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 get_starting_conformations(moving_h, cutoff=50, log=null_out):
"""
modify only ramachandran outliers.
"""
variants = []
r = ramachandran_eval.RamachandranEval()
phi_psi_atoms = utils.get_phi_psi_atoms(moving_h)
for phi_psi_pair, rama_key in phi_psi_atoms:
if (utils.rama_evaluate(phi_psi_pair, r, rama_key) == ramalyze.RAMALYZE_OUTLIER):
variants.append(ramalyze.get_favored_regions(rama_key))
else:
variants.append([(None, None)])
result = []
print >> log, "variants", variants
if variants.count([(None, None)]) == len(variants):
print "Nothing to CCD"
return result
all_angles_combination = list(itertools.product(*variants))
i = 0
for comb in all_angles_combination:
print >> log, "Model %d, angles:" % i, comb
if is_not_none_combination(comb):
result.append(set_rama_angles(moving_h, list(comb)))
i += 1
return result[:cutoff]
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 get_starting_conformations(moving_h, cutoff=50, log=null_out()):
"""
modify only ramachandran outliers.
"""
variants = []
r = rama_eval()
phi_psi_atoms = utils.get_phi_psi_atoms(moving_h)
for phi_psi_pair, rama_key in phi_psi_atoms:
if (utils.rama_evaluate(phi_psi_pair, r, rama_key) == ramalyze.RAMALYZE_OUTLIER):
vs = get_sampled_rama_favored_angles(rama_key, r)
# print len(vs)
# print vs
# STOP()
variants.append(vs)
# variants.append(ramalyze.get_favored_regions(rama_key))
else:
variants.append([(None, None)])
result = []
print >> log, "variants", variants
if variants.count([(None, None)]) == len(variants):
print "Nothing to CCD"
return result
all_angles_combination = list(itertools.product(*variants))
i = 0
n_added = 0
n_all_combination = len(all_angles_combination)
i_max = min(cutoff, n_all_combination)
while n_added < i_max:
comb = all_angles_combination[i]
if is_not_none_combination(comb):
result.append(set_rama_angles(moving_h, list(comb)))
print >> log, "Model %d, angles:" % i, comb
n_added += 1
i += 1
return result
def get_all_starting_conformations(moving_h, change_radius, cutoff=50, log=null_out()):
variants = []
r = rama_eval()
phi_psi_atoms = utils.get_phi_psi_atoms(moving_h)
n_rama = len(phi_psi_atoms)
change_angles = range((n_rama)//2-change_radius, (n_rama)//2+change_radius+1)
# print " change_angles", change_angles
for i, (phi_psi_pair, rama_key) in enumerate(phi_psi_atoms):
if i in change_angles or (utils.rama_evaluate(phi_psi_pair, r, rama_key) == ramalyze.RAMALYZE_OUTLIER):
if utils.rama_evaluate(phi_psi_pair, r, rama_key) == ramalyze.RAMALYZE_OUTLIER:
vs = get_sampled_rama_favored_angles(rama_key, r)
else:
vs = ramalyze.get_favored_regions(rama_key)
variants.append(vs)
# variants.append(ramalyze.get_favored_regions(rama_key))
else:
variants.append([(None, None)])
print >> log, "variants", variants
all_angles_combination = list(itertools.product(*variants))
result = []
i = 0
n_added = 0
n_all_combination = len(all_angles_combination)
i_max = min(cutoff, n_all_combination)
while n_added < i_max:
comb = all_angles_combination[i]
if is_not_none_combination(comb):
result.append(set_rama_angles(moving_h, list(comb)))
print >> log, "Model %d, angles:" % i, comb
n_added += 1
i += 1
# STOP()
return result
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 get_all_starting_conformations(moving_h,
change_radius,
n_outliers,
direction_forward=True,
cutoff=50,
change_all=True,
log=null_out(),
check_omega=False):
if log is None:
log = StringIO()
variants = []
result = []
r = rama_eval()
phi_psi_atoms = utils.get_phi_psi_atoms(moving_h, omega=True)
# print "N residue groups in h", [x.resseq for x in moving_h.residue_groups()]
if len(phi_psi_atoms) == 0:
print >> log, "Strange input to starting conformations!!!"
return result
n_rama = len(phi_psi_atoms)
# print "n_rama", n_rama
change_angles = [None]
if change_all:
change_angles = range(
(n_rama) // 2 - change_radius - n_outliers // 2,
(n_rama) // 2 + change_radius + 1 + n_outliers // 2)
# if change_angles[0] < 0:
# change_angles = range(change_angles[-1]-change_angles[0])
has_twisted = False
if check_omega:
omegas = [x[2] for x in phi_psi_atoms]
for o in omegas:
if o is not None and abs(abs(o) - 180) > 30:
has_twisted = True
print >> log, "n_outliers", n_outliers
for i, (phi_psi_pair, rama_key, omega) in enumerate(phi_psi_atoms):
angle_is_outlier = utils.rama_evaluate(
phi_psi_pair, r, rama_key) == ramalyze.RAMALYZE_OUTLIER
twisted = omega is not None and ((abs(abs(omega) - 180) > 30)
and check_omega)
print >> log, "in cycle, N, outlier?, change?, twisted?", i, angle_is_outlier, i in change_angles, twisted
if angle_is_outlier and n_outliers < 3:
vs = get_sampled_rama_favored_angles(rama_key, r)
elif (i in change_angles) or angle_is_outlier or has_twisted:
# vs = get_sampled_rama_favored_angles(rama_key, r)
vs = ramalyze.get_favored_regions(rama_key)
else:
vs = [(None, None)]
variants.append(vs)
print >> log, "variants", variants
all_angles_combination = list(itertools.product(*variants))
# filter none combinations
# print "len(all_angles_combination)", len(all_angles_combination)
all_angles_combination_f = []
for comb in all_angles_combination:
if is_not_none_combination(comb):
all_angles_combination_f.append(comb)
print >> log, "len(all_angles_combination_f)", len(
all_angles_combination_f)
return all_angles_combination_f
def get_all_starting_conformations(moving_h, change_radius, cutoff=50, log=null_out):
variants = []
r = ramachandran_eval.RamachandranEval()
phi_psi_atoms = utils.get_phi_psi_atoms(moving_h)
n_rama = len(phi_psi_atoms)
change_angles = range((n_rama)//2-change_radius, (n_rama)//2+change_radius+1)
# print " change_angles", change_angles
for i, (phi_psi_pair, rama_key) in enumerate(phi_psi_atoms):
if i in change_angles or (utils.rama_evaluate(phi_psi_pair, r, rama_key) == ramalyze.RAMALYZE_OUTLIER):
variants.append(ramalyze.get_favored_regions(rama_key))
else:
variants.append([(None, None)])
print >> log, "variants", variants
all_angles_combination = list(itertools.product(*variants))
result = []
i = 0
for comb in all_angles_combination:
if is_not_none_combination(comb):
result.append(set_rama_angles(moving_h, list(comb)))
print >> log, "Model %d, angles:" % i, comb
i += 1
# STOP()
return result[:cutoff]
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
def get_all_starting_conformations(moving_h,
change_radius,
include_allowed,
n_outliers,
direction_forward=True,
cutoff=50,
change_all=True,
log=null_out(),
check_omega=False):
if log is None:
log = StringIO()
variants = []
result = []
r = rama_eval()
phi_psi_atoms = utils.get_phi_psi_atoms(moving_h, omega=True)
# print "N residue groups in h", [x.resseq for x in moving_h.residue_groups()]
if len(phi_psi_atoms) == 0:
print("Strange input to starting conformations!!!", file=log)
return result
n_rama = len(phi_psi_atoms)
# print "n_rama", n_rama
change_angles = [None]
if change_all:
change_angles = range(
(n_rama) // 2 - change_radius - n_outliers // 2,
(n_rama) // 2 + change_radius + 1 + n_outliers // 2)
# if change_angles[0] < 0:
# change_angles = range(change_angles[-1]-change_angles[0])
has_twisted = False
if check_omega:
omegas = [x[2] for x in phi_psi_atoms]
for o in omegas:
if o is not None and abs(abs(o) - 180) > 30:
has_twisted = True
print("n_outliers", n_outliers, file=log)
for i, (phi_psi_pair, rama_key, omega) in enumerate(phi_psi_atoms):
angle_is_outlier = utils.rama_evaluate(
phi_psi_pair, r, rama_key) == ramalyze.RAMALYZE_OUTLIER
angle_is_outlier = angle_is_outlier or (
include_allowed and utils.rama_evaluate(
phi_psi_pair, r, rama_key) == ramalyze.RAMALYZE_ALLOWED)
twisted = omega is not None and ((abs(abs(omega) - 180) > 30)
and check_omega)
print("in cycle, N, outlier?, change?, twisted?",
i,
angle_is_outlier,
i in change_angles,
twisted,
file=log)
if angle_is_outlier and n_outliers < 3:
vs = get_sampled_rama_favored_angles(rama_key, r)
elif (i in change_angles) or angle_is_outlier or has_twisted:
# vs = get_sampled_rama_favored_angles(rama_key, r)
vs = ramalyze.get_favored_regions(rama_key)
else:
vs = [(None, None)]
variants.append(vs)
print("variants", variants, file=log)
# Filtering them, since could be
# [len(x) for x in variants] = [129, 129, 4, 129, 129]
# resulting in 1107691524 all_angles_combination
n_comb = numpy.prod([len(x) for x in variants])
if n_comb > cutoff:
# still aiming for ~1000
n_in_each = int(1000**(1 / len(variants)))
variants = [
random.sample(x, n_in_each) if len(x) > n_in_each else x
for x in variants
]
all_angles_combination = list(itertools.product(*variants))
# filter none combinations
# print "len(all_angles_combination)", len(all_angles_combination)
all_angles_combination_f = []
for comb in all_angles_combination:
if is_not_none_combination(comb):
all_angles_combination_f.append(comb)
print("len(all_angles_combination_f)",
len(all_angles_combination_f),
file=log)
return all_angles_combination_f
