Emap2sec to MRC.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import os\n",
    "import mrcfile\n",
    "import csv\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "filepath = \"ChainA_simulated_resample_phase2pred.txt\"\n",
    "df = pd.read_csv(filepath, sep=' |,', engine='python')\n",
    "df.drop(df.columns[3],axis=1,inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "        180  103   90  1  0.2907393  0.3802863  0.30566594  0.02330846\n",
      "0       181  103   90  1   0.308517   0.369448    0.292441    0.029594\n",
      "1       182  103   90  1   0.309514   0.362327    0.299106    0.029052\n",
      "2       183  103   90  1   0.330668   0.343932    0.290840    0.034560\n",
      "3       184  103   90  1   0.330855   0.343784    0.290682    0.034679\n",
      "4       185  103   90  1   0.330946   0.343733    0.290558    0.034762\n",
      "...     ...  ...  ... ..        ...        ...         ...         ...\n",
      "541762  226   68  175  2   0.317804   0.250222    0.387394    0.044580\n",
      "541763  227   68  175  2   0.317466   0.250439    0.387960    0.044135\n",
      "541764  228   68  175  2   0.294985   0.294741    0.359653    0.050621\n",
      "541765  229   68  175  2   0.310936   0.297494    0.351076    0.040493\n",
      "541766  230   68  175  2   0.292954   0.310799    0.349195    0.047052\n",
      "\n",
      "[541767 rows x 8 columns]\n"
     ]
    }
   ],
   "source": [
    "print(df) # x: 180 - 230, y: 68 - 103, z: 90 - 175 "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "df.to_csv(\"Input_emd_8097_chainA_resampled.csv\", index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def conv_phase_to_mrc1(phasefile,reffile,keyidx,outmapfile):\n",
    "    if os.path.isfile(outmapfile):\n",
    "        return True\n",
    "    INPUT=[]\n",
    "    with open(phasefile) as f:\n",
    "        reader = csv.reader(f)\n",
    "        for row in reader:\n",
    "            #xyz:[0,3]\n",
    "            INPUT.append([int(float(row[0])),int(float(row[1])),int(float(row[2])),float(row[keyidx+3])])\n",
    "    with mrcfile.open(reffile) as mrc:\n",
    "        nx,ny,nz,nxs,nys,nzs,mx,my,mz = mrc.header.nx,mrc.header.ny,mrc.header.nz,mrc.header.nxstart,mrc.header.nystart,mrc.header.nzstart,mrc.header.mx,mrc.header.my,mrc.header.mz\n",
    "        orig=mrc.header.origin\n",
    "        data=mrc.data\n",
    "        data_new= data #init\n",
    "        #update data by INPUT\n",
    "        #mrc_new = mrcfile.new(outmapfile,data=data_new, overwrite=True)\n",
    "        \n",
    "        mrc_new = mrcfile.new(outmapfile,overwrite=True)\n",
    "        \n",
    "        mrc_new.set_data(np.zeros((nx * 2, ny * 2, nz * 2),dtype=np.float32))\n",
    "        mrc_new.header.nxstart=nxs\n",
    "        mrc_new.header.nystart=nys\n",
    "        mrc_new.header.nzstart=nzs\n",
    "        \n",
    "        for x,y,z,prob in INPUT:\n",
    "            mrc_new.data[z,y,x]=prob\n",
    "        vsize=mrc_new.voxel_size\n",
    "        vsize.flags.writeable = True\n",
    "        mrc_new.voxel_size=vsize         \n",
    "         #             mrc_new.header.xorg=float(xx[0]) - float(mx)/2.0\n",
    "        \n",
    "        mrc_new.update_header_stats()\n",
    "        \n",
    "        print(\"original\", mrc.voxel_size)\n",
    "        mrc.print_header()\n",
    "        \n",
    "        print(\"new\", mrc_new.voxel_size)\n",
    "        mrc_new.print_header()\n",
    "        \n",
    "        mrc_new.close()    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "original (1.0700002, 1.0700002, 1.0700002)\n",
      "nx              : 221\n",
      "ny              : 201\n",
      "nz              : 191\n",
      "mode            : 2\n",
      "nxstart         : 0\n",
      "nystart         : 0\n",
      "nzstart         : 0\n",
      "mx              : 221\n",
      "my              : 201\n",
      "mz              : 191\n",
      "cella           : (236.47003, 215.07004, 204.37003)\n",
      "cellb           : (90., 90., 90.)\n",
      "mapc            : 1\n",
      "mapr            : 2\n",
      "maps            : 3\n",
      "dmin            : 0.0\n",
      "dmax            : 0.5139835476875305\n",
      "dmean           : 0.00250758184120059\n",
      "ispg            : 0\n",
      "nsymbt          : 0\n",
      "extra1          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "exttyp          : b''\n",
      "nversion        : 0\n",
      "extra2          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "origin          : (0., 0., 0.)\n",
      "map             : b'MAP '\n",
      "machst          : [68 65  0  0]\n",
      "rms             : 0.0\n",
      "nlabl           : 1\n",
      "label           : [b'Chimera 1.15_b42258 Wed Jun  9 12:56:42 2021' b'' b'' b'' b'' b'' b''\n",
      " b'' b'' b'']\n",
      "new (0., 0., 0.)\n",
      "nx              : 382\n",
      "ny              : 402\n",
      "nz              : 442\n",
      "mode            : 2\n",
      "nxstart         : 0\n",
      "nystart         : 0\n",
      "nzstart         : 0\n",
      "mx              : 382\n",
      "my              : 402\n",
      "mz              : 442\n",
      "cella           : (0., 0., 0.)\n",
      "cellb           : (90., 90., 90.)\n",
      "mapc            : 1\n",
      "mapr            : 2\n",
      "maps            : 3\n",
      "dmin            : 0.0\n",
      "dmax            : 0.956852912902832\n",
      "dmean           : 0.002342719119042158\n",
      "ispg            : 1\n",
      "nsymbt          : 0\n",
      "extra1          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "exttyp          : b''\n",
      "nversion        : 20140\n",
      "extra2          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "origin          : (0., 0., 0.)\n",
      "map             : b'MAP '\n",
      "machst          : [68 68  0  0]\n",
      "rms             : 0.03068394586443901\n",
      "nlabl           : 1\n",
      "label           : [b'Created by mrcfile.py                                       2021-09-13 19:52:14 '\n",
      " b'' b'' b'' b'' b'' b'' b'' b'' b'']\n",
      "original (1.0700002, 1.0700002, 1.0700002)\n",
      "nx              : 221\n",
      "ny              : 201\n",
      "nz              : 191\n",
      "mode            : 2\n",
      "nxstart         : 0\n",
      "nystart         : 0\n",
      "nzstart         : 0\n",
      "mx              : 221\n",
      "my              : 201\n",
      "mz              : 191\n",
      "cella           : (236.47003, 215.07004, 204.37003)\n",
      "cellb           : (90., 90., 90.)\n",
      "mapc            : 1\n",
      "mapr            : 2\n",
      "maps            : 3\n",
      "dmin            : 0.0\n",
      "dmax            : 0.5139835476875305\n",
      "dmean           : 0.00250758184120059\n",
      "ispg            : 0\n",
      "nsymbt          : 0\n",
      "extra1          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "exttyp          : b''\n",
      "nversion        : 0\n",
      "extra2          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "origin          : (0., 0., 0.)\n",
      "map             : b'MAP '\n",
      "machst          : [68 65  0  0]\n",
      "rms             : 0.0\n",
      "nlabl           : 1\n",
      "label           : [b'Chimera 1.15_b42258 Wed Jun  9 12:56:42 2021' b'' b'' b'' b'' b'' b''\n",
      " b'' b'' b'']\n",
      "new (0., 0., 0.)\n",
      "nx              : 382\n",
      "ny              : 402\n",
      "nz              : 442\n",
      "mode            : 2\n",
      "nxstart         : 0\n",
      "nystart         : 0\n",
      "nzstart         : 0\n",
      "mx              : 382\n",
      "my              : 402\n",
      "mz              : 442\n",
      "cella           : (0., 0., 0.)\n",
      "cellb           : (90., 90., 90.)\n",
      "mapc            : 1\n",
      "mapr            : 2\n",
      "maps            : 3\n",
      "dmin            : 0.0\n",
      "dmax            : 0.8712306618690491\n",
      "dmean           : 0.0011219173902645707\n",
      "ispg            : 1\n",
      "nsymbt          : 0\n",
      "extra1          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "exttyp          : b''\n",
      "nversion        : 20140\n",
      "extra2          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "origin          : (0., 0., 0.)\n",
      "map             : b'MAP '\n",
      "machst          : [68 68  0  0]\n",
      "rms             : 0.01718294620513916\n",
      "nlabl           : 1\n",
      "label           : [b'Created by mrcfile.py                                       2021-09-13 19:52:17 '\n",
      " b'' b'' b'' b'' b'' b'' b'' b'' b'']\n",
      "original (1.0700002, 1.0700002, 1.0700002)\n",
      "nx              : 221\n",
      "ny              : 201\n",
      "nz              : 191\n",
      "mode            : 2\n",
      "nxstart         : 0\n",
      "nystart         : 0\n",
      "nzstart         : 0\n",
      "mx              : 221\n",
      "my              : 201\n",
      "mz              : 191\n",
      "cella           : (236.47003, 215.07004, 204.37003)\n",
      "cellb           : (90., 90., 90.)\n",
      "mapc            : 1\n",
      "mapr            : 2\n",
      "maps            : 3\n",
      "dmin            : 0.0\n",
      "dmax            : 0.5139835476875305\n",
      "dmean           : 0.00250758184120059\n",
      "ispg            : 0\n",
      "nsymbt          : 0\n",
      "extra1          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "exttyp          : b''\n",
      "nversion        : 0\n",
      "extra2          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "origin          : (0., 0., 0.)\n",
      "map             : b'MAP '\n",
      "machst          : [68 65  0  0]\n",
      "rms             : 0.0\n",
      "nlabl           : 1\n",
      "label           : [b'Chimera 1.15_b42258 Wed Jun  9 12:56:42 2021' b'' b'' b'' b'' b'' b''\n",
      " b'' b'' b'']\n",
      "new (0., 0., 0.)\n",
      "nx              : 382\n",
      "ny              : 402\n",
      "nz              : 442\n",
      "mode            : 2\n",
      "nxstart         : 0\n",
      "nystart         : 0\n",
      "nzstart         : 0\n",
      "mx              : 382\n",
      "my              : 402\n",
      "mz              : 442\n",
      "cella           : (0., 0., 0.)\n",
      "cellb           : (90., 90., 90.)\n",
      "mapc            : 1\n",
      "mapr            : 2\n",
      "maps            : 3\n",
      "dmin            : 0.0\n",
      "dmax            : 0.9982191920280457\n",
      "dmean           : 0.003119435627013445\n",
      "ispg            : 1\n",
      "nsymbt          : 0\n",
      "extra1          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "exttyp          : b''\n",
      "nversion        : 20140\n",
      "extra2          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "origin          : (0., 0., 0.)\n",
      "map             : b'MAP '\n",
      "machst          : [68 68  0  0]\n",
      "rms             : 0.042691417038440704\n",
      "nlabl           : 1\n",
      "label           : [b'Created by mrcfile.py                                       2021-09-13 19:52:21 '\n",
      " b'' b'' b'' b'' b'' b'' b'' b'' b'']\n",
      "original (1.0700002, 1.0700002, 1.0700002)\n",
      "nx              : 221\n",
      "ny              : 201\n",
      "nz              : 191\n",
      "mode            : 2\n",
      "nxstart         : 0\n",
      "nystart         : 0\n",
      "nzstart         : 0\n",
      "mx              : 221\n",
      "my              : 201\n",
      "mz              : 191\n",
      "cella           : (236.47003, 215.07004, 204.37003)\n",
      "cellb           : (90., 90., 90.)\n",
      "mapc            : 1\n",
      "mapr            : 2\n",
      "maps            : 3\n",
      "dmin            : 0.0\n",
      "dmax            : 0.5139835476875305\n",
      "dmean           : 0.00250758184120059\n",
      "ispg            : 0\n",
      "nsymbt          : 0\n",
      "extra1          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "exttyp          : b''\n",
      "nversion        : 0\n",
      "extra2          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "origin          : (0., 0., 0.)\n",
      "map             : b'MAP '\n",
      "machst          : [68 65  0  0]\n",
      "rms             : 0.0\n",
      "nlabl           : 1\n",
      "label           : [b'Chimera 1.15_b42258 Wed Jun  9 12:56:42 2021' b'' b'' b'' b'' b'' b''\n",
      " b'' b'' b'']\n",
      "new (0., 0., 0.)\n",
      "nx              : 382\n",
      "ny              : 402\n",
      "nz              : 442\n",
      "mode            : 2\n",
      "nxstart         : 0\n",
      "nystart         : 0\n",
      "nzstart         : 0\n",
      "mx              : 382\n",
      "my              : 402\n",
      "mz              : 442\n",
      "cella           : (0., 0., 0.)\n",
      "cellb           : (90., 90., 90.)\n",
      "mapc            : 1\n",
      "mapr            : 2\n",
      "maps            : 3\n",
      "dmin            : 0.0\n",
      "dmax            : 0.9999864101409912\n",
      "dmean           : 0.001397743122652173\n",
      "ispg            : 1\n",
      "nsymbt          : 0\n",
      "extra1          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "exttyp          : b''\n",
      "nversion        : 20140\n",
      "extra2          : b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'\n",
      "origin          : (0., 0., 0.)\n",
      "map             : b'MAP '\n",
      "machst          : [68 68  0  0]\n",
      "rms             : 0.027099203318357468\n",
      "nlabl           : 1\n",
      "label           : [b'Created by mrcfile.py                                       2021-09-13 19:52:25 '\n",
      " b'' b'' b'' b'' b'' b'' b'' b'' b'']\n"
     ]
    }
   ],
   "source": [
    "structures = [1, 2, 3, 4]\n",
    "csv_path = \"Input_emd_8097_chainA_resampled.csv\"\n",
    "mrc_path = \"ChainA_simulated_resample.mrc\"\n",
    "map_name = \"emd_8097_chainA\"\n",
    "\n",
    "for i in structures:\n",
    "    if i == 1:\n",
    "        name = \"_helix.mrc\"\n",
    "    elif i == 2:\n",
    "        name = \"_coil.mrc\"\n",
    "    elif i == 3:\n",
    "        name = \"_strand.mrc\"\n",
    "    else:\n",
    "        name = \"_DNA.mrc\"\n",
    "      \n",
    "    conv_phase_to_mrc1(csv_path, mrc_path, i, map_name + name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
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   },
   "outputs": [],
   "source": []
  }
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