コード例 #1
0
ファイル: molecule.py プロジェクト: NRGunby/UCONGA
 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)
コード例 #2
0
ファイル: molecule.py プロジェクト: NRGunby/UCONGA
 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)