octadist.util

octadist.src.util.find_bonds(atom, coord, cutoff_global=2.0, cutoff_hydrogen=1.2)[source]

Find all bond distance and filter the possible bonds.

Compute distance of all bonds
Screen bonds out based on global cutoff distance
Screen H bonds out based on local cutoff distance

Parameters:

atom (list) – List of atomic labels of molecule.
coord (list) – List of atomic coordinates of molecule.
cutoff_global (int or float) – Global cutoff for screening bonds. Default is 2.0.
cutoff_hydrogen (int or float) – Cutoff for screening hydrogen bonds. Default is 1.2.

Returns:

filtered_pair_2 (list) – List of pair of atoms of selected bonds in molecule after screening
filtered_bond_2 (array_like) – Array of bond distances of selected bonds in molecule after screening.

Examples

>>> atom = ['Fe', 'N', 'N', 'N', 'O', 'O', 'O']
>>> coord = [[2.298354000, 5.161785000, 7.971898000],
             [1.885657000, 4.804777000, 6.183726000],
             [1.747515000, 6.960963000, 7.932784000],
             [4.094380000, 5.807257000, 7.588689000],
             [0.539005000, 4.482809000, 8.460004000],
             [2.812425000, 3.266553000, 8.131637000],
             [2.886404000, 5.392925000, 9.848966000]]
>>> pair_bond, bond_dist = find_bonds(atom, coord)
>>> pair_bond
[['Fe', 'N'], ['Fe', 'N'], ['Fe', 'N'], ['Fe', 'O'], ['Fe', 'O'], ['Fe', 'O']]
>>> bond_dist
[[[2.298354 5.161785 7.971898]
  [1.885657 4.804777 6.183726]]
 [[2.298354 5.161785 7.971898]
  [1.747515 6.960963 7.932784]]
 [[2.298354 5.161785 7.971898]
  [4.09438  5.807257 7.588689]]
 [[2.298354 5.161785 7.971898]
  [0.539005 4.482809 8.460004]]
 [[2.298354 5.161785 7.971898]
  [2.812425 3.266553 8.131637]]
 [[2.298354 5.161785 7.971898]
  [2.886404 5.392925 9.848966]]]

octadist.src.util.find_faces_octa(c_octa)[source]

Find the eight faces of octahedral structure.

1. Choose 3 atoms out of 6 ligand atoms. The total number of combination is 20.
2. Orthogonally project metal center atom onto the face: m ----> m'
3. Calculate the shortest distance between original metal center to its projected point.
4. Sort the 20 faces in ascending order of the shortest distance.
5. Delete 12 faces that closest to metal center atom (first 12 faces).
6. The remaining 8 faces are the (reference) face of octahedral structure.
7. Find 8 opposite faces.

Reference plane              Opposite plane
   [[1 2 3],                    [[4 5 6],
    [1 2 4],        --->         [3 5 6],
      ...                          ...
    [2 3 5]]                     [1 4 6]]

Parameters:

c_octa (array_like) – Atomic coordinates of octahedral structure.

Returns:

a_ref_f (list) – Atomic labels of reference face.
c_ref_f (array_like) – Atomic coordinates of reference face.
a_oppo_f (list) – Atomic labels of opposite face.
c_oppo_f (array_like) – Atomic coordinates of opposite face.

See also

octadist.src.plane.find_eq_of_plane: Find the equation of the plane.
octadist.src.projection.project_atom_onto_plane: Orthogonal projection of point onto the plane.

Examples

>>> coord = [[14.68572, 18.49228, 6.66716],
             [14.86476, 16.48821, 7.43379],
             [14.44181, 20.59400, 6.21555],
             [13.37473, 17.23453, 5.45099],
             [16.26114, 18.54903, 8.20527],
             [13.04897, 19.25464, 7.93122],
             [16.09157, 18.96170, 5.02956]]
>>> a_ref, c_ref, a_oppo, c_oppo = find_faces_octa(coord)
>>> a_ref
[[1, 3, 6], [1, 4, 6], [2, 3, 6], [2, 3, 5],
 [2, 4, 5], [1, 4, 5], [1, 3, 5], [2, 4, 6]]
>>> c_ref
[[[14.86476 16.48821  7.43379]
  [13.37473 17.23453  5.45099]
  [16.09157 18.9617   5.02956]],
 ...,
 ...,
 [[14.44181 20.594    6.21555]
  [16.26114 18.54903  8.20527]
  [16.09157 18.9617   5.02956]]]
>>> a_octa
[[2, 4, 5], [2, 3, 5], [1, 4, 5], [1, 4, 6],
 [1, 3, 6], [2, 3, 6], [2, 4, 6], [1, 3, 5]]
>>> c_octa
[[[14.44181 20.594    6.21555]
  [16.26114 18.54903  8.20527]
  [13.04897 19.25464  7.93122]],
 ...,
 ...,
 [[14.86476 16.48821  7.43379]
  [13.37473 17.23453  5.45099]
  [13.04897 19.25464  7.93122]]]