octadist.calc

class octadist.src.calc.CalcDistortion(coord)[source]

Calculate octahedral histortion parameters:

Bond distance : calc_d_bond()
Mean bond distance : calc_d_mean()
Bond angle around metal center atom : calc_bond_angle()
zeta parameter : calc_zeta()
Delta parameter : calc_delta()
Sigma parameter : calc_sigma()
Minimum Tehta parameter : calc_theta_min()
Maximum Theta parameter : calc_theta_max()
Mean Theta parametes : calc_theta()
Volume : calc_vol()

Parameters:: coord (array_like) – Atomic coordinates of octahedral structure.

Examples

>>> coord = [[2.298354000, 5.161785000, 7.971898000],  # <- Metal atom
             [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]]
>>> test = CalcDistortion(coord)
>>> test.sigma
47.926528379270124

calc_d_bond()[source]

Calculate metal-ligand bond distance and return value in Angstrom.

See also

calc_d_mean: Calculate mean metal-ligand bond length.

calc_d_mean()[source]

Calculate mean distance parameter and return value in Angstrom.

See also

calc_d_bond: Calculate metal-ligand bonds length.

calc_bond_angle()[source]

Calculate 12 cis and 3 trans unique angles in octahedral structure.

See also

calc_sigma: Calculate Sigma parameter.

calc_zeta()[source]

Calculate zeta parameter [1] and return value in Angstrom.

See also

calc_d_bond: Calculate metal-ligand bonds length.
calc_d_mean: Calculate mean metal-ligand bond length.

References

calc_delta()[source]

Calculate Delta parameter, also known as Tilting distortion parameter [2].

See also

calc_d_bond: Calculate metal-ligand bonds length.
calc_d_mean: Calculate mean metal-ligand bond length.

References

calc_sigma()[source]

Calculate Sigma parameter [3] and return value in degree.

See also

calc_bond_angle: Calculate bond angles between ligand-metal-ligand.

References

determine_faces()[source]

Refine the order of ligand atoms in order to find the plane for projection.

Returns:

coord_metal (array_like) – Coordinate of metal atom.
coord_lig (array_like) – Coordinate of ligand atoms.

See also

calc_theta: Calculate mean Theta parameter

Examples

>>> bef = np.array([
            [4.0674, 7.2040, 13.6117]
            [4.3033, 7.3750, 11.7292]
            [3.8326, 6.9715, 15.4926]
            [5.8822, 6.4461, 13.4312]
            [3.3002, 5.3828, 13.6316]
            [4.8055, 8.9318, 14.2716]
            [2.3184, 8.0165, 13.1152]
            ])
>>> metal, coord = self.determine_faces(bef)
>>> metal
[ 4.0674  7.204  13.6117]
>>> coord_lig
[[ 4.3033  7.375  11.7292]      # Front face
 [ 4.8055  8.9318 14.2716]      # Front face
 [ 5.8822  6.4461 13.4312]      # Front face
 [ 2.3184  8.0165 13.1152]      # Back face
 [ 3.8326  6.9715 15.4926]      # Back face
 [ 3.3002  5.3828 13.6316]]     # Back face

calc_theta()[source]

Calculate Theta parameter [4] and value in degree.

See also

calc_theta_min: Calculate minimum Theta parameter.
calc_theta_max: Calculate maximum Theta parameter.
octadist.src.linear.angle_btw_vectors: Calculate cosine angle between two vectors.
octadist.src.linear.angle_sign: Calculate cosine angle between two vectors sensitive to CW/CCW direction.
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.

References

calc_theta_min()[source]

Calculate minimum Theta parameter and return value in degree.

See also

calc_theta: Calculate mean Theta parameter

calc_theta_max()[source]

Calculate maximum Theta parameter and return value in degree.

See also

calc_theta: Calculate mean Theta parameter

calc_vol()[source]: Calculate the octahedron volume and return value in cubic Angstrom.