.. _Documentation:

Documentation
==============

.. _doc_invariants:

Knot, link, theta-curve and handcuff type indentification (invariants calculation)
-----------------------------------------------------------------------------------

.. _doc_alexander:
.. autofunction:: topoly.alexander
.. _doc_jones:
.. autofunction:: topoly.jones
.. _doc_conway:
.. autofunction:: topoly.conway
.. _doc_homfly:
.. autofunction:: topoly.homfly
.. _doc_yamada:
.. autofunction:: topoly.yamada
.. _doc_kauffman_bracket:
.. autofunction:: topoly.kauffman_bracket
.. _doc_kauffman_polynomial:
.. autofunction:: topoly.kauffman_polynomial
.. _doc_blmho:
.. autofunction:: topoly.blmho
.. _doc_aps:
.. autofunction:: topoly.aps
.. _doc_writhe:
.. autofunction:: topoly.writhe
.. _doc_gln:
.. autofunction:: topoly.gln


.. _doc_joined:

Calculating invariants of conjoined structures
-----------------------------------------------
.. _doc_getpoly:
.. autofunction:: topoly.getpoly
.. _doc_exportpoly:
.. autofunction:: topoly.exportpoly


.. _doc_lasso:

Lasso type indentification (minimal surface calculation)
-----------------------------------------------------------

.. _doc_lasso_type:
.. autofunction:: topoly.lasso_type
.. _doc_make_surface:
.. autofunction:: topoly.make_surface


.. _doc_find:

Finding loops, theta-curves and handcuffs in structure
-------------------------------------------------------

.. _doc_find_loops:
.. autofunction:: topoly.find_loops
.. _doc_find_thetas:
.. autofunction:: topoly.find_thetas
.. _doc_find_handcuffs:
.. autofunction:: topoly.find_handcuffs


.. _doc_generate:

Random polygons generation
----------------------------
.. _doc_generate_walk:
.. autofunction:: topoly.generate_walk
.. _doc_generate_loop:
.. autofunction:: topoly.generate_loop
.. _doc_generate_lasso:
.. autofunction:: topoly.generate_lasso
.. _doc_generate_link:
.. autofunction:: topoly.generate_link
.. _doc_generate_handcuff:
.. autofunction:: topoly.generate_handcuff
.. _doc_generate_theta:
.. autofunction:: topoly.generate_theta


.. _doc_matrix:

Knot map manipulating functions
--------------------------------

.. _doc_plot_matrix:
.. autofunction:: topoly.plot_matrix
.. _doc_find_spots:
.. autofunction:: topoly.find_spots
.. _doc_translate_matrix:
.. autofunction:: topoly.translate_matrix


.. _doc_vis:

Visualization
--------------
.. _doc_xyz2vmd:
.. autofunction:: topoly.xyz2vmd
.. _doc_plot_graph:
.. autofunction:: topoly.plot_graph


.. _doc_manipulation:

Data manipulation
-------------------

.. _doc_translate_code:
.. autofunction:: topoly.translate_code
.. _doc_find_matching:
.. autofunction:: topoly.find_matching
.. _doc_import_structure:
.. autofunction:: topoly.import_structure
.. _doc_reduce_structure:
.. autofunction:: topoly.reduce_structure
.. _doc_close_curve:
.. autofunction:: topoly.close_curve


.. _doc.params:

Parameters for various functions (topoly.params)
---------------------------------------------------------------
.. _doc_Closure:
.. autoclass:: topoly.params.Closure
   :members:
.. _doc_ReduceMethod:
.. autoclass:: topoly.params.ReduceMethod
   :members:
.. _doc_SurfacePlotFormat:
.. autoclass:: topoly.params.SurfacePlotFormat
   :members:
.. _doc_PlotFormat:
.. autoclass:: topoly.params.PlotFormat
   :members:
.. _doc_OutputFormat:
.. autoclass:: topoly.params.OutputFormat
   :members:
.. _doc_PrecisionSurface:
.. autoclass:: topoly.params.PrecisionSurface
   :members:
.. _doc_DensitySurface:
.. autoclass:: topoly.params.DensitySurface
   :members:
.. _doc_Bridges:
.. autoclass:: topoly.params.Bridges
   :members:
.. _doc_OutputType:
.. autoclass:: topoly.params.OutputType
   :members:
.. _doc_Colors:
.. autoclass:: topoly.params.Colors
   :members: