From 5aa06c09d1e7134745d11772dbe644ea9444f2a2 Mon Sep 17 00:00:00 2001 From: fiona-naughton Date: Fri, 1 Nov 2024 13:00:27 +1100 Subject: [PATCH] add archive links for original fortran helanal --- docs/source/getting_started.rst | 4 +++- docs/source/properties_computed.rst | 10 +++++++--- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst index e9d83dc..cd05103 100644 --- a/docs/source/getting_started.rst +++ b/docs/source/getting_started.rst @@ -82,7 +82,7 @@ Further Options 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. @@ -94,3 +94,5 @@ them when using this module in published work. 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 diff --git a/docs/source/properties_computed.rst b/docs/source/properties_computed.rst index c50251e..8ad0d69 100644 --- a/docs/source/properties_computed.rst +++ b/docs/source/properties_computed.rst @@ -1,9 +1,10 @@ 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}`, @@ -111,3 +112,6 @@ All angles are in degrees. 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