John H. jrhaberstroh

Data Scientist

jrhaberstroh / MDAnalysis modify atom file

Last active February 22, 2017 06:24

Simple MDAnalysis script to read in coordinates, modify them, and write them back out

	from MDAnalysis import *

	filename_in ="fakefile_{}.gro".format("in")
	filename_out="fakefile_{}.gro".format("out")

	ref = Universe(filename)

	R = [[1, 0, 0], [0, 0, 1], [0, 1, 0]]
	ref.atoms.translate(-ref.atoms.center_of_mass())
	ref.atoms.rotate(R)

jrhaberstroh / aminoacid_dihedrals.txt

Last active July 25, 2016 01:14

Ordered list of atomtypes from amino acid residues. Can be used to construct all sidechain dihedral angles.

	# Names of atom types involved in dihedral angles for amino acids.
	# Atom names based on conventions from GROMACS 4.6.7 amber99sb-ildn.ff/aminoacids.rtp
	ARG C CA CB CG CD NE CZ NH1
	LYS C CA CB CG CD CE NZ
	MET C CA CB CG SD CE
	GLU C CA CB CG SD OE1
	GLN C CA CB CG SD OE1
	ILE C CA CB CG1 CD
	LEU C CA CB CG CD1
	ASP C CA CB CG OD1

jrhaberstroh / newbash

Created July 24, 2016 21:14

	#!/bin/bash

	help()
	{
	sed --silent -e '/^: <<.*HELPDOC/,/^HELPDOC$/p' ${BASH_SOURCE[0]} \| tail -n+2 \| head -n-1
	}

	SRCDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )

	: <<'HELPDOC'

jrhaberstroh / newpy

Created July 24, 2016 21:13

	#!/bin/bash

	help()
	{
	sed --silent -e '/^: <<.*HELPDOC/,/^HELPDOC$/p' ${BASH_SOURCE[0]} \| tail -n+2 \| head -n-1
	}

	SRCDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )

	: <<'HELPDOC'

jrhaberstroh / safesaveplot

Created July 24, 2016 21:11

	# START: SAFESAVEPLOT
	if not args.o is None:
	import matplotlib
	matplotlib.use("agg")
	import matplotlib.pyplot as plt
	def safesaveplot(out=None, suffix=None, transparent=False, clf=True):
	fig = plt.gcf()
	if out:
	plt.savefig(out+suffix, transparent=transparent)
	if clf:

jrhaberstroh / pip_upgrade.sh

Created October 22, 2015 17:55

Upgrades all outdated python packages