rmcgibbo

all:
	gcc -DHEADER client.c lib.c -o withheader
	gcc          client.c lib.c -o withoutheader

rmcgibbo

make an empty list called medoids

for cluster i:
  let t be a trajectory containing all of the structures assigned to cluster i
  let D = the full len(t) x len(t) pairwise RMSD distance matrix
  set medoid[i] = argmin( rowsums (D) )

rmcgibbo

import numpy as np
import sys
import rpy2.rinterface as ri
import rpy2.robjects as ro
from rpy2.robjects.numpy2ri import numpy2ri
ro.conversion.py2ri = numpy2ri
from IPython.extensions.rmagic import RInterpreterError, Rconverter
from IPython.utils.py3compat import str_to_unicode, unicode_to_str, PY3

__all__ = ['r']

rmcgibbo

rmcgibbo

rmcgibbo

rmcgibbo

import numpy as np
from msmbuilder.metrics import AbstractDistanceMetric, Vectorized
# multithreaded distance and angle engines
from msmbuilder.geometry import angle, contact
import itertools

class HydrogenBond(Vectorized, AbstractDistanceMetric):
    """ 
    Distance metric class for calculating distance between frames based
    on their hydrogen bond contact maps, which are NON-SYMMETRIC matrices

rmcgibbo

from __future__ import division
import numpy  as np
import IPython as ip
import matplotlib.pyplot as pp
import warnings
from collections import namedtuple
import scipy.optimize

#symbolic algebra
import theano

rmcgibbo

#!/bin/sh

# probably need to set up some PBS directives up here...

N_PROCS=4

# Set up a little python "shim" using mpi4py that farms
# out a set of command line commands to multiple nodes
# using MPI. This shim gets written to a little file
rm -f ./temp_shim.py

rmcgibbo

#!/bin/sh

# start up the controller on the main node
ipcontroller --ip="*" &
sleep 5

mpirun --hostfile $PBS_NODEFILE --bynode ipengine &
sleep 5