def to_cml(self):
'''
Creates a cml molecule element
Uses the original (i.e. non-aromatised)
'''
original_bonds = self.bonds
for each_tuple in self.aromatised_bonds:
i, j, k = each_tuple
original_bonds[i][j] = k
original_bonds[j][i] = k
root = ET.Element(lbl_molecule)
atom_array = ET.Element(lbl_atom_array)
for each in self.atoms:
atom_array.append(each.to_cml())
root.append(atom_array)
bond_array = ET.Element(lbl_bond_array)
for i_idx, i in enumerate(original_bonds):
for j_idx, j in enumerate(i):
if j and (i_idx > j_idx):
bond = ET.Element(lbl_bond)
bond.set(lbl_order, str(j))
bond.set(lbl_atom_refs,
' '.join([py_to_id(l) for l in [i_idx, j_idx]]))
bond_array.append(bond)
root.append(bond_array)
return ET.tostring(root)
def set_torsion(self, id1, id2, id3, id4, torsion):
'''
Rotates atom 1 and all its children aound that atom2-atom3 bond
so that the 1-2-3-4 torsion is the supplied value (in radians)
'''
# Start by finding the children of atom 2(all closer to it than atom 3)
children = []
for idx, i in enumerate(self.distances):
if i[id2] < i[id3]:
children.append(idx)
at2 = self.atoms[id2]
axis = at2.get_vector(self.atoms[id3])
angle = self.get_torsion(id1, id2, id3, id4) - torsion
matrix = linalg.rotation_axis_angle(axis, angle)
back_again = at2.coords
there = [-1 * i for i in back_again]
for at_idx in children:
at = self.atoms[at_idx]
at.translate(there)
c = at.coords.transpose()
new_c = matrix.dot(c)
at.coords = new_c.transpose()
at.translate(back_again)
d = self.get_torsion(id1, id2, id3, id4)
try:
assert abs(sin(d) - sin(torsion)) < 1e-3
assert abs(cos(d) - cos(torsion)) < 1e-3
except AssertionError:
msg = 'Failed to set torsion %s' %'->'.join([py_to_id(i) for i in (id1, id2, id3, id4)])
msg += '\n Should be %f, is %f' %(degrees(torsion), degrees(d))
raise RuntimeError(msg)