.cdl = use_cdl
params.clash_guard.nonbonded_distance_threshold = None
processed_pdb_file = pdb_interpretation.process(
params = params,
mon_lib_srv = server.server(),
ener_lib = server.ener_lib(),
file_name = file_name,
strict_conflict_handling = True,
restraints_loading_flags = restraints_loading_flags,
force_symmetry = True,
substitute_non_crystallographic_unit_cell_if_necessary=True,
log = log)
grm = processed_pdb_file.geometry_restraints_manager()
use_segids = utils.use_segids_in_place_of_chainids(
hierarchy=processed_pdb_file.all_chain_proxies.pdb_hierarchy)
if do_bonds_and_angles or do_kinemage:
rc = get_bond_and_angle_outliers(
pdb_hierarchy=processed_pdb_file.all_chain_proxies.pdb_hierarchy,
xray_structure=processed_pdb_file.xray_structure(),
geometry_restraints_manager=grm,
use_segids=use_segids,
outliers_only=outliers_only)
#get chain types
chain_types = {}
for chain in processed_pdb_file.all_chain_proxies.\
pdb_hierarchy.models()[0].chains() :
if use_segids:
chain_id = utils.get_segid_as_chainid(chain=chain)
else:
chain_id = chain.id
main_conf = chain.conformers()[0]
if chain_types.get(chain_id) not in ["NA", "PROTEIN"]:
if (main_conf.is_na()) :
chain_types[chain_id] = "NA"
elif (main_conf.is_protein()):
chain_types[chain_id] = "PROTEIN"
else:
chain_types[chain_id] = "UNK"
outliers = []
#bonds
for result in rc.bonds.results:
atom_info = result.atoms_info[0]
# label:chain:number:ins:alt:type:measure:value:sigmas:class
atoms_str = get_atoms_str(atoms_info=result.atoms_info)
altloc = get_altloc(atoms_info=result.atoms_info)
chain_id = atom_info.chain_id
outliers.append( [chain_id,
atom_info.resseq,
atom_info.icode,
altloc,
atom_info.resname,
atoms_str,
result.model,
result.score,
chain_types[atom_info.chain_id]] )
#angles
for result in rc.angles.results:
atom_info = result.atoms_info[0]
# label:chain:number:ins:alt:type:measure:value:sigmas:class
atoms_str = get_atoms_str(atoms_info=result.atoms_info)
altloc = get_altloc(atoms_info=result.atoms_info)
chain_id = atom_info.chain_id
outliers.append( [chain_id,
atom_info.resseq,
atom_info.icode,
altloc,
atom_info.resname,
atoms_str,
result.model,
result.score,
chain_types[atom_info.chain_id]] )
if do_bonds_and_angles:
for outlier in outliers:
print >> out, "%s:%2s:%s:%s:%s:%s:%s:%.3f:%.3f:%s" % (
basename, outlier[0], outlier[1], outlier[2], outlier[3],
outlier[4], outlier[5], outlier[6], outlier[7], outlier[8])
elif do_kinemage:
print >> out, rc.bonds.kinemage_header
for result in rc.bonds.results:
print >> out, result.as_kinemage()
print >> out, rc.angles.kinemage_header
for result in rc.angles.results:
print >> out, result.as_kinemage()
out.close()
elif do_rna_backbone:
from mmtbx.validation import utils
rna_bb = utils.get_rna_backbone_dihedrals(processed_pdb_file)
print >> out, rna_bb
if out_file is not None:
out.close()
def run (args, params=None, out=sys.stdout, log=sys.stderr) :
# params keyword is for running program from GUI dialog
if ( ((len(args) == 0) and (params is None)) or
((len(args) > 0) and ((args[0] == "-h") or (args[0] == "--help"))) ):
show_usage()
return
# parse command-line arguments
if (params is None):
pcl = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="file_name")
work_params = pcl.work.extract()
# or use parameters defined by GUI
else:
work_params = params
pdb_files = work_params.file_name
work_params.secondary_structure.enabled=True
assert work_params.format in ["phenix", "phenix_refine", "phenix_bonds",
"pymol", "refmac", "kinemage", "pdb"]
if work_params.quiet :
out = cStringIO.StringIO()
pdb_combined = iotbx.pdb.combine_unique_pdb_files(file_names=pdb_files)
pdb_structure = iotbx.pdb.input(source_info=None,
lines=flex.std_string(pdb_combined.raw_records))
cs = pdb_structure.crystal_symmetry()
corrupted_cs = False
if cs is not None:
if [cs.unit_cell(), cs.space_group()].count(None) > 0:
corrupted_cs = True
cs = None
elif cs.unit_cell().volume() < 10:
corrupted_cs = True
cs = None
if cs is None:
if corrupted_cs:
print >> out, "Symmetry information is corrupted, "
else:
print >> out, "Symmetry information was not found, "
print >> out, "putting molecule in P1 box."
from cctbx import uctbx
atoms = pdb_structure.atoms()
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=atoms.extract_xyz(),
buffer_layer=3)
atoms.set_xyz(new_xyz=box.sites_cart)
cs = box.crystal_symmetry()
from mmtbx.monomer_library import pdb_interpretation, server
import mmtbx
import mmtbx.command_line.geometry_minimization
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
defpars = mmtbx.command_line.geometry_minimization.master_params().extract()
defpars.pdb_interpretation.automatic_linking.link_carbohydrates=False
defpars.pdb_interpretation.c_beta_restraints=False
defpars.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
pdb_inp = pdb_structure,
crystal_symmetry = cs,
params = defpars.pdb_interpretation,
force_symmetry = True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
geometry = processed_pdb_file.geometry_restraints_manager()
geometry.pair_proxies(processed_pdb_file.xray_structure().sites_cart())
pdb_hierarchy.atoms().reset_i_seq()
if len(pdb_hierarchy.models()) != 1 :
raise Sorry("Multiple models not supported.")
ss_from_file = None
if hasattr(pdb_structure, "extract_secondary_structure"):
ss_from_file = pdb_structure.extract_secondary_structure()
m = manager(pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry,
sec_str_from_pdb_file=ss_from_file,
params=work_params.secondary_structure,
verbose=work_params.verbose)
# bp_p = nucleic_acids.get_basepair_plane_proxies(
# pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.base_pair,
# geometry)
# st_p = nucleic_acids.get_stacking_proxies(
# pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.stacking_pair,
# geometry)
# hb_b, hb_a = nucleic_acids.get_basepair_hbond_proxies(pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.base_pair)
result_out = cStringIO.StringIO()
# prefix_scope="refinement.pdb_interpretation"
# prefix_scope=""
prefix_scope=""
if work_params.format == "phenix_refine":
prefix_scope = "refinement.pdb_interpretation"
elif work_params.format == "phenix":
prefix_scope = "pdb_interpretation"
ss_phil = None
working_phil = m.as_phil_str(master_phil=sec_str_master_phil)
phil_diff = sec_str_master_phil.fetch_diff(source=working_phil)
if work_params.format in ["phenix", "phenix_refine"]:
comment = "\n".join([
"# These parameters are suitable for use in e.g. phenix.real_space_refine",
"# or geometry_minimization. To use them in phenix.refine add ",
"# 'refinement.' if front of pdb_interpretation."])
if work_params.format == "phenix_refine":
comment = "\n".join([
"# These parameters are suitable for use in phenix.refine only.",
"# To use them in other Phenix tools remove ",
"# 'refinement.' if front of pdb_interpretation."])
print >> result_out, comment
if (prefix_scope != "") :
print >> result_out, "%s {" % prefix_scope
if work_params.show_all_params :
working_phil.show(prefix=" ", out=result_out)
else :
phil_diff.show(prefix=" ", out=result_out)
if (prefix_scope != "") :
print >> result_out, "}"
elif work_params.format == "pdb":
print >> result_out, m.actual_sec_str.as_pdb_str()
elif work_params.format == "phenix_bonds" :
raise Sorry("Not yet implemented.")
elif work_params.format in ["pymol", "refmac", "kinemage"] :
m.show_summary(log=out)
(hb_proxies, hb_angle_proxies, planarity_proxies,
parallelity_proxies) = m.create_all_new_restraints(
pdb_hierarchy=pdb_hierarchy,
grm=geometry,
log=out)
if hb_proxies.size() > 0:
if work_params.format == "pymol" :
bonds_in_format = hb_proxies.as_pymol_dashes(
pdb_hierarchy=pdb_hierarchy)
elif work_params.format == "kinemage" :
bonds_in_format = hb_proxies.as_kinemage(
pdb_hierarchy=pdb_hierarchy)
else :
bonds_in_format = hb_proxies.as_refmac_restraints(
pdb_hierarchy=pdb_hierarchy)
print >> result_out, bonds_in_format
result = result_out.getvalue()
filename = "%s_ss.eff" %os.path.basename(work_params.file_name[0])
outf = open(filename, "w")
outf.write(result)
outf.close()
print >> out, result
return os.path.abspath(filename)
def exercise_1():
pdb_raw = """\
ATOM 1134 N LYS A 82 5.933 36.285 21.572 1.00 70.94 N
ATOM 1135 CA LYS A 82 6.564 37.423 20.931 1.00 76.69 C
ATOM 1136 C LYS A 82 5.553 38.547 20.756 1.00 78.75 C
ATOM 1137 O LYS A 82 5.325 39.038 19.654 1.00 86.47 O
ATOM 1138 CB LYS A 82 7.179 37.024 19.583 1.00 82.32 C
ATOM 1139 CG LYS A 82 8.190 38.035 19.048 0.00 70.34 C
ATOM 1140 CD LYS A 82 9.429 38.129 19.944 0.00 67.69 C
ATOM 1141 CE LYS A 82 9.983 39.545 20.014 0.00 64.44 C
ATOM 1142 NZ LYS A 82 10.933 39.832 18.908 0.00 61.45 N
ATOM 1143 H LYS A 82 5.139 36.115 21.291 1.00 85.12 H
ATOM 1144 HA LYS A 82 7.279 37.749 21.501 1.00 92.03 H
ATOM 1145 HB2 LYS A 82 6.469 36.939 18.928 1.00 98.78 H
ATOM 1146 HB3 LYS A 82 7.636 36.175 19.687 1.00 98.78 H
ATOM 1147 HG2 LYS A 82 8.476 37.762 18.163 0.00 84.41 H
ATOM 1148 HG3 LYS A 82 7.775 38.912 19.011 0.00 84.41 H
ATOM 1149 HD2 LYS A 82 9.193 37.853 20.843 0.00 81.23 H
ATOM 1150 HD3 LYS A 82 10.122 37.551 19.589 0.00 81.23 H
ATOM 1151 HE2 LYS A 82 9.249 40.177 19.952 0.00 77.33 H
ATOM 1152 HE3 LYS A 82 10.453 39.662 20.854 0.00 77.33 H
ATOM 1153 HZ1 LYS A 82 11.237 40.666 18.977 0.00 73.75 H
ATOM 1154 HZ2 LYS A 82 10.523 39.738 18.123 0.00 73.75 H
ATOM 1155 HZ3 LYS A 82 11.621 39.269 18.944 0.00 73.75 H
ATOM 1156 N LYS A 83 4.936 38.927 21.866 1.00 75.79 N
ATOM 1157 CA LYS A 83 4.177 40.172 21.966 1.00 82.80 C
ATOM 1158 C LYS A 83 4.081 40.508 23.460 1.00 86.23 C
ATOM 1159 O LYS A 83 2.978 40.521 24.017 1.00 79.81 O
ATOM 1160 CB LYS A 83 2.790 40.044 21.332 1.00 79.16 C
ATOM 1161 CG LYS A 83 2.038 41.342 21.175 0.00 70.42 C
ATOM 1162 CD LYS A 83 2.072 41.803 19.735 0.00 66.90 C
ATOM 1163 CE LYS A 83 1.295 43.089 19.552 0.00 62.46 C
ATOM 1164 NZ LYS A 83 1.004 43.350 18.118 0.00 60.73 N
ATOM 1165 H LYS A 83 4.940 38.470 22.594 1.00 90.95 H
ATOM 1166 HA LYS A 83 4.658 40.885 21.518 1.00 99.36 H
ATOM 1167 HB2 LYS A 83 2.251 39.459 21.887 1.00 95.00 H
ATOM 1168 HB3 LYS A 83 2.890 39.655 20.449 1.00 95.00 H
ATOM 1169 HG2 LYS A 83 1.113 41.213 21.435 0.00 84.51 H
ATOM 1170 HG3 LYS A 83 2.453 42.024 21.726 0.00 84.51 H
ATOM 1171 HD2 LYS A 83 2.992 41.962 19.471 0.00 80.28 H
ATOM 1172 HD3 LYS A 83 1.672 41.123 19.171 0.00 80.28 H
ATOM 1173 HE2 LYS A 83 0.452 43.024 20.027 0.00 74.95 H
ATOM 1174 HE3 LYS A 83 1.818 43.830 19.896 0.00 74.95 H
ATOM 1175 HZ1 LYS A 83 0.521 42.683 17.780 0.00 72.87 H
ATOM 1176 HZ2 LYS A 83 1.764 43.417 17.661 0.00 72.87 H
ATOM 1177 HZ3 LYS A 83 0.548 44.109 18.034 0.00 72.87 H
ATOM 3630 N ASN A 242 -5.454 -3.027 1.145 0.00 67.69 N
ATOM 3631 CA ASN A 242 -4.759 -2.535 -0.037 0.00 65.44 C
ATOM 3632 C ASN A 242 -5.734 -2.397 -1.208 0.00 63.57 C
ATOM 3633 O ASN A 242 -6.425 -3.357 -1.552 0.00 63.94 O
ATOM 3634 CB ASN A 242 -3.626 -3.503 -0.392 0.00 63.13 C
ATOM 3635 CG ASN A 242 -2.802 -3.044 -1.576 0.00 63.58 C
ATOM 3636 OD1 ASN A 242 -2.524 -1.862 -1.731 0.00 65.52 O
ATOM 3637 ND2 ASN A 242 -2.399 -3.988 -2.416 0.00 62.17 N
ATOM 3638 H ASN A 242 -5.562 -3.880 1.129 0.00 81.22 H
ATOM 3639 HA ASN A 242 -4.375 -1.665 0.151 0.00 78.53 H
ATOM 3640 HB2 ASN A 242 -3.032 -3.587 0.370 0.00 75.76 H
ATOM 3641 HB3 ASN A 242 -4.007 -4.368 -0.611 0.00 75.76 H
ATOM 3642 HD21 ASN A 242 -1.929 -3.779 -3.104 0.00 74.60 H
ATOM 3643 HD22 ASN A 242 -2.609 -4.810 -2.272 0.00 74.60 H
ATOM 2 CA ALYS A 32 10.574 8.177 11.768 0.40 71.49 C
ATOM 3 CB ALYS A 32 9.197 8.686 12.246 0.40 74.71 C
ATOM 2 CA BLYS A 32 10.574 8.177 11.768 0.40 71.49 C
ATOM 3 CB BLYS A 32 9.197 8.686 12.246 0.40 74.71 C
ATOM 5 CA AVAL A 33 11.708 5.617 14.332 0.50 71.42 C
ATOM 6 CB AVAL A 33 11.101 4.227 14.591 0.50 71.47 C
ATOM 5 CA BVAL A 33 11.708 5.617 14.332 0.40 71.42 C
ATOM 6 CB BVAL A 33 11.101 4.227 14.591 0.40 71.47 C
TER
ATOM 1 N GLU X 18 -13.959 12.159 -6.598 1.00260.08 N
ATOM 2 CA GLU X 18 -13.297 13.465 -6.628 1.00269.83 C
ATOM 3 C GLU X 18 -11.946 13.282 -7.309 1.00269.18 C
ATOM 4 CB GLU X 18 -13.128 14.035 -5.210 1.00261.96 C
ATOM 5 CG GLU X 18 -14.455 14.401 -4.522 1.00263.56 C
ATOM 6 CD GLU X 18 -14.291 15.239 -3.242 1.00264.89 C
ATOM 7 OE1 GLU X 18 -14.172 14.646 -2.143 1.00264.24 O
ATOM 8 OE2 GLU X 18 -14.309 16.498 -3.306 1.00264.37 O1-
HETATM 614 S SO4 B 101 14.994 20.601 10.862 0.00 7.02 S
HETATM 615 O1 SO4 B 101 14.234 20.194 12.077 0.00 7.69 O
HETATM 616 O2 SO4 B 101 14.048 21.062 9.850 0.00 9.28 O
HETATM 617 O3 SO4 B 101 15.905 21.686 11.261 0.00 8.01 O
HETATM 618 O4 SO4 B 101 15.772 19.454 10.371 0.00 8.18 O
TER
HETATM 122 O HOH S 1 5.334 8.357 8.032 1.00 0.00 O
HETATM 123 O HOH S 2 5.396 15.243 10.734 1.00202.95 O
HETATM 124 O HOH S 3 -25.334 18.357 18.032 0.00 20.00 O
"""
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=pdb_raw)
xrs = pdb_in.input.xray_structure_simple()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=pdb_in.hierarchy.as_pdb_string(crystal_symmetry=xrs),
crystal_symmetry=xrs,
log=null_out())
pdb_in.hierarchy.atoms().reset_i_seq()
mstats = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ignore_hd=True)
out = StringIO()
mstats.show(out=out)
#print out.getvalue()
assert not show_diff(
out.getvalue(), """\
Overall:
Number of atoms = 50 (anisotropic = 0)
B_iso: mean = 96.0 max = 269.8 min = 0.0
Occupancy: mean = 0.47 max = 1.00 min = 0.00
warning: 22 atoms with zero occupancy
69 total B-factor or occupancy problem(s) detected
Atoms or residues with zero occupancy:
LYS A 82 CG occ=0.00
LYS A 82 CD occ=0.00
LYS A 82 CE occ=0.00
LYS A 82 NZ occ=0.00
LYS A 83 CG occ=0.00
LYS A 83 CD occ=0.00
LYS A 83 CE occ=0.00
LYS A 83 NZ occ=0.00
ASN A 242 (all) occ=0.00
SO4 B 101 (all) occ=0.00
HOH S 3 O occ=0.00
Macromolecules:
Number of atoms = 42 (anisotropic = 0)
B_iso: mean = 108.0 max = 269.8 min = 60.7
Occupancy: mean = 0.51 max = 1.00 min = 0.00
warning: 16 atoms with zero occupancy
59 total B-factor or occupancy problem(s) detected
Ligands:
Number of atoms = 5 (anisotropic = 0)
B_iso: mean = 8.0 max = 9.3 min = 7.0
Occupancy: mean = 0.00 max = 0.00 min = 0.00
warning: 5 atoms with zero occupancy
6 total B-factor or occupancy problem(s) detected
Waters:
Number of atoms = 3 (anisotropic = 0)
B_iso: mean = 74.3 max = 202.9 min = 0.0
Occupancy: mean = 0.67 max = 1.00 min = 0.00
warning: 1 atoms with zero occupancy
4 total B-factor or occupancy problem(s) detected
(Hydrogen atoms not included in overall counts.)
""")
assert (len(mstats.all.bad_adps) == 1)
assert (mstats.all.n_zero_b == 1)
mstats2 = loads(dumps(mstats))
out1 = StringIO()
out2 = StringIO()
mstats.show(out=out1)
mstats2.show(out=out2)
assert (out1.getvalue() == out2.getvalue())
# now with ignore_hd=False
mstats3 = model_properties.model_statistics(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=processed_pdb_file.all_chain_proxies,
ignore_hd=False)
out2 = StringIO()
mstats3.show(out=out2)
assert (out2.getvalue() != out.getvalue())
assert (""" LYS A 83 HZ3 occ=0.00""" in out2.getvalue())
outliers = mstats3.all.as_gui_table_data(include_zoom=True)
assert (len(outliers) == 86)
# test with all_chain_proxies undefined
mstats4 = model_properties.model_statistics(pdb_hierarchy=pdb_in.hierarchy,
xray_structure=xrs,
all_chain_proxies=None,
ignore_hd=False)
outliers = mstats4.all.as_gui_table_data(include_zoom=True)
assert (len(outliers) == 86)
def exercise_2(mon_lib_srv, ener_lib):
for use_reference in [True, False, None]:
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=flex.std_string(pdb_str_2.splitlines()),
strict_conflict_handling=True,
force_symmetry=True,
log=None)
grm = processed_pdb_file.geometry_restraints_manager()
xrs2 = processed_pdb_file.xray_structure(show_summary=False)
awl2 = processed_pdb_file.all_chain_proxies.pdb_hierarchy.atoms_with_labels(
)
pdb_inp3 = iotbx.pdb.input(source_info=None, lines=pdb_str_3)
xrs3 = pdb_inp3.xray_structure_simple()
ph3 = pdb_inp3.construct_hierarchy()
ph3.atoms().reset_i_seq()
awl3 = ph3.atoms_with_labels()
sites_cart_reference = flex.vec3_double()
selection = flex.size_t()
reference_names = ["CG", "CD", "NE", "CZ", "NH1", "NH2"]
for a2, a3 in zip(tuple(awl2), tuple(awl3)):
assert a2.resname == a3.resname
assert a2.name == a3.name
assert a2.i_seq == a3.i_seq
if (a2.resname == "ARG" and a2.name.strip() in reference_names):
selection.append(a2.i_seq)
sites_cart_reference.append(a3.xyz)
assert selection.size() == len(reference_names)
selection_bool = flex.bool(xrs2.scatterers().size(), selection)
if (use_reference):
grm.adopt_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart=sites_cart_reference,
selection=selection,
sigma=0.01))
elif (use_reference is None):
grm.adopt_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart=sites_cart_reference,
selection=selection,
sigma=0.01))
grm.remove_reference_coordinate_restraints_in_place(
selection=selection)
d1 = flex.mean(
flex.sqrt((xrs2.sites_cart().select(selection) -
xrs3.sites_cart().select(selection)).dot()))
print "distance start (use_reference: %s): %6.4f" % (
str(use_reference), d1)
assert d1 > 4.0
assert approx_equal(
flex.max(
flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())),
0)
from cctbx import geometry_restraints
import mmtbx.refinement.geometry_minimization
import scitbx.lbfgs
grf = geometry_restraints.flags.flags(default=True)
sites_cart = xrs2.sites_cart()
minimized = mmtbx.refinement.geometry_minimization.lbfgs(
sites_cart=sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=grm,
sites_cart_selection=flex.bool(sites_cart.size(), selection),
geometry_restraints_flags=grf,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=5000))
xrs2.set_sites_cart(sites_cart=sites_cart)
d2 = flex.mean(
flex.sqrt((xrs2.sites_cart().select(selection) -
xrs3.sites_cart().select(selection)).dot()))
print "distance final (use_reference: %s): %6.4f" % (
str(use_reference), d2)
if (use_reference): assert d2 < 0.005, "failed: %f<0.05" % d2
else: assert d2 > 4.0, d2
assert approx_equal(
flex.max(
flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())),
0)