Naoyuki Miyashita yukimya

yukimya / DisMatPlot.run

Created September 8, 2014 07:34

shell script of a movie making for Distant Matrix (calcDisMat.py)

	#!/bin/sh
	#gnuplot -e "plot.gn"
	mkdir tmp
	gnuplot DisMatPlot.gn
	ffmpeg -i "tmp/dd."%d".dis.jpeg" "tmp/dd.dis.movie.mpeg"
	ffmpeg -i "tmp/dd."%d".dif.jpeg" "tmp/dd.dif.movie.mpeg"

yukimya / DisMatPlot.gn

Created September 8, 2014 07:31

Plot Distant Matrix by gnuplot

	# This is for calcDisMatPlot.py
	# create jpeg file
	# written by Naoyuki Miyashita 09/07/2014
	# GPL v3

	se pm3d at b
	unse surface
	se view 0,0
	se size 0.7,1.0
	unse key

yukimya / calcDisMat.py

Last active August 29, 2015 14:06

Dinstant Matrix

	# GPL v 3.0
	# script name: setupDisMat.py
	# written by Naoyuki Miyashita on 09/07/2014
	# Naoyuki Miyashita (c) 2014
	#
	#-----------------------------------
	# Use lProam, pylab, numpy
	#-----------------------------------
	# ussage:
	# python calcDisMat.py 4 input.pdb input.dcd "name CA" output

yukimya / mkMu_07mkNPTEqu.sh

Created July 22, 2014 10:50

	#!/bin/sh
	# GPL v. 3
	# Program mkMu: 06mkAllEqu.sh
	#
	#
	# written by Naoyuki Miyashita 7/22/2014
	inputPrefix="04_ddng"
	inpPrefix="06.eq"
	outPrefix="07.eq"

yukimya / mkMu_06mkAllEqu.sh

Created July 22, 2014 08:35

	#!/bin/sh
	# GPL v. 3
	# Program mkMu: 06mkAllEqu.sh
	#
	#
	# written by Naoyuki Miyashita 7/22/2014
	inputPrefix="04_ddng"
	inpPrefix="05.min"
	outPrefix="06.eq"

yukimya / mkMu_05mkAllMini.sh

Last active August 29, 2015 14:04

	#!/bin/sh
	# GPL v. 3
	# Program mkMu: 05mkVacMini.sh
	#
	#
	# written by Naoyuki Miyashita 7/22/2014
	inputPrefix="04_ddng"
	outPrefix="05.min"

	Temp=310

yukimya / mkMu_04addWaterION.sh

Last active August 29, 2015 14:04

add water and IONs

	#!/bin/sh
	# GPL v. 3
	# Program mkMu: 04addWaterION.sh
	#
	#
	# written by Naoyuki Miyashita 7/22/2014

	#INPUT
	inputPrefix="01_dd"
	inpdcd="03.min/r.03.min.dcd"

yukimya / mkMu_03mkVacMini2.sh

Created July 22, 2014 07:13

minimization for protein in vac.-- constraints

	#!/bin/sh
	# GPL v. 3
	# Program mkMu: 03mkVacMini2.sh
	#
	#
	# written by Naoyuki Miyashita 7/22/2014
	inputPrefix="01_dd"
	inpPrefix="02.min"
	outPrefix="03.min"

yukimya / mkMu_02mkVacMini.sh

Last active August 29, 2015 14:04

minimization of Vac Protein

	#!/bin/sh
	# GPL v. 3
	# Program mkMu: 02mkVacMini.sh
	#
	#
	# written by Naoyuki Miyashita 7/22/2014
	inputPrefix="01_dd"
	outPrefix="02.min"

	Temp=310

yukimya / mkMu_01mkVacPSF.sh

Created July 22, 2014 04:54

make Mutant structure

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


	# Input