sunhwan

from IPython.core.magic import register_cell_magic
from IPython.display import SVG, display

import requests

diagrams_supported = set(['blockdiag', 'seqdiag', 'mermaid', 'actdiag', 
                          'nwdiag', 'packetdiag', 'rackdiag', 'erd',
                          'nomnoml', 'plantuml', 'umlet', 'wavedrom', 
                          'bpmn', 'bytefield', 'pikchr', 'graphviz',
                          'vega', 'vega-lite', 'ditaa', 'svgbob'])

sunhwan

[aws]
aws_region_name = us-east-1

[aliases]
ssh = ssh {CFN_USER}@{MASTER_IP} {ARGS}

[global]
cluster_template = default
update_check = true
sanity_check = true

sunhwan

from numpy.random import choice

class KMedoid:
    def __init__(self, k, verbose=False):
        self.k = k
        self.maxiter = 100
        self.verbose = verbose
        
    def assign_labels(self, S):
        return np.argmin(S, axis=1)

sunhwan

import argparse
import re
import base64
from io import BytesIO

import cairosvg
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem.Draw.MolDrawing import MolDrawing, DrawingOptions #Only needed if modifying defaults

sunhwan

import argparse
from pathlib import Path
import re
import sys
from multiprocessing import Pool
from functools import partial

from tqdm import tqdm
import mdtraj as md
import numpy as np

sunhwan

#!/bin/sh

if [[ "${1}" == "http"* ]] ; then
	doi="${1}"
else
	doi="http://dx.doi.org/${1}"
fi

# Stopped working around 2015-10-04.
# curl -sLH "Accept: text/bibliography; style=bibtex" "${doi}" | sed 's/^ *//'

sunhwan

import sys
import numpy as np

debug = False
if len(sys.argv) > 1: debug = True

input = sys.stdin
pmf_filename = input.readline().strip() # stores pmf
rho_filename = input.readline().strip() # stores average density
bia_filename = input.readline().strip() # stores biased distribution

sunhwan

# configuration for replica exchange scripts

# run simulation: 
#   mkdir output
#   (cd output; mkdir 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15)
#   mpirun -np 16 -hostfile hostfile $bindir/namd2 +replicas 16 job0.conf +stdout output/%d/job0.%d.log
# the number of MPI ranks (-np) must be a multiple of the number of replicas (+replicas)

# to continue:
#   mpirun -np 16 -hostfile hostfile $bindir/namd2 +replicas 16 job1.conf +stdout output/%d/job1.%d.log

sunhwan

import argparse
import re
import sys

_s = re.compile('\s+')

def parse_psf(psffile):
    psf = open(psffile)
    psf.readline(); psf.readline()
    ntitle = int(psf.readline().strip().split()[0])

sunhwan

import subprocess as sp
pid = sp.Popen(['ssh', 'purdue', 'tail -f work/glycan/benchmarks/rexmd/aarex/server.log'], stdin=sp.PIPE, stdout=sp.PIPE, close_fds=True)
stdin, stdout = pid.stdin, pid.stdout

while 1:
    print stdout.readline()