Testing

Automated testing

We are working towards automated unit and integration tests (see issue #2) but we do not have any yet.

Manual tests

(see #11)

Data files

I dumped the testing trajectory to figshare: Molecular dynamics trajectory of I-FABP for testing and benchmarking solvent dynamics analysis; will also have DOI 10.6084/m9.figshare.7058030.

The test data are too big (75 MB) to be included in the repo but you can download them from https://figshare.com/articles/Molecular_dynamics_trajectory_of_I-FABP_for_testing_and_benchmarking_solvent_dynamics_analysis/7058030 with the commands

curl -L https://ndownloader.figshare.com/articles/7058030/versions/1 --output files.zip
unzip files.zip

(For proper tests we could just take the first few frames.)

Test script

I ran the three scripts on relatively simple input, a MD simulation of apo I-FABP, using HOP_TESTRUN.sh:

#!/bin/bash

# get test data from https://doi.org/10.6084/m9.figshare.7058030
# or 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
DELTA=2.0


rm -rf $TESTDIR

hop-generate-densities.py -s ${PSF} -f ${DCD} -A "name OH2" -D ${TESTDIR} \
			  --delta=$DELTA --threshold=$CUTOFF || exit 1
hop-generate-hoptraj.py -s ${PSF} -f ${DCD} -o ${TESTDIR}/hoptraj \
			  ${TESTDIR}/water.pickle || exit 1
hop-generate-hopgraph.py  -s ${TESTDIR}/hoptraj.psf -f ${TESTDIR}/hoptraj.dcd \
			  -o ${TESTDIR}/hopgraph ${TESTDIR}/water.pickle || exit 1

Results

The output generally looks ok (see image below) but we need to check the numerical values for the hopping rates (in analysis/rates.txt).