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 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:

  1. Program name, version, and release.
  2. Full author names.
  3. 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.

  1. Name of authors
  2. Official program website
  3. 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]