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Robert T. McGibbon rmcgibbo

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rmcgibbo / assignments.md
Created February 6, 2014 07:12 
>>> from mdtraj import io
>>> io.loadh('/Users/rmcgibbo/Downloads/Assignments.h5')['arr_0]
>>> assigments = io.loadh('/Users/rmcgibbo/Downloads/Assignments.h5')['arr_0']
>>> np.unique(assigments)
array([-1,  0,  4,  5,  6,  7,  8,  9])
@rmcgibbo
rmcgibbo / config.py
Created February 26, 2014 06:28
import bisect
import collections
class Configuration(collections.Mapping):
'''dict-like object that allows multiple values per key. each key is
associated with a 'priority' __getitem__ always return the entry with the
highest priority
'''
def __init__(self):
self._items = collections.defaultdict(lambda : [])
@rmcgibbo
rmcgibbo / output.log
Last active August 29, 2015 13:56
$ python testInstallation.py
There are 4 Platforms available:
/home/rmcgibbo/local/openmm/openmmapi/src/NonbondedForceImpl.cpp:267:26: runtime error: signed integer overflow: 188464 * 23558 cannot be represented in type 'int'
1 Reference - Successfully computed forces
/home/rmcgibbo/local/openmm/libraries/csha1/src/SHA1.cpp:80:2: runtime error: unsigned integer overflow: 3354000705 + 1518500249 cannot be represented in type 'unsigned int'
/home/rmcgibbo/local/openmm/libraries/csha1/src/SHA1.cpp:80:2: runtime error: unsigned integer overflow: 577533658 + 3903086636 cannot be represented in type 'unsigned int'
/home/rmcgibbo/local/openmm/libraries/csha1/src/SHA1.cpp:80:22: runtime error: unsigned integer overflow: 4227596030 + 1869443177 cannot be represented in type 'unsigned int'
/home/rmcgibbo/local/openmm/libraries/csha1/src/SHA1.cpp:80:22: runtime error: unsigned integer overflow: 3320572160 + 3698794201 cannot be represented in type 'unsigned int'
/home/rmcgibbo/local/openmm/libraries/csha1/src/SHA1.cpp:
@rmcgibbo
rmcgibbo / gist:9319779
Created March 3, 2014 07:03
$ python testInstallation.py
llvm-symbolizer: Unknown command line argument '--default-arch=x86_64'. Try: '/usr/bin/llvm-symbolizer -help'
llvm-symbolizer: Did you mean '-disable-ssc=x86_64'?
==13656==WARNING: external symbolizer didn't start up correctly!
==13656==WARNING: Trying to symbolize code, but external symbolizer is not initialized!
/home/rmcgibbo/local/openmm/olla/src/Platform.cpp:201:13: runtime error: call to function (unknown) through pointer to incorrect function type 'void (*)()'
(/home/rmcgibbo/opt/openmm-master/lib/plugins/libOpenMMAmoebaReference.so+0x586890): note: (unknown) defined here
/home/rmcgibbo/local/openmm/olla/src/Platform.cpp:201:13: runtime error: call to function (unknown) through pointer to incorrect function type 'void (*)()'
(/home/rmcgibbo/opt/openmm-master/lib/plugins/libOpenMMCUDA.so+0x599370): note: (unknown) defined here
/home/rmcgibbo/local/openmm/olla/src/Platform.cpp:201:13: runtime error: call to function (unknown) through pointer to incorrect function type 'void
@rmcgibbo
rmcgibbo / protL_nat.pdb
Created March 28, 2014 21:23
TITLE Gyas ROwers Mature At Cryogenic Speed
MODEL 1
ATOM 1 N MET A 1 4.331 -2.627 4.691 1.00 0.00 N
ATOM 2 H1 MET A 1 5.097 -3.176 5.026 1.00 0.00
ATOM 3 H2 MET A 1 3.880 -3.107 3.938 1.00 0.00
ATOM 4 H3 MET A 1 4.671 -1.744 4.367 1.00 0.00
ATOM 5 CA MET A 1 3.379 -2.414 5.770 1.00 0.00 C
ATOM 6 HA MET A 1 3.910 -1.927 6.464 1.00 0.00
ATOM 7 CB MET A 1 2.200 -1.573 5.271 1.00 0.00 C
ATOM 8 HB1 MET A 1 1.424 -1.719 5.885 1.00 0.00
@rmcgibbo
rmcgibbo / pme-electrostatics.py
Created April 6, 2014 08:23
Two interacting point charges.
from simtk.openmm import *
from pylab import *
system = System()
system.addParticle(0)
system.addParticle(0)
system.setDefaultPeriodicBoxVectors([10,0,0], [0, 10, 0], [0, 0, 10])
force = NonbondedForce()
force.setNonbondedMethod(NonbondedForce.PME)
force.addParticle(1.0, 1.0, 0.0)
@rmcgibbo
rmcgibbo / transmat.txt
Created May 3, 2014 06:02
8.219178082191781753e-03 1.369863013698630061e-02 6.849315068493150305e-03 1.643835616438356351e-02 1.095890410958904118e-02 8.219178082191781753e-03 8.219178082191781753e-03 6.849315068493150305e-03 9.589041095890411467e-03 1.095890410958904118e-02 1.095890410958904118e-02 1.917808219178082293e-02 9.589041095890411467e-03 8.219178082191781753e-03 4.109589041095890877e-03 1.506849315068493206e-02 1.506849315068493206e-02 1.232876712328767090e-02 6.849315068493150305e-03 9.589041095890411467e-03 6.849315068493150305e-03 1.095890410958904118e-02 8.219178082191781753e-03 1.643835616438356351e-02 1.095890410958904118e-02 4.109589041095890877e-03 1.643835616438356351e-02 6.849315068493150305e-03 8.219178082191781753e-03 9.589041095890411467e-03 6.849315068493150305e-03 6.849315068493150305e-03 2.054794520547945091e-02 1.780821917808219149e-02 1.095890410958904118e-02 2.739726027397260295e-03 9.589041095890411467e-03 5.479452054794520591e-03 1.369863013698630061e-02 1.095890410958904118e-02 1.232876712328767090e-02
@rmcgibbo
rmcgibbo / gist.py
Created May 14, 2014 04:02
import numpy as np
from mixtape.vmhmm import inverse_mbessel_ratio
def fit_vonmises(data):
"""
Parameters
----------
data : np.array, shape=(n_samples, n_features)
@rmcgibbo
rmcgibbo / ipcluster.sh
Created May 22, 2014 21:54
#!/bin/bash
#PBS -S /bin/bash
#PBS -e /dev/null
#PBS -o /dev/null
#PBS -l nodes=4:ppn=16
#PBS -l walltime=10:00:00
#PBS -V
#PBS -q MP
cd $PBS_O_WORKDIR
@rmcgibbo
rmcgibbo / convert-project.py
Last active August 29, 2015 14:06
from __future__ import print_function
import os
import sys
import json
import argparse
import traceback
from fnmatch import fnmatch
import mdtraj as md