def calculate_chi(residue, j):
res_chi_topology = get_res_chi_topology(residue.type)
if j < len(res_chi_topology):
p = [residue.atom(atom_type).pos for atom_type in res_chi_topology[j]]
angle = vector3d.pos_dihedral(p[0], p[1], p[2], p[3])
return vector3d.normalize_angle(angle)
raise ValueError, "No Chi%d angle for res %d" % (j, i)
def calculate_chi(residue, j):
res_chi_topology = get_res_chi_topology(residue.type)
if j < len(res_chi_topology):
p = [residue.atom(atom_type).pos for atom_type in res_chi_topology[j]]
angle = vector3d.pos_dihedral(p[0], p[1], p[2], p[3])
return vector3d.normalize_angle(angle)
raise ValueError, "No Chi%d angle for res %d" % (j, i)
def chi(self, i, j):
res = self.residue(i)
if _chi_topology.has_key(res.type):
if j < len(_chi_topology[res.type]):
p = [res.atom(atom_type).pos
for atom_type in _chi_topology[res.type][j]]
angle = vector3d.pos_dihedral(p[0], p[1], p[2], p[3])
return vector3d.normalize_angle(angle)
raise ValueError, "No Chi%d angle for res %s-%d" % (j, res.type, i)
def chi(self, i, j):
res = self.residue(i)
if _chi_topology.has_key(res.type):
if j < len(_chi_topology[res.type]):
p = [res.atom(atom_type).pos
for atom_type in _chi_topology[res.type][j]]
angle = vector3d.pos_dihedral(p[0], p[1], p[2], p[3])
return vector3d.normalize_angle(angle)
raise ValueError, "No Chi%d angle for res %s-%d" % (j, res.type, i)
def psi(self, i):
if "NME" in self.residue(i).type:
raise ValueError, "Can't calculate psi of NME"
if i < self.n_residue() - 1:
p1 = self.residue(i).atom("N").pos
p2 = self.residue(i).atom("CA").pos
p3 = self.residue(i).atom("C").pos
p4 = self.residue(i+1).atom("N").pos
angle = vector3d.pos_dihedral(p1, p2, p3, p4)
else:
p1 = self.residue(i).atom("N").pos
p2 = self.residue(i).atom("CA").pos
p3 = self.residue(i).atom("C").pos
p4 = self.residue(i).atom("O").pos
angle = math.pi + vector3d.pos_dihedral(p1, p2, p3, p4)
return vector3d.normalize_angle(angle)
def psi(self, i):
if "NME" in self.residue(i).type:
raise ValueError, "Can't calculate psi of NME"
if i < self.n_residue() - 1:
p1 = self.residue(i).atom("N").pos
p2 = self.residue(i).atom("CA").pos
p3 = self.residue(i).atom("C").pos
p4 = self.residue(i+1).atom("N").pos
angle = vector3d.pos_dihedral(p1, p2, p3, p4)
else:
p1 = self.residue(i).atom("N").pos
p2 = self.residue(i).atom("CA").pos
p3 = self.residue(i).atom("C").pos
p4 = self.residue(i).atom("O").pos
angle = math.pi + vector3d.pos_dihedral(p1, p2, p3, p4)
return vector3d.normalize_angle(angle)
def phi(self, i):
if "ACE" in self.residue(i).type:
raise ValueError, "Can't calculate phi of ACE"
if i == 0:
if "PRO" in self.residue(i).type:
atoms = [(i, "CD1"), (i, "N"), (i, "CA"), (i, "C")]
elif self.residue(i).has_atom("H"):
atoms = [(i, "H"), (i, "N"), (i, "CA"), (i, "C")]
elif self.residue(i).has_atom("H1"):
atoms = [(i, "H1"), (i, "N"), (i, "CA"), (i, "C")]
else:
raise ValueError, "Can't find atoms to calculate phi"
else:
if "ACE" in self.residue(i-1).type:
atoms = [(i-1, "CH3"), (i, "N"), (i, "CA"), (i, "C")]
else:
atoms = [(i-1, "C"), (i, "N"), (i, "CA"), (i, "C")]
p = [self.residue(j).atom(a_type).pos for j, a_type in atoms]
return vector3d.normalize_angle(vector3d.pos_dihedral(p[0], p[1], p[2], p[3]))
def phi(self, i):
if "ACE" in self.residue(i).type:
raise ValueError, "Can't calculate phi of ACE"
if i == 0:
if "PRO" in self.residue(i).type:
atoms = [(i, "CD1"), (i, "N"), (i, "CA"), (i, "C")]
elif self.residue(i).has_atom("H"):
atoms = [(i, "H"), (i, "N"), (i, "CA"), (i, "C")]
elif self.residue(i).has_atom("H1"):
atoms = [(i, "H1"), (i, "N"), (i, "CA"), (i, "C")]
else:
raise ValueError, "Can't find atoms to calculate phi"
else:
if "ACE" in self.residue(i-1).type:
atoms = [(i-1, "CH3"), (i, "N"), (i, "CA"), (i, "C")]
else:
atoms = [(i-1, "C"), (i, "N"), (i, "CA"), (i, "C")]
p = [self.residue(j).atom(a_type).pos for j, a_type in atoms]
return vector3d.normalize_angle(vector3d.pos_dihedral(p[0], p[1], p[2], p[3]))