def get_phi_psi_correction(result,
residue,
phi_psi,
display_phi_psi_correction=False,
verbose=False):
rc = None
key = (round_to_ten(phi_psi[0]), round_to_ten(phi_psi[1]))
if residue.resname=='PRO':
correction = PRO_phi_psi.get(key, None)
elif residue.resname in ['VAL', 'THR', 'ILE']:
correction = VAL_THR_ILE_phi_psi.get(key, None)
else:
correction = others_phi_psi.get(key, None)
if correction:
correction = radial_deviation(*tuple(correction), input_in_radians=True)
current = radial_deviation(result.deviation, result.dihedral)
rc = current-correction
start = (current.r>=0.25)
finish = (rc.r>=0.25)
if verbose:
print('current %s is corrected with %s' % (current, correction)),
print(' to give %s\n' % rc)
if display_phi_psi_correction and (start or finish):
show_phi_psi_correction(residue, phi_psi, current, correction, rc)
return rc.r, rc.t/pi*180, start, finish
else:
return None
def show_phi_psi_correction(residue, phi_psi, current, correction, rc, units=100):
import matplotlib.pyplot as plt
xs = [current.t, correction.t, rc.t]
ys = [current.r, correction.r, rc.r]
labels = ['default', 'correction', 'result']
for i, (x, y) in enumerate(zip(xs, ys)):
y*=units
plt.polar(x, y, 'ro')
plt.text(x, y,
'%s' % (labels[i]),
)
key = (round_to_ten(phi_psi[0]), round_to_ten(phi_psi[1]))
plt.title('%s (%5.1f, %5.1f) (%4.0f, %4.0f)\n%s minus %s equals %s' %(
residue.id_str(),
phi_psi[0],
phi_psi[1],
key[0],
key[1],
current,
correction,
rc,
)
)
plt.show()
def get_cdl_key(self,
exact=False,
only_psi_phi_pairs=True,
force_plus_one=False,
omega_cdl=False,
verbose=False):
dihedrals=self.get_phi_psi_angles(only_psi_phi_pairs=only_psi_phi_pairs,
omega_cdl=omega_cdl,
verbose=verbose,
)
if dihedrals is None: return None
key = []
for phi_or_psi in dihedrals:
if exact:
key.append(phi_or_psi)
else:
key.append(round_to_ten(phi_or_psi))
return tuple(key)
def get_cdl_key(self,
exact=False,
only_psi_phi_pairs=True,
force_plus_one=False,
omega_cdl=False,
verbose=False):
dihedrals=self.get_phi_psi_angles(only_psi_phi_pairs=only_psi_phi_pairs,
omega_cdl=omega_cdl,
verbose=verbose,
)
key = []
for phi_or_psi in dihedrals:
if exact:
key.append(phi_or_psi)
else:
key.append(round_to_ten(phi_or_psi))
#print self, self.get_ramalyze_key(verbose=1)
return tuple(key)