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User Documentation

  • Getting Started
    • Why OctaDist?
    • Features
      • Structural distortion analysis
      • Molecular visualizations
      • Tools and Utilities
      • Capabilities
      • Architectures
    • Distortion parameters
    • System requirements
  • Download OctaDist
    • Stable Version
    • Development Version
    • Release Archives
  • Install OctaDist
    • Windows
    • Linux
    • macOS
    • PyPI
    • Anaconda
    • Python Package
  • Build OctaDist
    • Prerequisites
    • Build the tarball, wheel, and egg
    • Compile OctaDist to EXE
  • Run OctaDist
    • Run OctaDist GUI using EXE
    • Run OctaDist GUI on the terminal
    • Run OctaDist CLI
  • Example Calculations
    • Supported File Format
    • Running the tests
      • Example 1
      • Example 2
      • Example 3
      • Example 4
      • Example 5
      • Example 6
      • Example 7
  • Benchmarks
    • 1. Perfect octahedral complex
    • 2. [Fe(1-bpp)2][BF4]2 complex in low-spin state
    • 3. [Fe(1-bpp)2][BF4]2 complex in high-spin state
    • 4. Very distorted structure
  • Error and Fixing
    • 1. OctaDist Startup Slow on Windows?
    • 2. Missing some packages
    • 3. tkinter is not properly configured to Python
    • 4. Failed to build PEP517
    • 5. MPL error
    • 6. Cannot connect to X11 server
  • Modules
    • Program structure
    • Application Program Interface (API)
    • Source code
      • octadist.main
        • OctaDist
        • main()
      • octadist.gui
        • run_gui()
      • octadist.cli
        • check_file()
        • find_coord()
        • calc_param()
        • run_cli()
      • octadist.calc
        • CalcDistortion
      • octadist.draw
        • DrawComplex_Matplotlib
        • DrawComplex_Plotly
        • DrawProjection
        • DrawTwistingPlane
      • octadist.elements
        • number_to_symbol()
        • number_to_radii()
        • number_to_color()
      • octadist.io
        • is_cif()
        • get_coord_cif()
        • is_xyz()
        • get_coord_xyz()
        • is_gaussian()
        • get_coord_gaussian()
        • is_nwchem()
        • get_coord_nwchem()
        • is_orca()
        • get_coord_orca()
        • is_qchem()
        • get_coord_qchem()
        • count_line()
        • extract_coord()
        • find_metal()
        • extract_octa()
      • octadist.linear
        • angle_sign()
        • angle_btw_vectors()
        • angle_btw_planes()
        • triangle_area()
      • octadist.plane
        • find_eq_of_plane()
        • find_fit_plane()
      • octadist.plot
        • Plot
      • octadist.popup
        • err_no_file()
        • err_invalid_ftype()
        • err_no_coord()
        • err_less_ligands()
        • err_no_metal()
        • err_no_calc()
        • err_only_2_files()
        • err_not_equal_atom()
        • err_atom_not_match()
        • err_many_files()
        • err_wrong_format()
        • err_no_editor()
        • err_visualizer_not_found()
        • err_cannot_update()
        • info_save_results()
        • info_new_update()
        • info_using_dev()
        • info_no_update()
        • warn_no_metal()
        • warn_not_octa()
      • octadist.projection
        • project_atom_onto_line()
        • project_atom_onto_plane()
      • octadist.scripting
        • ScriptingConsole
      • octadist.structure
        • DataComplex
        • StructParam
        • SurfaceArea
      • octadist.tools
        • CalcJahnTeller
        • CalcRMSD
      • octadist.util
        • find_bonds()
        • find_faces_octa()
  • Development
    • Contribution
    • OctaDist Testing
    • Bug report
    • Code maintenance
  • Authors
  • License
OctaDist
  • Download OctaDist
  • Edit on GitHub

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  • Stable Version
  • Development Version
  • Release Archives
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© Copyright 2019-2024, Rangsiman Ketkaew et al.. Revision c38c5646.

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