def set_rama_angles(moving_h, angles):
"""
angles = [(phi, psi), (phi, psi), ... (phi, psi)]
phi or psi == None means we don't change this angle
returns deep-copied hierarchy with new angles. Change occurs from first to
last angle so starting point would be in the same place.
This function should produce up to all possible favored conformations.
This function doesn't change moving_h
"""
# print "angles", angles
# STOP()
result_h = moving_h.deep_copy()
result_h.reset_atom_i_seqs()
phi_psi_atoms = utils.get_phi_psi_atoms(moving_h)
assert len(phi_psi_atoms) == len(angles)
for ps_atoms, target_angle_pair in zip(phi_psi_atoms, angles):
phi_psi_pair = ps_atoms[0]
phi_psi_angles = utils.get_pair_angles(phi_psi_pair)
# phi
if target_angle_pair[0] is not None:
utils.rotate_atoms_around_bond(
result_h,
phi_psi_pair[0][1],
phi_psi_pair[0][2],
angle=-phi_psi_angles[0]+target_angle_pair[0])
# psi
if target_angle_pair[1] is not None:
utils.rotate_atoms_around_bond(
result_h,
phi_psi_pair[1][1],
phi_psi_pair[1][2],
angle=-phi_psi_angles[1]+target_angle_pair[1])
return result_h
def __call__(self, hsh_tuple):
temp_annot = iotbx.pdb.secondary_structure.annotation(
helices=hsh_tuple[0], sheets=hsh_tuple[1])
helix = len(hsh_tuple[0]) > 0
# print temp_annot.as_pdb_str().replace('\n',' '),
ss_params = mmtbx.secondary_structure.manager.get_default_ss_params()
ss_params.secondary_structure.enabled = True
ss_params.secondary_structure.protein.remove_outliers = False
ss_params.secondary_structure.protein.helix = []
ss_params.secondary_structure.protein.sheet = []
ss_params.secondary_structure.nucleic_acid.enabled = False
ss_m_log = StringIO()
ss_manager = mmtbx.secondary_structure.manager(
pdb_hierarchy=self.pdb_h,
atom_selection_cache=self.asc,
sec_str_from_pdb_file=temp_annot,
params=ss_params.secondary_structure,
show_summary_on=False,
log=ss_m_log)
h_bond_proxies, hb_angles = ss_manager.create_protein_hbond_proxies(
log=ss_m_log)
cutoff_bad = self.bad_hbond_cutoff
cutoff_mediocre = self.mediocre_hbond_cutoff
n_hbonds = 0
n_bad_hbonds = 0
n_mediocre_hbonds = 0
hb_lens = []
for hb_p in h_bond_proxies:
# print dir(hb_p)
n_hbonds += 1
hb_len = self.atoms[hb_p.i_seqs[0]].distance(
self.atoms[hb_p.i_seqs[1]])
hb_lens.append(hb_len)
if hb_len > cutoff_bad:
n_bad_hbonds += 1
elif hb_len > cutoff_mediocre:
n_mediocre_hbonds += 1
# Ramachandran outliers and wrong areas
sele = self.asc.selection(temp_annot.as_atom_selections()[0])
ss_h = self.pdb_h.select(sele)
phi_psi_atoms = get_phi_psi_atoms(ss_h)
n_outliers = 0
n_wrong_region = 0
for phi_psi_pair, rama_key in phi_psi_atoms:
phi, psi = get_pair_angles(phi_psi_pair)
r_eval = self.r.evaluate_angles(rama_key, phi, psi)
if r_eval == ramalyze.RAMALYZE_OUTLIER:
n_outliers += 1
else:
reg = pp2_helix_sheet_rama_region(phi, psi, self.pp2m)
if (helix and reg != 'A') or (not helix and reg != 'B'):
n_wrong_region += 1
# print " Wrong region:", phi_psi_pair[0][2].id_str(), reg, helix
del ss_manager
del ss_params
return n_hbonds, n_bad_hbonds, n_mediocre_hbonds, hb_lens, n_outliers, n_wrong_region
def set_rama_angles(moving_h, angles):
"""
angles = [(phi, psi), (phi, psi), ... (phi, psi)]
phi or psi == None means we don't change this angle
returns deep-copied hierarchy with new angles. Change occurs from first to
last angle so starting point would be in the same place.
This function should produce up to all possible favored conformations.
This function doesn't change moving_h
"""
# print "angles", angles
# STOP()
result_h = moving_h.deep_copy()
result_h.reset_atom_i_seqs()
phi_psi_atoms = utils.get_phi_psi_atoms(moving_h)
assert len(phi_psi_atoms) == len(angles)
for ps_atoms, target_angle_pair in zip(phi_psi_atoms, angles):
phi_psi_pair = ps_atoms[0]
phi_psi_angles = utils.get_pair_angles(phi_psi_pair)
# phi
if target_angle_pair[0] is not None:
utils.rotate_atoms_around_bond(
result_h,
phi_psi_pair[0][1],
phi_psi_pair[0][2],
angle=-phi_psi_angles[0]+target_angle_pair[0])
# psi
if target_angle_pair[1] is not None:
utils.rotate_atoms_around_bond(
result_h,
phi_psi_pair[1][1],
phi_psi_pair[1][2],
angle=-phi_psi_angles[1]+target_angle_pair[1])
return result_h
def helix_sheet_rama_region(cls, phi_psi_pair):
# result 1 - helix, 2 - sheet, 0 - other
# cutoff: phi < 70 - helix, phi>=70 - sheet
phi_psi_angles = get_pair_angles(phi_psi_pair, round_coords=False)
if phi_psi_angles[1] < 70:
return 1
else:
return 2
def set_rama_angles(moving_h,
angles,
direction_forward=True,
check_omega=False):
"""
angles = [(phi, psi), (phi, psi), ... (phi, psi)]
phi or psi == None means we don't change this angle
returns deep-copied hierarchy with new angles. Change occurs from first to
last angle so starting point would be in the same place.
This function should produce up to all possible favored conformations.
This function doesn't change moving_h
direction_forward==True - set from beginning to end - the end residue moves
direction_forward==False - set from end to beginning, the first residue moves
"""
# print "angles", angles
# STOP()
result_h = moving_h.deep_copy()
result_h.reset_atom_i_seqs()
fixed_omega = False
phi_psi_atoms = utils.get_phi_psi_atoms(moving_h, omega=True)
assert len(phi_psi_atoms) == len(angles), "%d != %d" % (len(phi_psi_atoms),
len(angles))
if not direction_forward:
phi_psi_atoms.reverse()
angles.reverse()
for ps_atoms, target_angle_pair in zip(phi_psi_atoms, angles):
phi_psi_pair = ps_atoms[0]
# print "phi_psi_pair", phi_psi_pair
omega = ps_atoms[2]
phi_psi_angles = utils.get_pair_angles(phi_psi_pair)
# print "ps_atoms, target_angle_pair", phi_psi_angles, target_angle_pair
# phi
if target_angle_pair[0] is not None and phi_psi_angles[0] is not None:
rotation_angle = -phi_psi_angles[0] + target_angle_pair[0]
# print "rot angle", rotation_angle
# if not direction_forward:
# rotation_angle = -rotation_angle
utils.rotate_atoms_around_bond(result_h,
phi_psi_pair[0][1],
phi_psi_pair[0][2],
angle=rotation_angle,
direction_forward=direction_forward)
# psi
if target_angle_pair[1] is not None and phi_psi_angles[1] is not None:
rotation_angle = -phi_psi_angles[1] + target_angle_pair[1]
# print "rot angle", rotation_angle
# if not direction_forward:
# rotation_angle = -rotation_angle
utils.rotate_atoms_around_bond(result_h,
phi_psi_pair[1][1],
phi_psi_pair[1][2],
angle=rotation_angle,
direction_forward=direction_forward)
# omega
if omega is not None and abs(abs(omega) - 180) > 10 and check_omega:
rotation_angle = -omega + 180
# print "Omega rotation:", omega, rotation_angle
utils.rotate_atoms_around_bond(result_h,
phi_psi_pair[0][0],
phi_psi_pair[0][1],
angle=rotation_angle,
direction_forward=direction_forward)
fixed_omega = True
# print utils.list_rama_outliers_h(result_h)
# result_h.write_pdb_file(file_name="variant_%s.pdb" % direction_forward)
# STOP()
return result_h, fixed_omega