octadist.tools
- class octadist.src.tools.CalcJahnTeller(atom, coord, cutoff_global=2.0, cutoff_hydrogen=1.2, master=None, icon=None)[source]
Calculate angular Jahn-Teller distortion parameter [1].
- Parameters:
atom (array_like) – Atomic labels of full complex.
coord (array_like) – Atomic coordinates of full complex.
master (None, object) – If None, use tk.Tk(). If not None, use tk.Toplevel(master).
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.
icon (str, optional) – If None, use tkinter default icon. If not None, use user-defined icon.
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]] >>> test = CalcJahnTeller(atom=atom, coord=coord) >>> test.start_app() >>> test.find_bond() >>> test.show_app()
References
- find_bond()[source]
Find bonds.
See also
octadist.src.util.find_bonds
Find atomic bonds.
- class octadist.src.tools.CalcRMSD(coord_1, coord_2, atom_1=None, atom_2=None, master=None, icon=None)[source]
Calculate root mean squared displacement of atoms in complex, RMSD [2].
- Parameters:
coord_1 (array_like) – Atomic coordinates of structure 1.
coord_2 (array_like) – Atomic coordinates of structure 2.
atom_1 (list or tuple, optional) – Atomic symbols of structure 1.
atom_2 (list or tuple, optional) – Atomic symbols of structure 2. If no atom_2 specified, assign it with None.
- Returns:
rmsd_normal (float) – Normal RMSD.
rmsd_translate (float) – Translate RMSD (re-centered).
rmsd_rotate (float) – Kabsch RMSD (rotated).
References
[2] Kromann. https://github.com/charnley/rmsd.
Examples
>>> # Example of structure 1 >>> comp1 = [[10.1873, 5.7463, 5.615], [8.494, 5.9735, 4.8091], [9.6526, 6.4229, 7.3079], [10.8038, 7.5319, 5.1762], [9.6229, 3.9221, 6.0083], [12.0065, 5.5562, 6.3497], [10.8046, 4.9471, 3.9219]]
>>> # Example of structure 1 >>> comp2 = [[12.0937, 2.4505, 3.4207], [12.9603, 2.2952, 1.7286], [13.4876, 1.6182, 4.4230], [12.8522, 4.3174, 3.9894], [10.9307, 0.7697, 2.9315], [10.7878, 2.2987, 5.1071], [10.6773, 3.7960, 2.5424]]
>>> test = CalcRMSD(coord_1=comp1, coord_2=comp2) >>> test.calc_rmsd() >>> test.rmsd_normal 6.758144 >>> test.rmsd_translate 0.305792 >>> test.rmsd_rotate 0.277988