def run(filename=None):
assert filename is None
hpdl_database = get_hpdl_database()
if 0:
print "HPDL"
print hpdl_database
for aa in sorted(hpdl_database):
print " %s" % aa
for key, value in sorted(hpdl_database[aa].items()):
print " %s : %s" % (key, value)
assert 0
#
for pdb, lines in pdbs.items():
print pdb
filename="hpdl_%s.pdb" % pdb
f=file(filename, "wb")
f.write(lines)
f.close()
cmd = "phenix.pdb_interpretation %s write_geo=1 hpdl=%s" % (filename, True)
print cmd
easy_run.call(cmd)
if filename.find("his_double")>-1: key="ND1 and NE2 protonated"
elif filename.find("his_nd1")>-1: key="Only ND1 protonated"
elif filename.find("his_ne2")>-1: key="Only NE2 protonated"
if refine_geo_parser:
check_ideals("%s.geo" % filename, hpdl_database[key])
print "OK"
def update_restraints(hierarchy,
geometry, # restraints_manager,
current_geometry=None, # xray_structure!!
sites_cart=None,
esd_factor=1.,
log=None,
verbose=False,
):
#
def _set_or_reset_bond_restraints(geometry,
lookup,
verbose=False,
):
count = 0
for i_seqs, values in lookup.items():
if len(i_seqs)!=2: continue
bond=geometry.bond_params_table.lookup(*list(i_seqs))
assert bond
if verbose:
print " i_seqs %-15s initial %12.3f %12.3f final %12.3f %12.3f" % (
i_seqs,
bond.distance_ideal,
bond.weight,
values[0],
1/values[1]**2,
)
bond.distance_ideal=values[0]
bond.weight = 1/values[1]**2
count+=1
return count
#
def _set_or_reset_angle_restraints(geometry,
lookup,
verbose=False,
):
count = 0
for angle_proxy in geometry.angle_proxies:
if angle_proxy.i_seqs in lookup:
if verbose: print " i_seqs %-15s initial %12.3f %12.3f" % (
angle_proxy.i_seqs,
angle_proxy.angle_ideal,
angle_proxy.weight,
),
assert angle_proxy.angle_ideal<181
angle_proxy.angle_ideal = lookup[angle_proxy.i_seqs][0]
angle_proxy.weight = esd_factor/lookup[angle_proxy.i_seqs][1]**2
if verbose: print "final %12.3f %12.3f" % (
#angle_proxy.i_seqs,
angle_proxy.angle_ideal,
angle_proxy.weight,
)
count += 1
return count
#
t0=time.time()
sites_cart = None
if current_geometry:
sites_cart = current_geometry.sites_cart()
i_seqs_restraints = {}
#
def _alt_loc_atom_generator(residue_group, atom_group):
atoms = []
for ag in residue_group.atom_groups():
if ag.altloc.strip()=="" or ag.altloc.strip()==atom_group.altloc.strip():
for atom in ag.atoms(): yield atom
#
hpdl_database = get_hpdl_database() #include_hydrogens=False)
count=0
counts = {}
for model in hierarchy.models():
#if verbose: print 'model: "%s"' % model.id
for chain in model.chains():
#if verbose: print 'chain: "%s"' % chain.id
for residue_group in chain.residue_groups():
for atom_group in residue_group.atom_groups():
if atom_group.resname!="HIS": continue
protonation = get_histidine_protonation(atom_group)
if verbose or 1:
rc = predict_protonation(atom_group)
if rc is None:
s = "%s" % rc
else:
s = "%0.1f, %0.1f" % tuple(rc)
print >> log, '%satom group "%s" has %-22s (%s)' % (
' '*6,
atom_group.id_str(),
protonation,
s,
)
#interpret_his1_his2(*tuple(rc))
counts.setdefault(protonation, 0)
if protonation is None: continue
counts[protonation]+=1
count+=1
restraints = hpdl_database[protonation]
for names, values in restraints.items():
i_seqs = []
for name in names:
# need to test this...
for atom in _alt_loc_atom_generator(residue_group, atom_group):
if name.strip()==atom.name.strip():
i_seqs.append(atom.i_seq)
break
if len(i_seqs)!=len(names): continue
i_seqs_restraints[tuple(i_seqs)] = values
if len(i_seqs)!=2:
i_seqs.reverse()
i_seqs_restraints[tuple(i_seqs)] = values
count_b = _set_or_reset_bond_restraints(geometry,
i_seqs_restraints,
verbose=verbose,
)
count_a = _set_or_reset_angle_restraints(geometry,
i_seqs_restraints,
verbose=verbose,
)
#
print >> log, " Number of bonds, angles adjusted : %d, %d in %s HIS" % (
count_b,
count_a,
count,
)
def update_restraints(
hierarchy,
geometry, # restraints_manager,
current_geometry=None, # xray_structure!!
sites_cart=None,
esd_factor=1.,
log=None,
verbose=False,
):
#
def _set_or_reset_bond_restraints(
geometry,
lookup,
ignore_esd=True,
log=None,
verbose=False,
):
count = 0
for i_seqs, values in lookup.items():
if len(i_seqs) != 2: continue
bond = geometry.bond_params_table.lookup(*list(i_seqs))
assert bond
if verbose:
from math import sqrt
key = list(i_seqs)
key.append("names")
key = tuple(key)
names = lookup.get(key, "")
old_bond_ideal = bond.distance_ideal
old_bond_weight = bond.weight
print >> log, " i_seqs %-15s %s initial %8.3f %8.3f %8.3f final %8.3f %8.3f %8.3f" % (
i_seqs,
names,
bond.distance_ideal,
bond.weight,
1 / sqrt(bond.weight),
values[0],
1 / values[1]**2,
values[1],
)
if bond.distance_ideal != old_bond_ideal or bond.weight != old_bond_weight:
print >> log, 'RESETTING'
bond.distance_ideal = values[0]
if not ignore_esd:
bond.weight = 1 / values[1]**2
count += 1
return count
#
def _set_or_reset_angle_restraints(
geometry,
lookup,
ignore_esd=True,
log=None,
verbose=False,
):
count = 0
for angle_proxy in geometry.angle_proxies:
if angle_proxy.i_seqs in lookup:
if verbose:
old_angle_ideal = angle_proxy.angle_ideal
old_angle_weight = angle_proxy.weight
print >> log, " i_seqs %-15s initial %12.3f %12.3f" % (
angle_proxy.i_seqs,
angle_proxy.angle_ideal,
angle_proxy.weight,
),
assert angle_proxy.angle_ideal < 181
angle_proxy.angle_ideal = lookup[angle_proxy.i_seqs][0]
if not ignore_esd:
angle_proxy.weight = esd_factor / lookup[
angle_proxy.i_seqs][1]**2
if verbose:
print >> log, "final %12.3f %12.3f" % (
angle_proxy.angle_ideal,
angle_proxy.weight,
)
if old_angle_ideal != angle_proxy.angle_ideal or old_angle_weight != angle_proxy.weight:
print >> log, "RESETTING"
count += 1
return count
#
t0 = time.time()
sites_cart = None
if current_geometry:
sites_cart = current_geometry.sites_cart()
i_seqs_restraints = {}
#
def _alt_loc_atom_generator(residue_group, atom_group):
atoms = []
for ag in residue_group.atom_groups():
if ag.altloc.strip() == "" or ag.altloc.strip(
) == atom_group.altloc.strip():
for atom in ag.atoms():
yield atom
#
hpdl_database = get_hpdl_database() #include_hydrogens=False)
count = 0
counts = {}
for model in hierarchy.models():
#if verbose: print 'model: "%s"' % model.id
for chain in model.chains():
#if verbose: print 'chain: "%s"' % chain.id
for residue_group in chain.residue_groups():
for atom_group in residue_group.atom_groups():
if atom_group.resname != "HIS": continue
protonation = get_histidine_protonation(atom_group)
if verbose or 1:
rc = predict_protonation(atom_group)
if rc is None:
s = "%s" % rc
else:
s = "%0.1f, %0.1f" % tuple(rc)
print >> log, '%satom group "%s" has %-22s (%s)' % (
' ' * 6,
atom_group.id_str(),
protonation,
s,
)
#interpret_his1_his2(*tuple(rc))
counts.setdefault(protonation, 0)
if protonation is None: continue
counts[protonation] += 1
count += 1
restraints = hpdl_database[protonation]
for names, values in restraints.items():
i_seqs = []
atoms = []
for name in names:
# need to test this...
for atom in _alt_loc_atom_generator(
residue_group, atom_group):
if name.strip() == atom.name.strip():
i_seqs.append(atom.i_seq)
atoms.append(atom.name)
break
if len(i_seqs) != len(names): continue
i_seqs_restraints[tuple(i_seqs)] = values
if len(i_seqs) != 2:
i_seqs.reverse()
i_seqs_restraints[tuple(i_seqs)] = values
if verbose:
i_seqs.append("names")
i_seqs_restraints[tuple(i_seqs)] = atoms
count_b = _set_or_reset_bond_restraints(
geometry,
i_seqs_restraints,
log=log,
#verbose=verbose,
)
count_a = _set_or_reset_angle_restraints(
geometry,
i_seqs_restraints,
log=log,
#verbose=verbose,
)
#
print >> log, " Number of bonds, angles adjusted : %d, %d in %s HIS" % (
count_b,
count_a,
count,
)