octadist.draw
- class octadist.src.draw.DrawComplex_Matplotlib(atom=None, coord=None, cutoff_global=2.0, cutoff_hydrogen=1.2)[source]
Display 3D structure of octahedral complex with label for each atoms using Matplotlib.
- Parameters:
atom (list) – Atomic symbols of octahedral structure. Default is None.
coord (list or array_like or tuple or bool) – Atomic coordinates of octahedral structure. Default is None.
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.
See also
draw.DrawComplex_Plotly
Use Plotly engine to draw a complex.
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 = DrawComplex_Matplotlib(atom=atom, coord=coord) >>> test.add_atom() >>> test.add_bond() >>> test.add_legend() >>> test.show_plot()
- plot_title(title='Full complex', font_size='12')[source]
Add plot title at top position.
- Parameters:
title (str) – Top title of the plot. Default is “Full complex”.
fontsize (int or float or str) – Font size of title. Default is “12”.
- add_bond()[source]
Calculate bond distance, screen bond, and add them to show in figure.
See also
octadist.src.util.find_bonds
Find atomic bonds.
- add_face(coord)[source]
Find the faces of octahedral structure and add those faces to show in figure.
See also
octadist.src.util.find_faces_octa
Find all faces of octahedron.
- add_legend()[source]
Add atoms legend to show in figure.
References
- Remove duplicate labels in legend.
- Fix size of point in legend.
- config_plot(show_title=True, show_axis=True, show_grid=True, **kwargs)[source]
Setting configuration for figure.
- Parameters:
show_title (bool) – If True, show title of figure. If False, not show title of figure.
show_axis (bool) – If True, show axis of figure. If False, not show axis of figure.
show_grid (bool) – If True, show grid of figure. If False, not show grid of figure.
kwargs (dict, optional) – title_name : title name of figure. title_size : text size of title. label_size : text size of axis labels.
- class octadist.src.draw.DrawComplex_Plotly(atom=None, coord=None, cutoff_global=2.0, cutoff_hydrogen=1.2)[source]
Display 3D structure of octahedral complex in web browser using Plotly.
- Parameters:
atom (list) – Atomic symbols of octahedral structure. Default is None.
coord (list or array_like or tuple or bool) – Atomic coordinates of octahedral structure. Default is None.
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.
See also
draw.DrawComplex_Matplotlib
Use Matplotlib engine to draw a complex.
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 = DrawComplex_Plotly(atom=atom, coord=coord) >>> test.add_atom() >>> test.add_bond() >>> test.show_plot()
- plot_title(title='Full complex', font_size='12')[source]
Add plot title at top position.
- Parameters:
title (str) – Top title of the plot. Default is “Full complex”.
fontsize (int or float or str) – Font size of title. Default is “12”.
- add_bond()[source]
Calculate bond distance, screen bond, and add them to show in figure.
See also
octadist.src.util.find_bonds
Find atomic bonds.
- class octadist.src.draw.DrawProjection(atom=None, coord=None)[source]
Display the selected 4 faces of octahedral complex.
- Parameters:
atom (list) – Atomic symbols of octahedral structure. Default is None.
coord (list or array_like or tuple) – Atomic coordinates of octahedral structure. Default is None.
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 = DrawProjection(atom=atom, coord=coord) >>> test.add_atom() >>> test.add_symbol() >>> test.add_plane() >>> test.show_plot()
- plot_title(title='4 pairs of opposite planes', font_size='x-large')[source]
Add plot title at top position.
- Parameters:
title (str) – Top title of the plot. Default is “Full complex”.
fontsize (int or float or str) – Font size of title. Default is “x-large”.
- add_plane()[source]
Add the projection planes to show in figure.
See also
octadist.src.util.find_faces_octa
Find all faces of octahedron.
- class octadist.src.draw.DrawTwistingPlane(atom=None, coord=None, symbol_fontsize=15)[source]
Display twisting triangular faces and vector projection.
- Parameters:
atom (list) – Atomic symbols of octahedral structure. Default is None.
coord (list or array or tuple) – Atomic coordinates of octahedral structure. Default is None.
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 = DrawTwistingPlane(atom=atom, coord=coord) >>> test.add_plane() >>> test.add_symbol() >>> test.add_bond() >>> test.show_plot()
- plot_title(title='Projected twisting triangular faces', font_size='x-large')[source]
Add plot title at top position.
- Parameters:
title (str) – Top title of the plot. Default is “Projected twisting triangular faces”.
fontsize (int or float or str) – Font size of title. Default is “x-large”.
- add_plane()[source]
Add the projection planes to show in figure.
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.