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#!/usr/bin/env bash | |
VERSION="1.1.8" | |
NAME="pbzip2-$VERSION" | |
FILENAME="$NAME.tar.gz" | |
URL="http://compression.ca/pbzip2/$FILENAME" | |
if [[ ! -f "$FILENAME" ]]; then | |
echo "Download $NAME..." | |
curl -o $FILENAME $URL | |
fi |
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#!/usr/bin/env bash | |
BASE=$(pwd) | |
HOST=$1 | |
if [[ "$HOST" = "" ]]; then | |
echo "usage: rsync_pull HOST_ADDRESS" | |
exit 1 | |
fi | |
askYesOrNo() { |
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#!/usr/bin/env bash | |
BASE=$(pwd) | |
HOST=$1 | |
if [[ "$HOST" = "" ]]; then | |
echo "usage: rsync_pull HOST_ADDRESS" | |
exit 1 | |
fi | |
askYesOrNo() { |
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# coding=utf-8 | |
""" | |
""" | |
__author__ = 'Alisue <lambdalisue@hashnote.net>' | |
try: | |
from PySide import QtCore | |
from PySide import QtGui | |
except ImportError: | |
from PyQt4 import QtCore | |
from PyQt4 import QtGui |
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# coding: utf-8 | |
#=============================================================================== | |
# Name: track_atoms.py | |
# Description: draw tracking arrows for atoms trajectory (iterate states) | |
# Author: Alisue <lambdalisue@hashnote.net> | |
# License: MIT license | |
# Required: colour, natsort, pymol, chempy | |
# (C) 2014, hashnote.net, Alisue | |
#=============================================================================== | |
import re |
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#!/usr/bin/env python | |
# coding=utf-8 | |
""" | |
Colors | |
""" | |
__author__ = 'Alisue <lambdalisue@hashnote.net>' | |
import collections | |
Colors = collections.namedtuple('Colors', [ | |
"LIGHT_PINK", "LIGHT_BROWN", "LIGHT_PURPLE", "LIGHT_ORANGE", | |
"LIGHT_BLUE", "LIGHT_GREEN", "LIGHT_RED", "LIGHT_BLACK", |
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# coding=utf-8 | |
""" | |
Amino acid sequence manupulation library | |
""" | |
__author__ = 'Alisue <lambdalisue@hashnote.net>' | |
AMINOACIDS = list("ARNDCEQGHILKMFPSTWYV") | |
AMINOACIDS3 = ( | |
'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLU', 'GLN', 'GLY', 'HIS', 'ILE', 'LEU', | |
'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL', | |
) |
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# coding=utf-8 | |
""" | |
""" | |
__author__ = 'Alisue <lambdalisue@hashnote.net>' | |
def load_fasta(iterator): | |
""" | |
Load fasta file and return sequence list | |
>>> fasta = ''' | |
... >avGFP |
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# coding=utf-8 | |
""" | |
""" | |
__author__ = 'Alisue <lambdalisue@hashnote.net>' | |
# Refence: | |
# Eisenberg D., Schwarz E., Komarony M., Wall R. | |
# J. Mol. Biol. 179:125-142(1984). | |
HYDROPHOBICITIES = { | |
'A': 0.620, 'R': -2.530, 'N': -0.780, 'D': -0.900, 'C': 0.290, |
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# coding=utf-8 | |
""" | |
""" | |
__author__ = 'Alisue <lambdalisue@hashnote.net>' | |
import re | |
def find_alignment_offsets(sequence): | |
""" | |
Get alignment offset from alignment sequence |
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