- Jonathan Whitmore, PhD
- Data Scientist, SVDS
- @jbwhitmore
from __future__ import print_function | |
""" | |
simulatedtempering.py: Implements simulated tempering | |
This is part of the OpenMM molecular simulation toolkit originating from | |
Simbios, the NIH National Center for Physics-Based Simulation of | |
Biological Structures at Stanford, funded under the NIH Roadmap for | |
Medical Research, grant U54 GM072970. See https://simtk.org. |
This is just a quick list of resourses on TDA that I put together for @rickasaurus after he was asking for links to papers, books, etc on Twitter and is by no means an exhaustive list.
Both Carlsson's and Ghrist's survey papers offer a very good introduction to the subject
- Topology and Data by Gunnar Carlsson
- Barcodes: The Persistent Topology of Data by Robert Ghrist
- Extracting insights from the shape of complex data using topology A good introductory paper in Nature on the
Mapper
algorithm.
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 |
HEADER HEADER | |
ATOM 1 N LYS 1 38.807 20.601 18.408 1.00 .00 | |
ATOM 2 H1 LYS 1 39.388 20.210 17.695 1.00 .00 | |
ATOM 3 H2 LYS 1 37.905 20.169 18.376 1.00 .00 | |
ATOM 4 H3 LYS 1 39.223 20.439 19.303 1.00 .00 | |
ATOM 5 CA LYS 1 38.666 22.049 18.184 1.00 .00 | |
ATOM 6 HA LYS 1 39.651 22.511 18.241 .00 .00 | |
ATOM 7 CB LYS 1 38.086 22.288 16.784 1.00 .00 | |
ATOM 8 HB1 LYS X 1 37.069 21.897 16.759 1.00 .00 | |
ATOM 9 HB2 LYS 1 38.692 21.737 16.068 1.00 .00 |
import mdtraj as md | |
import numpy as np | |
n_frames = 100 | |
coords = np.random.multivariate_normal(mean=[0, 0, 0], cov=[[2, 1, 0], [0, 1, 0], [0 ,0, 1]], size=n_frames) | |
coords = np.reshape(coords, (n_frames, 1, 3)) | |
with md.XTCTrajectoryFile('output.xtc', 'w') as f: | |
f.write(coords) |
Created by Christopher Manning
[](http://bl.ocks.org/d/1703449/#/[0, 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144, 233, 377, 610, 987, 1597, 2584, 4181, 6765, 10946, 17711, 28657, 46368, 75025, 121393, 196418, 317811, 514229, 832040, 1346269, 2178309, 3524578, 5702887, 9227465, 14930352, 24157817, 39088169]43/0/1) [![Star](https://raw.github.co
Created by Christopher Manning
[](http://bl.ocks.org/d/1703449/#/[0, 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144, 233, 377, 610, 987, 1597, 2584, 4181, 6765, 10946, 17711, 28657, 46368, 75025, 121393, 196418, 317811, 514229, 832040, 1346269, 2178309, 3524578, 5702887, 9227465, 14930352, 24157817, 39088169]43/0/1) [![Star](https://raw.github.co
import time | |
import random | |
from IPython import parallel | |
# create client & view | |
rc = parallel.Client() | |
dv = rc[:] | |
# scatter 'id', so id=0,1,2 on engines 0,1,2 |