def get_rotamer_data(atom_group,
sa,
rotamer_evaluator,
rotamer_id,
all_dict,
sites_cart,
):
resname=substitute_residue_lookup.get(atom_group.resname,
atom_group.resname,
)
if resname not in rdl_database.keys(): return None
if resname in ["PRO", "GLY"]: return None
model_rot, m_chis, value = rotalyze.evaluate_rotamer(
atom_group=atom_group,
sidechain_angles=sa,
rotamer_evaluator=rotamer_evaluator,
rotamer_id=rotamer_id,
all_dict=all_dict,
sites_cart=sites_cart,
)
return model_rot, m_chis, value
def get_rotamer_data(atom_group,
sa,
rotamer_evaluator,
rotamer_id,
all_dict,
sites_cart,
):
resname=substitute_residue_lookup.get(atom_group.resname,
atom_group.resname,
)
if resname not in rdl_database.keys(): return None
if resname in ["PRO", "GLY"]: return None
model_rot, m_chis, value = rotalyze.evaluate_rotamer(
atom_group=atom_group,
sidechain_angles=sa,
rotamer_evaluator=rotamer_evaluator,
rotamer_id=rotamer_id,
all_dict=all_dict,
sites_cart=sites_cart,
)
return model_rot, m_chis, value
def search(self, atom_group, all_dict, m_chis, r_chis, rotamer,
sites_cart_moving, xray_structure, key):
include_ca_hinge = False
axis_and_atoms_to_rotate, tardy_labels= \
rotatable_bonds.axes_and_atoms_aa_specific(
residue=atom_group,
mon_lib_srv=self.mon_lib_srv,
remove_clusters_with_all_h=True,
include_labels=True,
log=None)
if (axis_and_atoms_to_rotate is None):
print >> self.log, "Skipped %s rotamer (TARDY error)" % key
return False
assert len(m_chis) == len(r_chis)
#exclude H-only clusters if necessary
while len(axis_and_atoms_to_rotate) > len(m_chis):
axis_and_atoms_to_rotate = \
axis_and_atoms_to_rotate[:-1]
assert len(m_chis) == len(axis_and_atoms_to_rotate)
counter = 0
residue_iselection = atom_group.atoms().extract_i_seq()
cur_ca = None
ca_add = None
ca_axes = []
for atom in atom_group.atoms():
if atom.name == " CA ":
cur_ca = atom.i_seq
if cur_ca is not None:
cur_c_alpha_hinges = self.c_alpha_hinges.get(cur_ca)
if cur_c_alpha_hinges is not None:
residue_length = len(tardy_labels)
for ca_pt in cur_c_alpha_hinges[0]:
residue_iselection.append(ca_pt)
tardy_labels.append(self.name_hash[ca_pt][0:4])
for bb_pt in cur_c_alpha_hinges[1]:
residue_iselection.append(bb_pt)
tardy_labels.append(self.name_hash[bb_pt][0:4])
end_pts = (residue_length, residue_length + 1)
group = []
for i, value in enumerate(tardy_labels):
if i not in end_pts:
group.append(i)
ca_add = [end_pts, group]
ca_axes.append(ca_add)
for ax in axis_and_atoms_to_rotate:
ca_axes.append(ax)
sites_cart_residue = \
sites_cart_moving.select(residue_iselection)
sites_cart_residue_start = sites_cart_residue.deep_copy()
selection = flex.bool(len(sites_cart_moving), residue_iselection)
rev_first_atoms = []
rev_start = rotamer_evaluator(
sites_cart_start=sites_cart_residue_start,
unit_cell=self.unit_cell,
two_mfo_dfc_map=self.target_map_data,
mfo_dfc_map=self.residual_map_data)
sidechain_only_iselection = flex.size_t()
for i_seq in residue_iselection:
atom_name = self.name_hash[i_seq][0:4]
if atom_name not in [' N ', ' CA ', ' C ', ' O ']:
sidechain_only_iselection.append(i_seq)
sites_cart_sidechain = \
sites_cart_moving.select(sidechain_only_iselection)
sites_frac_residue = self.unit_cell.fractionalize(sites_cart_sidechain)
sigma_cutoff = 1.0
sigma_residue = []
for rsf in sites_frac_residue:
if self.target_map_data.eight_point_interpolation(
rsf) < sigma_cutoff:
sigma_residue.append(False)
else:
sigma_residue.append(True)
sigma_count_start = 0
for sigma_state in sigma_residue:
if sigma_state:
sigma_count_start += 1
else:
break
for aa in axis_and_atoms_to_rotate:
axis = aa[0]
atoms = aa[1]
new_xyz = flex.vec3_double()
angle_deg = r_chis[counter] - m_chis[counter]
#skip angle rotations that are close to zero
if math.fabs(angle_deg) < 0.01:
counter += 1
continue
if angle_deg < 0:
angle_deg += 360.0
for atom in atoms:
new_xyz = rotate_point_around_axis(
axis_point_1=sites_cart_residue[axis[0]],
axis_point_2=sites_cart_residue[axis[1]],
point=sites_cart_residue[atom],
angle=angle_deg,
deg=True)
sites_cart_residue[atom] = new_xyz
counter += 1
#***** TEST *****
sites_cart_moving.set_selected(residue_iselection, sites_cart_residue)
cur_rotamer, cur_chis, cur_value = rotalyze.evaluate_rotamer(
atom_group=atom_group,
sidechain_angles=self.sa,
rotamer_evaluator=self.rotamer_evaluator,
rotamer_id=self.rotamer_id,
all_dict=all_dict,
sites_cart=sites_cart_moving)
assert rotamer == cur_rotamer
#****************
if len(ca_axes) == 0:
eval_axes = axis_and_atoms_to_rotate
else:
eval_axes = ca_axes
include_ca_hinge = True
for i_aa, aa in enumerate(eval_axes):
if (i_aa == len(eval_axes) - 1):
sites_aa = flex.vec3_double()
for aa_ in aa[1]:
sites_aa.append(sites_cart_residue[aa_])
elif i_aa == 0 and include_ca_hinge:
sites_aa = flex.vec3_double()
for aa_ in aa[1]:
sites_aa.append(sites_cart_residue[aa_])
else:
sites_aa = flex.vec3_double([sites_cart_residue[aa[1][0]]])
rev_i = rotamer_evaluator(sites_cart_start=sites_aa,
unit_cell=self.unit_cell,
two_mfo_dfc_map=self.target_map_data,
mfo_dfc_map=self.residual_map_data)
rev_first_atoms.append(rev_i)
rev = rotamer_evaluator(sites_cart_start=sites_cart_residue,
unit_cell=self.unit_cell,
two_mfo_dfc_map=self.target_map_data,
mfo_dfc_map=self.residual_map_data)
residue_sites_best = sites_cart_residue.deep_copy()
residue_sites_best, rotamer_id_best = \
torsion_search(
residue_evaluator=rev,
cluster_evaluators=rev_first_atoms,
axes_and_atoms_to_rotate=eval_axes,
rotamer_sites_cart=sites_cart_residue,
rotamer_id_best=rotamer,
residue_sites_best=residue_sites_best,
params = self.torsion_params,
rotamer_id = rotamer,
include_ca_hinge = include_ca_hinge)
sites_cart_moving.set_selected(residue_iselection, residue_sites_best)
xray_structure.set_sites_cart(sites_cart_moving)
cur_rotamer, cur_chis, cur_value = rotalyze.evaluate_rotamer(
atom_group=atom_group,
sidechain_angles=self.sa,
rotamer_evaluator=self.rotamer_evaluator,
rotamer_id=self.rotamer_id,
all_dict=all_dict,
sites_cart=sites_cart_moving)
rotamer_match = (cur_rotamer == rotamer)
if rev_start.is_better(sites_cart=residue_sites_best,
percent_cutoff=0.15, verbose=True) and \
rotamer_match:
sidechain_only_iselection = flex.size_t()
for i_seq in residue_iselection:
atom_name = self.name_hash[i_seq][0:4]
if atom_name not in [
' N ', ' CA ', ' C ', ' O ', ' OXT', ' H ', ' HA '
]:
sidechain_only_iselection.append(i_seq)
selection = flex.bool(len(sites_cart_moving),
sidechain_only_iselection)
selection_within = xray_structure.selection_within(
radius=1.0, selection=selection)
#check for bad steric clashes
created_clash = False
for i, state in enumerate(selection_within):
if state:
if i not in sidechain_only_iselection:
#print >> self.log, "atom clash: ", self.name_hash[i]
created_clash = True
if created_clash:
sites_cart_moving.set_selected(residue_iselection,
sites_cart_residue_start)
xray_structure.set_sites_cart(sites_cart_moving)
return False
sidechain_only_iselection = flex.size_t()
for i_seq in residue_iselection:
atom_name = self.name_hash[i_seq][0:4]
if atom_name not in [' N ', ' CA ', ' C ', ' O ']:
sidechain_only_iselection.append(i_seq)
sites_cart_sidechain = \
sites_cart_moving.select(sidechain_only_iselection)
sites_frac_residue = self.unit_cell.fractionalize(
sites_cart_sidechain)
sigma_cutoff = 1.0
sigma_residue = []
for rsf in sites_frac_residue:
if self.target_map_data.eight_point_interpolation(
rsf) < sigma_cutoff:
sigma_residue.append(False)
else:
sigma_residue.append(True)
sigma_count = 0
for sigma_state in sigma_residue:
if sigma_state:
sigma_count += 1
else:
break
if sigma_count < sigma_count_start:
sites_cart_moving.set_selected(residue_iselection,
sites_cart_residue_start)
xray_structure.set_sites_cart(sites_cart_moving)
return False
return True
else:
sites_cart_moving.set_selected(residue_iselection,
sites_cart_residue_start)
xray_structure.set_sites_cart(sites_cart_moving)
return False
def search(
self,
atom_group,
all_dict,
m_chis,
r_chis,
rotamer,
sites_cart_moving,
xray_structure,
key):
include_ca_hinge = False
axis_and_atoms_to_rotate, tardy_labels= \
rotatable_bonds.axes_and_atoms_aa_specific(
residue=atom_group,
mon_lib_srv=self.mon_lib_srv,
remove_clusters_with_all_h=True,
include_labels=True,
log=None)
if (axis_and_atoms_to_rotate is None) :
print >> self.log, "Skipped %s rotamer (TARDY error)" % key
return False
assert len(m_chis) == len(r_chis)
#exclude H-only clusters if necessary
while len(axis_and_atoms_to_rotate) > len(m_chis):
axis_and_atoms_to_rotate = \
axis_and_atoms_to_rotate[:-1]
assert len(m_chis) == len(axis_and_atoms_to_rotate)
counter = 0
residue_iselection = atom_group.atoms().extract_i_seq()
cur_ca = None
ca_add = None
ca_axes = []
for atom in atom_group.atoms():
if atom.name == " CA ":
cur_ca = atom.i_seq
if cur_ca is not None:
cur_c_alpha_hinges = self.c_alpha_hinges.get(cur_ca)
if cur_c_alpha_hinges is not None:
residue_length = len(tardy_labels)
for ca_pt in cur_c_alpha_hinges[0]:
residue_iselection.append(ca_pt)
tardy_labels.append(self.name_hash[ca_pt][0:4])
for bb_pt in cur_c_alpha_hinges[1]:
residue_iselection.append(bb_pt)
tardy_labels.append(self.name_hash[bb_pt][0:4])
end_pts = (residue_length, residue_length+1)
group = []
for i, value in enumerate(tardy_labels):
if i not in end_pts:
group.append(i)
ca_add = [end_pts, group]
ca_axes.append(ca_add)
for ax in axis_and_atoms_to_rotate:
ca_axes.append(ax)
sites_cart_residue = \
sites_cart_moving.select(residue_iselection)
sites_cart_residue_start = sites_cart_residue.deep_copy()
selection = flex.bool(
len(sites_cart_moving),
residue_iselection)
rev_first_atoms = []
rev_start = fit_rotamers.rotamer_evaluator(
sites_cart_start = sites_cart_residue_start,
unit_cell = self.unit_cell,
two_mfo_dfc_map = self.target_map_data,
mfo_dfc_map = self.residual_map_data)
sidechain_only_iselection = flex.size_t()
for i_seq in residue_iselection:
atom_name = self.name_hash[i_seq][0:4]
if atom_name not in [' N ', ' CA ', ' C ', ' O ']:
sidechain_only_iselection.append(i_seq)
sites_cart_sidechain = \
sites_cart_moving.select(sidechain_only_iselection)
sites_frac_residue = self.unit_cell.fractionalize(sites_cart_sidechain)
sigma_cutoff = 1.0
sigma_residue = []
for rsf in sites_frac_residue:
if self.target_map_data.eight_point_interpolation(rsf) < sigma_cutoff:
sigma_residue.append(False)
else:
sigma_residue.append(True)
sigma_count_start = 0
for sigma_state in sigma_residue:
if sigma_state:
sigma_count_start += 1
else:
break
for aa in axis_and_atoms_to_rotate:
axis = aa[0]
atoms = aa[1]
new_xyz = flex.vec3_double()
angle_deg = r_chis[counter] - m_chis[counter]
#skip angle rotations that are close to zero
if math.fabs(angle_deg) < 0.01:
counter += 1
continue
if angle_deg < 0:
angle_deg += 360.0
for atom in atoms:
new_xyz = rotate_point_around_axis(
axis_point_1=sites_cart_residue[axis[0]],
axis_point_2=sites_cart_residue[axis[1]],
point=sites_cart_residue[atom],
angle=angle_deg, deg=True)
sites_cart_residue[atom] = new_xyz
counter += 1
#***** TEST *****
sites_cart_moving.set_selected(
residue_iselection, sites_cart_residue)
cur_rotamer, cur_chis, cur_value = rotalyze.evaluate_rotamer(
atom_group=atom_group,
sidechain_angles=self.sa,
rotamer_evaluator=self.rotamer_evaluator,
rotamer_id=self.rotamer_id,
all_dict=all_dict,
sites_cart=sites_cart_moving)
assert rotamer == cur_rotamer
#****************
if len(ca_axes) == 0:
eval_axes = axis_and_atoms_to_rotate
else:
eval_axes = ca_axes
include_ca_hinge = True
for i_aa, aa in enumerate(eval_axes):
if(i_aa == len(eval_axes)-1):
sites_aa = flex.vec3_double()
for aa_ in aa[1]:
sites_aa.append(sites_cart_residue[aa_])
elif i_aa == 0 and include_ca_hinge:
sites_aa = flex.vec3_double()
for aa_ in aa[1]:
sites_aa.append(sites_cart_residue[aa_])
else:
sites_aa = flex.vec3_double([sites_cart_residue[aa[1][0]]])
rev_i = fit_rotamers.rotamer_evaluator(
sites_cart_start = sites_aa,
unit_cell = self.unit_cell,
two_mfo_dfc_map = self.target_map_data,
mfo_dfc_map = self.residual_map_data)
rev_first_atoms.append(rev_i)
rev = fit_rotamers.rotamer_evaluator(
sites_cart_start = sites_cart_residue,
unit_cell = self.unit_cell,
two_mfo_dfc_map = self.target_map_data,
mfo_dfc_map = self.residual_map_data)
residue_sites_best = sites_cart_residue.deep_copy()
residue_sites_best, rotamer_id_best = \
fit_rotamers.torsion_search(
residue_evaluator=rev,
cluster_evaluators=rev_first_atoms,
axes_and_atoms_to_rotate=eval_axes,
rotamer_sites_cart=sites_cart_residue,
rotamer_id_best=rotamer,
residue_sites_best=residue_sites_best,
params = self.torsion_params,
rotamer_id = rotamer,
include_ca_hinge = include_ca_hinge)
sites_cart_moving.set_selected(
residue_iselection, residue_sites_best)
xray_structure.set_sites_cart(sites_cart_moving)
cur_rotamer, cur_chis, cur_value = rotalyze.evaluate_rotamer(
atom_group=atom_group,
sidechain_angles=self.sa,
rotamer_evaluator=self.rotamer_evaluator,
rotamer_id=self.rotamer_id,
all_dict=all_dict,
sites_cart=sites_cart_moving)
rotamer_match = (cur_rotamer == rotamer)
if rev_start.is_better(sites_cart=residue_sites_best,
percent_cutoff=0.15, verbose=True) and \
rotamer_match:
sidechain_only_iselection = flex.size_t()
for i_seq in residue_iselection:
atom_name = self.name_hash[i_seq][0:4]
if atom_name not in [' N ', ' CA ', ' C ', ' O ',
' OXT', ' H ', ' HA ']:
sidechain_only_iselection.append(i_seq)
selection = flex.bool(
len(sites_cart_moving),
sidechain_only_iselection)
selection_within = xray_structure.selection_within(
radius = 1.0,
selection = selection)
#check for bad steric clashes
created_clash = False
for i, state in enumerate(selection_within):
if state:
if i not in sidechain_only_iselection:
#print >> self.log, "atom clash: ", self.name_hash[i]
created_clash = True
if created_clash:
sites_cart_moving.set_selected(
residue_iselection, sites_cart_residue_start)
xray_structure.set_sites_cart(sites_cart_moving)
return False
sidechain_only_iselection = flex.size_t()
for i_seq in residue_iselection:
atom_name = self.name_hash[i_seq][0:4]
if atom_name not in [' N ', ' CA ', ' C ', ' O ']:
sidechain_only_iselection.append(i_seq)
sites_cart_sidechain = \
sites_cart_moving.select(sidechain_only_iselection)
sites_frac_residue = self.unit_cell.fractionalize(sites_cart_sidechain)
sigma_cutoff = 1.0
sigma_residue = []
for rsf in sites_frac_residue:
if self.target_map_data.eight_point_interpolation(rsf) < sigma_cutoff:
sigma_residue.append(False)
else:
sigma_residue.append(True)
sigma_count = 0
for sigma_state in sigma_residue:
if sigma_state:
sigma_count += 1
else:
break
if sigma_count < sigma_count_start:
sites_cart_moving.set_selected(
residue_iselection, sites_cart_residue_start)
xray_structure.set_sites_cart(sites_cart_moving)
return False
return True
else:
sites_cart_moving.set_selected(
residue_iselection, sites_cart_residue_start)
xray_structure.set_sites_cart(sites_cart_moving)
return False
