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add archive links for original fortran helanal
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fiona-naughton committed Nov 1, 2024
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4 changes: 3 additions & 1 deletion docs/source/getting_started.rst
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Citations
---------

helanal implements the HELANAL algorithm from [Bansal2000]_, which itself
helanal is based on the `HELANAL algorithm`_ from [Bansal2000]_, which itself
uses the method of [Sugeta1967]_ to characterise each local axis. Please cite
them when using this module in published work.

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HELANAL - A program to characterise helix geometry in proteins.
*J Biomol Struct Dyn.* 17(5):811-819.
.. _`HELANAL algorithm`:
https://web.archive.org/web/20090226192455/http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.f
10 changes: 7 additions & 3 deletions docs/source/properties_computed.rst
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Computed Properties
===================

Helanal follows the procedure of Sugeta and Miyazawa [Sugeta1967]_. Properties
are computed for a 'window' of four consecutive :math:`C_α` atoms, and this
window is then slid along the length of the helix in one-residue steps.
Helanal follows the procedure of Sugeta and Miyazawa [Sugeta1967]_ and is based
on the `Fortran HELANAL implementation`_ by [Bansal2000]_.
Properties are computed for a 'window' of four consecutive :math:`C_α` atoms,
and this window is then slid along the length of the helix in one-residue steps.

For each window consisting of atoms :math:`c_i`, :math:`c_{i+1}`,
:math:`c_{i+2}`, :math:`c_{i+3}`, the vectors :math:`\mathbf{B_1}`,
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A summary of the results, including mean, sample standard deviation and mean
absolute deviation is also provided in ``results.summary``.

.. _`Fortran HELANAL implementation`:
https://web.archive.org/web/20090226192455/http://www.ccrnp.ncifcrf.gov/users/kumarsan/HELANAL/helanal.f

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