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
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.
- 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.
- 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_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.
- 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