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 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 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,
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 __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.default_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,
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 = ss_manager.selection_cache.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:
rama_score = get_rama_score(phi_psi_pair, self.r, rama_key)
if rama_evaluate(phi_psi_pair, self.r, rama_key) == ramalyze.RAMALYZE_OUTLIER:
n_outliers += 1
else:
reg = gather_ss_stats.helix_sheet_rama_region(phi_psi_pair)
if (reg == 1 and not helix) or (reg == 2 and helix):
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_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 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