octadist.main

class octadist.main.OctaDist[source]

OctaDist class initiates main program UI and create all widgets.

Program interface is structured as follows:

Program Menu
Frame 1
Frame 2	Frame 3
Frame 4

Frame 1 : Program name and short description
Frame 2 : Program console
Frame 3 : Textbox for showing summary output
Frame 4 : textbox for showing detailed output

Examples

>>> my_app = OctaDist()
>>> my_app.start_app()

create_logo()[source]

Create icon file from Base64 raw code.

This will be used only for Windows OS.

Other OS like Linux and macOS use default logo of Tkinter.

Examples

>>> if self.octadist_icon is True:
>>>     self.create_logo()
>>> else:
>>>     pass

start_master()[source]: Start application with UI settings.

add_menu()[source]: Add menu bar to master windows.

add_widgets()[source]

Add all widgets and components to master windows.

GUI style of widgets in master windows use ttk style.

show_text(text)[source]

Insert text to result box

Parameters:: text (str) – Text to show in result box.
Returns:: None (None)

welcome_msg()[source]

Show welcome message in result box:

Program name, version, and release.
Full author names.
Official website: https://octadist.github.io.

open_file()[source]: Open file dialog where the user will browse input files.

search_coord()[source]

Search and extract atomic symbols and coordinates from input file.

See also

octadist.src.io.extract_coord: Extract atomic symbols and atomic coordinates from input file.
octadist.src.io.extract_octa: Extract octahedral structure from complex.

show_coord()[source]: Show coordinates in box.

save_results()[source]: Save results as output file. Default file extension is .txt.

save_coord()[source]: Save atomic coordinates (Cartesian coordinate) of octahedral structure. Default file extension is .xyz.

calc_distortion()[source]

Calculate all distortion parameters:

D_mean
Zeta
Delta
Sigma
Theta
Volume

See also

octadist.src.calc.CalcDistortion.calc_d_mean: Calculate mean metal-ligand bond length.
octadist.src.calc.CalcDistortion.calc_zeta: Calculate Zeta parameter.
octadist.src.calc.CalcDistortion.calc_delta: Calculate Delta parameter.
octadist.src.calc.CalcDistortion.calc_sigma: Calculate Sigma parameter.
octadist.src.calc.CalcDistortion.calc_theta: Calculate Theta parameter.
octadist.src.calc.CalcDistortion.calc_vol: Calculate octahedron volume.

settings()[source]

Program settings allows the user to configure the values of variables that used in molecular display function.

For example, cutoff distance for screening bond distance between atoms.

copy_name()[source]

Copy input file name to clipboard.

See also

copy_path: Copy absolute path of input file to clibboard.
copy_results: Copy results to clibboard.
copy_octa: Copy octahedral structure coordinates to clibboard.

copy_path()[source]

Copy absolute path of input file to clipboard.

See also

copy_name: Copy input file name to clibboard.
copy_results: Copy results to clibboard.
copy_octa: Copy octahedral structure coordinates to clibboard.

copy_results()[source]

Copy the results and computed distortion parameters to clipboard.

See also

copy_name: Copy input file name to clibboard.
copy_path: Copy absolute path of input file to clibboard.
copy_octa: Copy octahedral structure coordinates to clibboard.

copy_octa()[source]

Copy atomic coordinates of octahedral structure to clipboard.

See also

copy_name: Copy input file name to clibboard.
copy_path: Copy absolute path of input file to clibboard.
copy_results: Copy results to clibboard.

edit_file()[source]: Edit file by specified text editor on Windows.

See also

settings

scripting_console()[source]

Start scripting interface for an interactive code.

User can access to class variable (dynamic variable).

Output box

Input box

See also

settings: Program settings.

draw_all_atom()[source]

Display 3D complex.

See also

octadist.src.draw.DrawComplex: Show 3D molecule.

draw_all_atom_and_face()[source]

Display 3D complex with the faces.

See also

octadist.src.draw.DrawComplex: Show 3D molecule.

draw_octa()[source]

Display 3D octahedral structure.

See also

octadist.src.draw.DrawComplex: Show 3D molecule.

draw_octa_and_face()[source]

Display 3D octahedral structure with the faces.

See also

octadist.src.draw.DrawComplex: Show 3D molecule.

draw_projection()[source]

Draw projection planes.

See also

octadist.src.draw.DrawProjection: Show graphical projections.

draw_twisting_plane()[source]

Draw twisting triangular planes.

See also

octadist.src.draw.DrawTwistingPlane: Show graphical triangular twisting planes.

show_data_complex()[source]

Show info of input complex.

See also

octadist.src.structure.DataComplex: Show data summary of complex.

show_param_octa()[source]

Show structural parameters of selected octahedral structure.

See also

octadist.src.structure.StructParam: Show structural parameter symmary of complex.

show_surface_area()[source]

Calculate the area of eight triangular faces of octahedral structure.

See also

octadist.src.structure.SurfaceArea: Show the area of the faces of octahedral structure.

plot_zeta_sigma()[source]

Plot relationship between zeta and sigma.

See also

octadist.src.plot.Plot: Show relationship plot.

plot_sigma_theta()[source]

Plot relationship between sigma and theta.

See also

octadist.src.plot.Plot: Show relationship plot.

tool_jahn_teller()[source]

Calculate Jahn-Teller distortion parameter.

See also

octadist.src.tools.CalcJahnTeller: Calculate Jahn-Teller distortion parameter.

tool_rmsd()[source]

Calculate root mean squared displacement of atoms in complex, RMSD.

See also

octadist.src.tools.CalcRMSD: Calculate RMSD.

static check_update()[source]

Check program update by comparing version of program user is using with that of the latest version released on github.

References

File: https://www.github.com/OctaDist/OctaDist/version_update.txt.

static callback(event)[source]

On-clink open web browser.

Parameters:: event (object) – Event object for callback.

static show_about()[source]

Show author details on a sub-window.

Name of authors
Official program website
Citation

static show_license()[source]

Show license details on a sub-window.

GNU General Public License version 3.0.

References

Link: https://www.gnu.org/licenses/gpl-3.0.en.html.

clear_cache()[source]: Clear program cache by nullifying all default variables and clear both of parameter and result boxes.

clear_param_box()[source]: Clear parameter box.

clear_result_box()[source]: Clear result box.

start_app()[source]: Start application.

octadist.main.main()[source]