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sampleModes docs fix #1318

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sampleModes docs fix #1318

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0852f92
sampleModes docs fix
jamesmkrieger Feb 22, 2021
788617d
another fix
jamesmkrieger Feb 23, 2021
2dc1fa8
Merge branch 'master' of github.com:prody/ProDy into website_fix
jamesmkrieger Dec 20, 2021
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4 changes: 2 additions & 2 deletions prody/dynamics/sampling.py
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Expand Up @@ -47,13 +47,13 @@ def sampleModes(modes, atoms=None, n_confs=1000, rmsd=1.0):

:math:`R_0` is the active coordinate set of *atoms*.
:math:`[r_1^k r_2^k ... r_m^k]` are normally distributed random numbers
generated for conformation :math:`k` using :func:`numpy.random.randn`.
generated for conformation :math:`k` using :func:`~numpy.random.randn`.

RMSD of the new conformation from :math:`R_0` can be calculated as

.. math::

RMSD^k = \\sqrt{ {\\left( s \\sum_{i=1}^{m} r_i^k \\lambda^{-0.5}_i u_i \\right)}^{2} / N } = \\frac{s}{ \\sqrt{N}} \\sqrt{ \\sum_{i=1}^{m} (r_i^k)^2 \\lambda^{-1}_i }
RMSD^k = \\sqrt{ {\\left( s \\sum_{i=1}^{m} r_i^k \\lambda^{-0.5}_i u_i \\right) }^{2} / N } = \\frac{s}{ \\sqrt{N}} \\sqrt{ \\sum_{i=1}^{m} (r_i^k)^2 \\lambda^{-1}_i }


Average :math:`RMSD` of the generated conformations from the initial conformation is:
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