def get_phi_psi_list(self):
"""
Return the list of phi/psi dihedral angles
"""
ppl = []
lng = len(self)
for i in range(0, lng):
res = self[i]
try:
n = res['N'].get_vector()
ca = res['CA'].get_vector()
c = res['C'].get_vector()
except:
# Some atoms are missing
# Phi/Psi cannot be calculated for this residue
ppl.append((None, None))
res.xtra["PHI"] = None
res.xtra["PSI"] = None
continue
# Phi
if i > 0:
rp = self[i - 1]
try:
cp = rp['C'].get_vector()
phi = calc_dihedral(cp, n, ca, c)
except:
phi = None
else:
# No phi for residue 0!
phi = None
# Psi
if i < (lng - 1):
rn = self[i + 1]
try:
nn = rn['N'].get_vector()
psi = calc_dihedral(n, ca, c, nn)
except:
psi = None
else:
# No psi for last residue!
psi = None
ppl.append((phi, psi))
# Add Phi/Psi to xtra dict of residue
res.xtra["PHI"] = phi
res.xtra["PSI"] = psi
return ppl
def get_phi_psi_list(self):
"""
Return the list of phi/psi dihedral angles
"""
ppl=[]
lng=len(self)
for i in range(0, lng):
res=self[i]
try:
n=res['N'].get_vector()
ca=res['CA'].get_vector()
c=res['C'].get_vector()
except:
# Some atoms are missing
# Phi/Psi cannot be calculated for this residue
ppl.append((None, None))
res.xtra["PHI"]=None
res.xtra["PSI"]=None
continue
# Phi
if i>0:
rp=self[i-1]
try:
cp=rp['C'].get_vector()
phi=calc_dihedral(cp, n, ca, c)
except:
phi=None
else:
# No phi for residue 0!
phi=None
# Psi
if i<(lng-1):
rn=self[i+1]
try:
nn=rn['N'].get_vector()
psi=calc_dihedral(n, ca, c, nn)
except:
psi=None
else:
# No psi for last residue!
psi=None
ppl.append((phi, psi))
# Add Phi/Psi to xtra dict of residue
res.xtra["PHI"]=phi
res.xtra["PSI"]=psi
return ppl
def get_tau_list(self):
"""List of tau torsions angles for all 4 consecutive Calpha atoms."""
ca_list=self.get_ca_list()
tau_list=[]
for i in range(0, len(ca_list)-3):
atom_list = (ca_list[i], ca_list[i+1], ca_list[i+2], ca_list[i+3])
v1, v2, v3, v4 = [a.get_vector() for a in atom_list]
tau=calc_dihedral(v1, v2, v3, v4)
tau_list.append(tau)
# Put tau in xtra dict of residue
res=ca_list[i+2].get_parent()
res.xtra["TAU"]=tau
return tau_list
def get_tau_list(self):
"""List of tau torsions angles for all 4 consecutive Calpha atoms."""
ca_list = self.get_ca_list()
tau_list = []
for i in range(0, len(ca_list) - 3):
atom_list = (ca_list[i], ca_list[i + 1], ca_list[i + 2],
ca_list[i + 3])
v1, v2, v3, v4 = [a.get_vector() for a in atom_list]
tau = calc_dihedral(v1, v2, v3, v4)
tau_list.append(tau)
# Put tau in xtra dict of residue
res = ca_list[i + 2].get_parent()
res.xtra["TAU"] = tau
return tau_list
