jrhaberstroh

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

# 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

#!/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

#!/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

# 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

#!/usr/bin/env bash
# ==============================================================================
usage() { cat <<- DOCUMENT

    usage: pip_upgrade [-h] [3]

    AUTHOR:      Sang Han
    CREATED:     08/23/2014
    REVISION:    1.0