def generate_protein_fragments(
hierarchy,
geometry,
backbone_only=False,
use_capping_hydrogens=False,
verbose=False,
):
from mmtbx.conformation_dependent_library.multi_residue_class import \
ThreeProteinResidues, RestraintsRegistry
registry = RestraintsRegistry()
threes = ThreeProteinResidues(geometry, registry=registry)
for residue in generate_residues_via_conformer(
hierarchy,
backbone_only=backbone_only,
verbose=verbose,
):
list.append(threes, residue)
if verbose: print 'THREE', threes
sub_unit = threes.provide_second_sub_unit_if_unlinked()
if verbose: print 'THREE, SUBUNIT', threes, sub_unit
if sub_unit:
threes.start = True
threes.end = True
yield threes
threes = sub_unit
threes.start = True
threes.end = True
yield threes
def update_restraints(
hierarchy,
geometry, # restraints_manager,
current_geometry=None, # xray_structure!!
sites_cart=None,
cdl_proxies=None,
ideal=True,
esd=True,
esd_factor=1.,
log=None,
verbose=False,
):
global registry
registry = RestraintsRegistry()
if current_geometry:
assert not sites_cart
sites_cart = current_geometry.sites_cart()
if sites_cart:
pdb_atoms = hierarchy.atoms()
# XXX PDB_TRANSITION VERY SLOW
for j_seq, atom in enumerate(pdb_atoms):
atom.xyz = sites_cart[j_seq]
threes = None
average_updates = 0
total_updates = 0
for threes in generate_protein_threes(
hierarchy,
geometry,
cdl_class=True,
omega_cdl=True,
#verbose=verbose,
):
threes.apply_updates = apply_updates
if threes.cis_group(omega_cdl=True):
if verbose and 0:
print 'cis ' * 20
print threes
continue
restraint_values = get_restraint_values(threes)
if restraint_values is None: continue
if restraint_values[0] == "I":
average_updates += 1
else:
total_updates += 1
threes.apply_updates(
threes,
restraint_values,
cdl_proxies,
ideal=ideal,
esd=esd,
esd_factor=esd_factor,
)
if registry.n:
threes.apply_average_updates(registry)
assert 0
geometry.reset_internals()
if verbose and threes and threes.errors:
if log:
log.write(
" Residues not completely updated with CDL restraints\n\n")
for line in threes.errors:
if log:
log.write("%s\n" % line)
else:
print line
return geometry
def update_restraints(
hierarchy,
geometry, # restraints_manager,
current_geometry=None, # xray_structure!!
sites_cart=None,
cdl_proxies=None,
ideal=True,
esd=True,
esd_factor=1.,
interpolate=False,
log=None,
verbose=False,
):
global registry
registry = RestraintsRegistry()
if current_geometry:
assert not sites_cart
sites_cart = current_geometry.sites_cart()
if sites_cart:
pdb_atoms = hierarchy.atoms()
#if atom_lookup:
# for j_seq, scatterer in enumerate(current_geometry.scatterers()):
# pdb_atoms[atom_lookup[scatterer.label]].xyz = sites_cart[j_seq]
#else:
# XXX PDB_TRANSITION VERY SLOW
for j_seq, atom in enumerate(pdb_atoms):
atom.xyz = sites_cart[j_seq]
#atom_lookup[atom.id_str()] = j_seq
threes = None
average_updates = 0
total_updates = 0
for threes in generate_protein_threes(
hierarchy,
geometry, #restraints_manager,
#verbose=verbose,
):
if threes.cis_group():
continue
if 0:
res_type_group = get_res_type_group(
threes[1].resname,
threes[2].resname,
)
if res_type_group is None: continue
key = threes.get_cdl_key() #verbose=verbose)
restraint_values = cdl_database[res_type_group][key]
print restraint_values
print len(restraint_values)
assert 0
else:
restraint_values = get_restraint_values(threes,
interpolate=interpolate)
#if 1:
# print threes, threes.are_linked(), res_type_group, key, restraint_values
if restraint_values is None: continue
if restraint_values[0] == "I":
#print threes, threes.are_linked(), res_type_group, key, restraint_values[:4]
average_updates += 1
else:
total_updates += 1
threes.apply_updates(
restraint_values,
cdl_proxies,
ideal=ideal,
esd=esd,
esd_factor=esd_factor,
)
if registry.n: threes.apply_average_updates(registry)
# restraints_manager.geometry.reset_internals()
geometry.reset_internals()
if verbose and threes and threes.errors:
if log:
log.write(
" Residues not completely updated with CDL restraints\n\n")
for line in threes.errors:
if log:
log.write("%s\n" % line)
else:
print line
# print 'average updates',average_updates,total_updates
# assert average_updates==0
return geometry #restraints_manager
from __future__ import division
import sys
import copy
from string import letters, digits
import iotbx.pdb
from mmtbx.conformation_dependent_library.cdl_database import cdl_database
import mmtbx.conformation_dependent_library.cdl_utils
from mmtbx.conformation_dependent_library.multi_residue_class import \
ThreeProteinResidues, RestraintsRegistry
chararcters_36 = letters[:26] + digits
registry = RestraintsRegistry()
def restraints_show(restraints_values):
from mmtbx.conformation_dependent_library.cdl_setup import headers
outl = ""
for i, item in enumerate(restraints_values):
if i % 2 == 0:
if i == 0:
s = " %s, %s : %s %s\n"
elif i < 15:
s = " %-25s%s: %9.2f %9.2f\n"
else:
s = " %-25s%s: %9.4f %9.4f\n"
outl += s % (
headers[i],
def backrub_move(
prev_res,
cur_res,
next_res,
angle,
move_oxygens=False,
accept_worse_rama=False,
rotamer_manager=None,
rama_manager=None):
import boost.python
ext = boost.python.import_ext("mmtbx_validation_ramachandran_ext")
from mmtbx_validation_ramachandran_ext import rama_eval
from scitbx.matrix import rotate_point_around_axis
from mmtbx.conformation_dependent_library.multi_residue_class import ThreeProteinResidues, \
RestraintsRegistry
if abs(angle) < 1e-4:
return
if prev_res is None or next_res is None:
return
saved_res = [{},{},{}]
for i, r in enumerate([prev_res, cur_res, next_res]):
for a in r.atoms():
saved_res[i][a.name.strip()] = a.xyz
if rotamer_manager is None:
rotamer_manager = RotamerEval()
prev_ca = prev_res.find_atom_by(name=" CA ")
cur_ca = cur_res.find_atom_by(name=" CA ")
next_ca = next_res.find_atom_by(name=" CA ")
if prev_ca is None or next_ca is None or cur_ca is None:
return
atoms_to_move = []
atoms_to_move.append(prev_res.find_atom_by(name=" C "))
atoms_to_move.append(prev_res.find_atom_by(name=" O "))
for atom in cur_res.atoms():
atoms_to_move.append(atom)
atoms_to_move.append(next_res.find_atom_by(name=" N "))
for atom in atoms_to_move:
assert atom is not None
new_xyz = rotate_point_around_axis(
axis_point_1 = prev_ca.xyz,
axis_point_2 = next_ca.xyz,
point = atom.xyz,
angle = angle,
deg = True)
atom.xyz = new_xyz
if move_oxygens:
registry = RestraintsRegistry()
if rama_manager is None:
rama_manager = rama_eval()
tpr = ThreeProteinResidues(geometry=None, registry=registry)
tpr.append(prev_res)
tpr.append(cur_res)
tpr.append(next_res)
phi_psi_angles = tpr.get_phi_psi_angles()
rama_key = tpr.get_ramalyze_key()
ev_before = rama_manager.evaluate_angles(rama_key, phi_psi_angles[0], phi_psi_angles[1])
theta1 = _find_theta(
ap1 = prev_ca.xyz,
ap2 = cur_ca.xyz,
cur_xyz = prev_res.find_atom_by(name=" O ").xyz,
needed_xyz = saved_res[0]["O"])
theta2 = _find_theta(
ap1 = cur_ca.xyz,
ap2 = next_ca.xyz,
cur_xyz = cur_res.find_atom_by(name=" O ").xyz,
needed_xyz = saved_res[1]["O"])
for a in [prev_res.find_atom_by(name=" C "),
prev_res.find_atom_by(name=" O "),
cur_res.find_atom_by(name=" C ")]:
new_xyz = rotate_point_around_axis(
axis_point_1 = prev_ca.xyz,
axis_point_2 = cur_ca.xyz,
point = a.xyz,
angle = theta1,
deg = True)
a.xyz = new_xyz
for a in [cur_res.find_atom_by(name=" C "),
cur_res.find_atom_by(name=" O "),
next_res.find_atom_by(name=" N ")]:
new_xyz = rotate_point_around_axis(
axis_point_1 = cur_ca.xyz,
axis_point_2 = next_ca.xyz,
point = a.xyz,
angle = theta2,
deg = True)
a.xyz = new_xyz
phi_psi_angles = tpr.get_phi_psi_angles()
rama_key = tpr.get_ramalyze_key()
ev_after = rama_manager.evaluate_angles(rama_key, phi_psi_angles[0], phi_psi_angles[1])
if ev_before > ev_after and not accept_worse_rama:
for a in [prev_res.find_atom_by(name=" C "),
prev_res.find_atom_by(name=" O "),
cur_res.find_atom_by(name=" C ")]:
new_xyz = rotate_point_around_axis(
axis_point_1 = prev_ca.xyz,
axis_point_2 = cur_ca.xyz,
point = a.xyz,
angle = -theta1,
deg = True)
a.xyz = new_xyz
for a in [cur_res.find_atom_by(name=" C "),
cur_res.find_atom_by(name=" O "),
next_res.find_atom_by(name=" N ")]:
new_xyz = rotate_point_around_axis(
axis_point_1 = cur_ca.xyz,
axis_point_2 = next_ca.xyz,
point = a.xyz,
angle = -theta2,
deg = True)
a.xyz = new_xyz
def update_restraints(hierarchy,
geometry,
current_geometry=None, # xray_structure!!
sites_cart=None,
cdl_proxies=None,
cis_pro_eh99=False, # use EH99 for cis-PRO
cdl_svl=False, # use CDL-SVL
ideal=True,
esd=True,
esd_factor=1.,
interpolate=False,
log=None,
verbose=False,
):
global registry
registry = RestraintsRegistry()
if current_geometry:
assert not sites_cart
sites_cart = current_geometry.sites_cart()
if sites_cart:
pdb_atoms = hierarchy.atoms()
# XXX PDB_TRANSITION VERY SLOW
for j_seq, atom in enumerate(pdb_atoms):
atom.xyz = sites_cart[j_seq]
threes = None
average_updates = 0
total_updates = 0
for threes in generate_protein_threes(
hierarchy,
geometry,
cdl_class=True,
retain_selection="name ca or name c or name n or name o or name cb or name h or name cd or name cg",
#verbose=verbose,
):
if cdl_svl:
restraint_values = get_restraint_values(threes,
cdl_svl=cdl_svl,
interpolate=interpolate)
# print('cdl_svl %s %s' % (threes,restraint_values))
else:
if threes.cis_group():
if cis_pro_eh99:
# returns cis-PRO EH99 values if asked
restraint_values = get_restraint_values(threes, interpolate=interpolate)
# print('cis-PRO EH99 %s %s' % (threes, restraint_values))
else:
continue
else:
restraint_values = get_restraint_values(threes, interpolate=interpolate)
# print('CDL %s %s' % (threes, restraint_values))
if restraint_values is None: continue
if restraint_values[0]=="I":
average_updates += 1
else:
total_updates += 1
threes.apply_updates(restraint_values,
cdl_proxies,
ideal=ideal,
esd=esd,
esd_factor=esd_factor,
)
if registry.n: threes.apply_average_updates(registry)
geometry.reset_internals()
if verbose and threes and threes.errors:
if log:
log.write(" Residues not completely updated with CDL restraints\n\n")
for line in threes.errors:
if log:
log.write("%s\n" % line)
else:
print(line)
# print 'average updates',average_updates,total_updates
# assert average_updates==0
return geometry #restraints_manager