def get_bb_angles(self, resnum):
""" Returns a list of [phi, psi, omega] angles for a residue.
Arguments:
resnum -- The number of the residue.
"""
length = self.get_length()
angles_deg = []
if resnum == 1:
res_1 = self._chain[resnum]
res_2 = self._chain[resnum + 1]
N1 = res_1['N'].get_vector()
CA1 = res_1['CA'].get_vector()
C1 = res_1['C'].get_vector()
N2 = res_2['N'].get_vector()
phi = None
psi = calc_dihedral(N1, CA1, C1, N2) * RAD_TO_DEG
omega = None
angles_deg = [phi, psi, omega]
elif resnum == length:
res_0 = self._chain[resnum - 1]
res_1 = self._chain[resnum]
CA0 = res_0['CA'].get_vector()
C0 = res_0['C'].get_vector()
N1 = res_1['N'].get_vector()
CA1 = res_1['CA'].get_vector()
C1 = res_1['C'].get_vector()
phi = calc_dihedral(C0, N1, CA1, C1) * RAD_TO_DEG
psi = None
omega = calc_dihedral(CA0, C0, N1, CA1) * RAD_TO_DEG
angles_deg = [phi, psi, omega]
else:
res_0 = self._chain[resnum - 1]
res_1 = self._chain[resnum]
res_2 = self._chain[resnum + 1]
CA0 = res_0['CA'].get_vector()
C0 = res_0['C'].get_vector()
N1 = res_1['N'].get_vector()
CA1 = res_1['CA'].get_vector()
C1 = res_1['C'].get_vector()
N2 = res_2['N'].get_vector()
phi = calc_dihedral(C0, N1, CA1, C1) * RAD_TO_DEG
psi = calc_dihedral(N1, CA1, C1, N2) * RAD_TO_DEG
omega = calc_dihedral(CA0, C0, N1, CA1) * RAD_TO_DEG
angles_deg = [phi, psi, omega]
return angles_deg
def get_bb_angles(self, resnum):
""" Returns a list of [phi, psi, omega] angles for a residue.
Arguments:
resnum -- The number of the residue.
"""
length = self.get_length()
angles_deg = []
if resnum == 1:
res_1 = self._chain[resnum]
res_2 = self._chain[resnum + 1]
N1 = res_1['N' ].get_vector()
CA1 = res_1['CA'].get_vector()
C1 = res_1['C' ].get_vector()
N2 = res_2['N' ].get_vector()
phi = None
psi = calc_dihedral(N1, CA1, C1, N2) * RAD_TO_DEG
omega = None
angles_deg = [phi, psi, omega]
elif resnum == length:
res_0 = self._chain[resnum - 1]
res_1 = self._chain[resnum]
CA0 = res_0['CA'].get_vector()
C0 = res_0['C' ].get_vector()
N1 = res_1['N' ].get_vector()
CA1 = res_1['CA'].get_vector()
C1 = res_1['C' ].get_vector()
phi = calc_dihedral(C0, N1, CA1, C1) * RAD_TO_DEG
psi = None
omega = calc_dihedral(CA0, C0, N1, CA1) * RAD_TO_DEG
angles_deg = [phi, psi, omega]
else:
res_0 = self._chain[resnum - 1]
res_1 = self._chain[resnum]
res_2 = self._chain[resnum + 1]
CA0 = res_0['CA'].get_vector()
C0 = res_0['C' ].get_vector()
N1 = res_1['N' ].get_vector()
CA1 = res_1['CA'].get_vector()
C1 = res_1['C' ].get_vector()
N2 = res_2['N' ].get_vector()
phi = calc_dihedral(C0, N1, CA1, C1) * RAD_TO_DEG
psi = calc_dihedral(N1, CA1, C1, N2) * RAD_TO_DEG
omega = calc_dihedral(CA0, C0, N1, CA1) * RAD_TO_DEG
angles_deg = [phi, psi, omega]
return angles_deg
def _get_chi(self, residue):
""" Returns a list of chi angles for a residue """
if residue.get_resname() == 'ALA':
return []
if residue.get_resname() == 'GLY':
return []
if residue.get_resname() == 'ARG':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['NE'].get_vector()
sc_atom7 = residue['CZ'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
chi4 = calc_dihedral(sc_atom4, sc_atom5, sc_atom6, sc_atom7)
return [chi1, chi2, chi3, chi4]
if residue.get_resname() == 'ASN':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['OD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'ASP':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['OD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'CYS':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['SG'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
if residue.get_resname() == 'GLU':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['OE1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
return [chi1, chi2, chi3]
if residue.get_resname() == 'GLN':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['OE1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
return [chi1, chi2, chi3]
if residue.get_resname() == 'HIS':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD2'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'ILE':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG1'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'LEU':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
sc_atom5_b = residue['CD2'].get_vector()
# Check for correct naming of CD1/CD2
check_angle = calc_dihedral(sc_atom5, sc_atom4, sc_atom3,
sc_atom5_b)
# If the naming of the CD1 and CD2 atoms is correct,
# the check_angle will be around -120 deg. If the names
# are swapped, the angle will be around 120 deg.
if check_angle > 0:
sc_atom5 = sc_atom5_b
print "WARNING: Correcting for incorrect naming of CD1 and CD2 in residue LEU%i." % residue.get_id(
)[1]
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'LYS':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['CE'].get_vector()
sc_atom7 = residue['NZ'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
chi4 = calc_dihedral(sc_atom4, sc_atom5, sc_atom6, sc_atom7)
return [chi1, chi2, chi3, chi4]
if residue.get_resname() == 'MET':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['SD'].get_vector()
sc_atom6 = residue['CE'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
return [chi1, chi2, chi3]
if residue.get_resname() == 'PHE':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'PRO':
# sc_atom1 = residue['N'].get_vector()
# sc_atom2 = residue['CA'].get_vector()
# sc_atom3 = residue['CB'].get_vector()
# sc_atom4 = residue['CG'].get_vector()
# sc_atom5 = residue['CD'].get_vector()
# chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
# chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
# chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom1)
# chi4 = calc_dihedral(sc_atom4, sc_atom5, sc_atom1, sc_atom2)
# return [chi1, chi2, chi3, chi4]
return []
if residue.get_resname() == 'SER':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['OG'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
if residue.get_resname() == 'THR':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['OG1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
if residue.get_resname() == 'TRP':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'TYR':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'VAL':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG1'].get_vector()
sc_atom4_b = residue['CG2'].get_vector()
# Check for correct naming of CG1/CG2
check_angle = calc_dihedral(sc_atom4, sc_atom3, sc_atom2,
sc_atom4_b)
# If the naming of the CG1 and CG2 atoms is correct,
# the check_angle will be around -120 deg. If the names
# are swapped, the angle will be around 120 deg.
if check_angle > 0:
sc_atom4 = sc_atom4_b
print "WARNING: Correcting for incorrect naming of CG1 and CG2 in residue VAL%i." % residue.get_id(
)[1]
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
else:
return "FAILLLL"
def _get_chi(self, residue):
""" Returns a list of chi angles for a residue """
if residue.get_resname() == 'ALA':
return []
if residue.get_resname() == 'GLY':
return []
if residue.get_resname() == 'ARG':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['NE'].get_vector()
sc_atom7 = residue['CZ'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
chi4 = calc_dihedral(sc_atom4, sc_atom5, sc_atom6, sc_atom7)
return [chi1, chi2, chi3, chi4]
if residue.get_resname() == 'ASN':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['OD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'ASP':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['OD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'CYS':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['SG'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
if residue.get_resname() == 'GLU':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['OE1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
return [chi1, chi2, chi3]
if residue.get_resname() == 'GLN':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['OE1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
return [chi1, chi2, chi3]
if residue.get_resname() == 'HIS':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD2'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'ILE':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG1'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'LEU':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
sc_atom5_b = residue['CD2'].get_vector()
# Check for correct naming of CD1/CD2
check_angle = calc_dihedral(sc_atom5, sc_atom4, sc_atom3, sc_atom5_b)
# If the naming of the CD1 and CD2 atoms is correct,
# the check_angle will be around -120 deg. If the names
# are swapped, the angle will be around 120 deg.
if check_angle > 0:
sc_atom5 = sc_atom5_b
print "WARNING: Correcting for incorrect naming of CD1 and CD2 in residue LEU%i." % residue.get_id()[1]
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'LYS':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['CE'].get_vector()
sc_atom7 = residue['NZ'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
chi4 = calc_dihedral(sc_atom4, sc_atom5, sc_atom6, sc_atom7)
return [chi1, chi2, chi3, chi4]
if residue.get_resname() == 'MET':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['SD'].get_vector()
sc_atom6 = residue['CE'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
return [chi1, chi2, chi3]
if residue.get_resname() == 'PHE':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'PRO':
# sc_atom1 = residue['N'].get_vector()
# sc_atom2 = residue['CA'].get_vector()
# sc_atom3 = residue['CB'].get_vector()
# sc_atom4 = residue['CG'].get_vector()
# sc_atom5 = residue['CD'].get_vector()
# chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
# chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
# chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom1)
# chi4 = calc_dihedral(sc_atom4, sc_atom5, sc_atom1, sc_atom2)
# return [chi1, chi2, chi3, chi4]
return []
if residue.get_resname() == 'SER':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['OG'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
if residue.get_resname() == 'THR':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['OG1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
if residue.get_resname() == 'TRP':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'TYR':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'VAL':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG1'].get_vector()
sc_atom4_b = residue['CG2'].get_vector()
# Check for correct naming of CG1/CG2
check_angle = calc_dihedral(sc_atom4, sc_atom3, sc_atom2, sc_atom4_b)
# If the naming of the CG1 and CG2 atoms is correct,
# the check_angle will be around -120 deg. If the names
# are swapped, the angle will be around 120 deg.
if check_angle > 0:
sc_atom4 = sc_atom4_b
print "WARNING: Correcting for incorrect naming of CG1 and CG2 in residue VAL%i." % residue.get_id()[1]
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
else:
return "FAILLLL"