octadist.main¶
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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()
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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.
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add_widgets
()[source]¶ Add all widgets and components to master windows.
GUI style of widgets in master windows use ttk style.
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show_text
(text)[source]¶ Insert text to result box
Parameters: text (str) – Text to show in result box. Returns: None (None)
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welcome_msg
()[source]¶ Show welcome message in result box:
- Program name, version, and release.
- Full author names.
- Official website: https://octadist.github.io.
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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.
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save_coord
()[source]¶ Save atomic coordinates (Cartesian coordinate) of octahedral structure. Default file extension is .xyz.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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draw_all_atom
()[source]¶ Display 3D complex.
See also
octadist.src.draw.DrawComplex()
- Show 3D molecule.
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draw_all_atom_and_face
()[source]¶ Display 3D complex with the faces.
See also
octadist.src.draw.DrawComplex()
- Show 3D molecule.
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draw_octa
()[source]¶ Display 3D octahedral structure.
See also
octadist.src.draw.DrawComplex()
- Show 3D molecule.
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draw_octa_and_face
()[source]¶ Display 3D octahedral structure with the faces.
See also
octadist.src.draw.DrawComplex()
- Show 3D molecule.
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draw_projection
()[source]¶ Draw projection planes.
See also
octadist.src.draw.DrawProjection()
- Show graphical projections.
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draw_twisting_plane
()[source]¶ Draw twisting triangular planes.
See also
octadist.src.draw.DrawTwistingPlane()
- Show graphical triangular twisting planes.
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show_data_complex
()[source]¶ Show info of input complex.
See also
octadist.src.structure.DataComplex()
- Show data summary of complex.
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show_param_octa
()[source]¶ Show structural parameters of selected octahedral structure.
See also
octadist.src.structure.StructParam()
- Show structural parameter symmary of complex.
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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.
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plot_zeta_sigma
()[source]¶ Plot relationship between zeta and sigma.
See also
octadist.src.plot.Plot()
- Show relationship plot.
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plot_sigma_theta
()[source]¶ Plot relationship between sigma and theta.
See also
octadist.src.plot.Plot()
- Show relationship plot.
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tool_jahn_teller
()[source]¶ Calculate Jahn-Teller distortion parameter.
See also
octadist.src.tools.CalcJahnTeller()
- Calculate Jahn-Teller distortion parameter.
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tool_rmsd
()[source]¶ Calculate root mean squared displacement of atoms in complex, RMSD.
See also
octadist.src.tools.CalcRMSD()
- Calculate RMSD.
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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.
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static
callback
(event)[source]¶ On-clink open web browser.
Parameters: event (object) – Event object for callback.
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static
show_about
()[source]¶ Show author details on a sub-window.
- Name of authors
- Official program website
- Citation
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static
show_license
()[source]¶ Show license details on a sub-window.
GNU General Public License version 3.0.
References