{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# SHAPESの実行\n",
    "まずは必要なモジュールをインポートする"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-12-23T01:42:57.306688Z",
     "start_time": "2019-12-23T01:42:57.272322Z"
    }
   },
   "outputs": [],
   "source": [
    "import shapes_main as shp\n",
    "import tkinter\n",
    "from tkinter import messagebox as tkMessageBox\n",
    "from tkinter import filedialog as tkFileDialog\n",
    "from tkinter import simpledialog as tkSimpleDialog"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "実際に`SHAPES`を実行してみる。\n",
    "\n",
    "`shapes_main.py` と `shapes_module.py` を同一ディレクトリにいれておき、 `shapes_main.py` をcallする。\n",
    "\n",
    "入力：`num_symm`、`num_aa,num_sols`、`nbeads`、`inFile`(GNOMアウトファイル)\n",
    "\n",
    "出力：`ビーズモデル(pdbファイル)`、`散乱強度(datファイル)`、`動径分布関数(datファイル)`、`偏比容ビーズモデル(pdbファイル)`\n",
    "\n",
    "出力は`ビーズモデル`だけでなく、`ビーズモデル`をタンパク質の体積で整形した`偏比容ビーズモデル`がある。\n",
    "プログラムは、あらかじめ出力を格納する"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2019-12-23T03:32:13.252281Z",
     "start_time": "2019-12-23T01:42:57.314624Z"
    },
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "root=tkinter.Tk()\n",
    "root.withdraw()\n",
    "\n",
    "### default parameters ###\n",
    "aList_summary=[]\n",
    "bias_z=0.0\n",
    "inflate=1.0\n",
    "\n",
    "surface_scale=0.0\n",
    "starting_pdb='no'\n",
    "pdbfile_in='none'\n",
    "##########################\n",
    "\n",
    "prefix='6lyz_'\n",
    "num_symm=1 #対称性\n",
    "num_aa=1.0 #スケール係数\n",
    "num_sols=10 #試行回数\n",
    "nbeads=129 #アミノ酸数\n",
    "inFile=tkFileDialog.askopenfilename(title='Open GNOM file',filetypes=[(\"アウトファイル\",\"*.out\")])\n",
    "print(\"GNOM file:\",inFile)\n",
    "shp.main(aList_summary,nbeads,num_sols,num_aa,num_symm,bias_z,inflate,prefix,surface_scale,starting_pdb,inFile,pdbfile_in)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "GNOM file: /media/fujisawa/2124879b-e9d4-4135-8fd5-9b114fd41989/home/backup/gifu_19/grad/SAXS_WG/report/source/M_M/6lyz.out\n",
    "Program: SHAPES version 1.3\n",
    "Author: John Badger\n",
    "Copyright: 2019, John Badger\n",
    "License: GNU GPLv3\n",
    "Number of runs: 1\n",
    "Number of amino acids: 129\n",
    "Input P(r) file name: /media/fujisawa/2124879b-e9d4-4135-8fd5-9b114fd41989/home/backup/gifu_19/grad/SAXS_WG/report/source/M_M/6lyz.out\n",
    "Scale aa to bead count: 1.0\n",
    "Point symmetry: 1\n",
    "Z-axis bias: 0.0\n",
    "PSV inflation factor: 1.0\n",
    "Number of points read from P(r): 113\n",
    "Grid sampling: 0.4464 Dmax: 50.0\n",
    "Number of intensity data points read: 200\n",
    "\n",
    "Reconstruction trial: 1\n",
    "Number of beads randomly placed: 129\n",
    "Minimize energy of initial positions\n",
    "Emin cycle: 0 Energy: 89797276708.35\n",
    "Emin cycle: 10 Energy: 997.36\n",
    "Emin cycle: 20 Energy: 233.82\n",
    "Initial rms P(r): 0.453\n",
    "Target volume: 2.30 Actual volume: 2.14 Beads outside volume: 0\n",
    "                :\n",
    "               略     \n",
    "                :\n",
    "Target volume: 1.15 Actual volume: 1.14 Beads outside volume: 2\n",
    "\n",
    "Final model statistics\n",
    "Delta P(r): 0.093\n",
    "VDW energy: -1.34\n",
    "Final PSV of protein envelope: 1.08\n",
    "Rvalue: 0.021 CHI-squared: 221.934\n",
    "Output intensity file: 6lyz_intensity_1.dat\n",
    "\n",
    "Completion time: Fri Apr 10 17:13:01 2020\n",
    "\n",
    "            これが10回続く"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "実行の結果は`prefix`を`6lyz_`としたので\n",
    "\n",
    "- 6lyz_intensity_#.dat： $I_{fit}(q)$\n",
    "- 6lyz_pr_calc_#.dat： $P(r)$\n",
    "- 6lyz_beads_#.dat: ビーズモデル\n",
    "- 6lyz_psv_shape_#.dat：偏比容ビーズモデル\n",
    "\n",
    "が生成される。#は番号を表す。\n",
    "\n",
    "\n"
   ]
  }
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