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# OpenDX density file written by
# $Id: sitemap.py 1706 2008-04-09 21:14:48Z oliver $
# File format: http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF
# Data are embedded in the header and tied to the grid positions.
# Unit of   length    is Angstrom.
# Unit of   density   is TIP3P-based.
# Data is written in C array order: In grid[x,y,z] the axis z is fastest
# varying, then y, then finally x, i.e. z is the innermost loop.
# Meta data stored with the python Grid object:
#    totaltime = 19998.998

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# test assert vs assert_
# run with
#      python assert_test.py
# and
#      python -O assert_test.py
#
# to see that assert is optimized away by -O

from numpy.testing import assert_

orbeckst

#!/bin/bash

# get test data from https://www.dropbox.com/sh/jp1n4zc7q5nxvzf/AABrM8iEypZE-g2gOFfOgahRa?dl=0 
# see https://github.com/Becksteinlab/hop/wiki/Testing#manual-tests

TESTDIR=analysis

PSF=ifabp_water.psf
DCD=rmsfit_ifabp_water_1.dcd
CUTOFF=1.3

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import numpy as np
import MDAnalysis as mda

u = mda.Universe("topol.tpr", "trj.xtc")
ca = u.select_atoms("name CA")
means = np.zeros((len(ca), 3))
sumsq = np.zeros_like(means)
for k, ts in enumerate(u.trajectory):
    sumsq += (k/(k+1.0)) * (ca.positions - means)**2
    means[:] = (k*means + ca.positions)/(k+1.0)

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#! /usr/bin/env python2.7

import MDAnalysis as mda
import MDAnalysis.analysis.hbonds 

def select_monomers(u, nmer=4):
    protein = u.select_atoms("protein")

    # note: bynum is 1-based so range starts at 1
    monomers = [u.select_atoms("protein and bynum " + str(i1) + ":" + str(i2)) for i1 in range(1, protein.n_atoms, protein.n_atoms/nmer) for i2 in [i1+protein.n_atoms/nmer - 1]]