yukimya

# GPL v 3.0 
# python library name: library of Protein analysis module(lProam)
# lProam.py
# written by Naoyuki Miyashita on 12/18/2013 
# Naoyuki Miyashita (c) 2013
#
#-----------------------------------
# please install 
# prody, pylab(matplotlib), numpy and scipy,
# before you use this scripts.

yukimya

# GPL v 3.0 
# script name: calcDistanceDCD.py
# written by Naoyuki Miyashita on 12/18/2013 
# Naoyuki Miyashita (c) 2013
#
#-----------------------------------
# Use lProam, pylab, numpy
#-----------------------------------
# ussage:
#

yukimya

# GPL v 3.0 
# script name: showPDF1d.py
# written by Naoyuki Miyashita on 12/18/2013 
# Naoyuki Miyashita (c) 2013
#
#-----------------------------------
# Use lProam, pylab, numpy
#-----------------------------------
# ussage:
# python showPDF1d.py \

yukimya

# DSSP_SECONCARY.PY
# Trajectories of Secondary Structure by DSSP
#-------------------------------------------------------------------------------
#    This source code is part of PROSTAC
#
#    Written by Naoyuki Miyashita
#    Copyright (c) 2013, Naoyuki Miyashita, Japan
#
#    This program is free software; you can redistribute it and/or
#    modify it under the terms of the GNU General Public License

yukimya

#!/bin/sh
#sed -e 's/[^3 ^4 ^5]/0/g' -e 's/[3 4 5]/1/g' $1 $1.helicity # for helicity
#sed -e 's/[^4 ]/0/g' -e 's/[4]/1/g' $1 # > $1.ahelix  # for alpha-helix
i=1
max=1
file_head="../data/out.condition."
file_ext=".out"

new_ext=".ahelix"
while [ $i -le $max ]

yukimya

# python script: averagin.py
# written by Naoyuki Miyashita

import subprocess
import numpy as np
import numpy.linalg
import string,os,sys,shutil,random

def readfile(filename):
    f=open(filename,"r")

yukimya

# GPL v 3.0
# script name: getSegment.py
# written by Naoyuki Miyashita on 1/06/2014
# Naoyuki Miyashita (c) 2014
#
#-----------------------------------
# Use lProam, pylab, numpy
#-----------------------------------
# ussage:
# setupTMDimerPosition.py input.pdb output.pdb distance \

yukimya

# GPL v 3.0
# script name: maxmin.py
# written by Naoyuki Miyashita on 12/20/2013
# Naoyuki Miyashita (c) 2013
#
#-----------------------------------
# Use lProam, pylab, numpy
#-----------------------------------
# ussage:
# python maxmin.py filename.pdb ¨selection¨

yukimya

#!/bin/sh
# GPL v.3
# Program mkMu:   mkMutation.sh
# Naoyuki Miyashita 7/22/2014
# 

#
# Input

outfile="00_mutation1.inp"

yukimya

#!/bin/sh
# GPL v. 3
# Program mkMu: 01mkVacPSF.sh
# 
# This program uses: lProam.py, getSegment.py
#
# written by Naoyuki Miyashita 7/22/2014


# Input