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

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.

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]¶