mpharrigan

"""Violin plot with just the median drawn

By default, when plotting a split violin plot, the inner
box plot is for both splits. You can change this with `inner='quartile'`
to plot the quartiles for each split, but by default it uses a dashed
line (small dashes) for the 25 and 75-%ile and another dashed line
(big dashes) for the median, which is very ugly and cluttered.

This patching the `draw_quartiles` function to just draw the median
as a solid line.

mpharrigan

12.2k atoms (cys-ala-val)

num	where	code	what	parallel	speed (approx)
1	xstream	amber	K40 GPU on Xstream	cuda	143
10	sherlock2	amber	gcc 6 + openblas	openmpi	28
10	sherlock2	amber	icc 2017 + mkl	openmpi (intel)	28
20	sherlock2	amber	gcc 6 + openblas	openmpi	40
20	sherlock2	amber	icc 2017 + mkl	openmpi (intel)	50
10	sherlock2	amber	icc 2017 + mkl	intel mpi	2.3 (something is probably wrong here)

mpharrigan

set M [transaxis z 45 deg]
$sel move $M
$sel writepdb file.pdb

mpharrigan

def graph(weights, cutoff=1e-5):
    
    trunc_weights = np.copy(weights)

    # Remove transitions below the cutoff
    if cutoff is not None:
        trunc_weights[trunc_weights < cutoff] = 0.0

    # Ignore self transitions
    diag_inds = np.arange(len(weights))

mpharrigan

CMakeFiles/TestCudaAmoebaTorsionTorsionForce.dir/TestCudaAmoebaTorsionTorsionForce.cpp.o: In function `testTorsionTorsion(int)':
/conda-dev-recipes/openmm/openmm/plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaTorsionTorsionForce.cpp:2589: undefined reference to `OpenMM::System::System()'
/conda-dev-recipes/openmm/openmm/plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaTorsionTorsionForce.cpp:2594: undefined reference to `OpenMM::LangevinIntegrator::LangevinIntegrator(double, double, double)'
/conda-dev-recipes/openmm/openmm/plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaTorsionTorsionForce.cpp:2596: undefined reference to `OpenMM::AmoebaTorsionTorsionForce::AmoebaTorsionTorsionForce()'
/conda-dev-recipes/openmm/openmm/plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaTorsionTorsionForce.cpp:2647: undefined reference to `OpenMM::AmoebaTorsionTorsionForce::addTorsionTorsion(int, int, int, int, int, int, int)'
/conda-dev-recipes/openmm/openmm/plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaTorsionTorsio

mpharrigan

ffmpeg -i molecule.%5d.ppm -c:v libx264 -preset slow -crf 18 molecule.mkv

# -i       input filenames
# -c:v     codec (libx264 --> H.264)
# -preset  duh
# -crf     quality factor, lower = better, 18 = practically lossless
#          output filename

# For colors, make sure you're using yuv444 which should be the default in newer ffmpeg

mpharrigan

ds = dataset("**/*.dcd", top='struct.pdb')
diheds = ds.fit_transform_with(DihedralFeaturizer(), 'diheds')
ticas = diheds.fit_transform_with(tICA(), 'ticas')
kmeans = KMeans(n_clusters=8)
clusters = ticas.fit_transform_with(kmeans, 'clusters')
msm = MSM().fit(clusters)
dump(msm, 'msm.pkl')

mpharrigan

# Basic usage / workflow
ds = dataset("**/*.dcd")

dihed = ds.derive('dihed', fmt='dir-npy')
dihed += DihedralFeaturizer().fit_transform(ds)

tica = dihed.derive('tica', fmt='hdf5')
tica += tICA().fit_transform(dihed)

clusters = tica.derive('clusters', fmt='hdf5')

mpharrigan

from __future__ import print_function
import simtk.openmm as mm
import simtk.openmm.app as app

d = dict(base_dir="RUN2",
         state='state.xml')


with open("{base_dir}/system.xml".format(**d)) as f:
    system = mm.XmlSerializer.deserialize(f.read())

mpharrigan

from mdtraj.formats.dcd import DCDTrajectoryFile
from mdtraj.formats.prmtop import load_prmtop
km = KMedoids(...)

# "centers" is a pandas DataFrame with metadata about each trajectory
# from which we are pulling structures

def get_top(struc):
    return centers.query("structure == @struc")['top_fn'].iloc[0]