{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "41fefda3",
   "metadata": {},
   "source": [
    "# Read the data in"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "158c3047-8006-45c6-8df3-d4fe153b7a11",
   "metadata": {},
   "outputs": [],
   "source": [
    "filepath = '/local/scratch/EnriqueTitanium/2019_10_04_Ti_550/Scan5/'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "fb1fa4de",
   "metadata": {},
   "outputs": [],
   "source": [
    "# open the alpha file for reading\n",
    "alphaFN = 'Ti550_scan5_13_10_norot2_alpha.ang'\n",
    "Alpha = open(filepath+alphaFN,\"r\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "d3ca62ab",
   "metadata": {},
   "outputs": [],
   "source": [
    "# read the alpha file to a list of lines\n",
    "alpha = Alpha.readlines()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "ff8fee17",
   "metadata": {},
   "outputs": [],
   "source": [
    "# open the beta file for reading\n",
    "betaFN = alphaFN.replace('_alpha.ang','_beta.ang')\n",
    "Beta = open(filepath+betaFN,\"r\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "c71660b6",
   "metadata": {},
   "outputs": [],
   "source": [
    "# read the beta file to a list of lines\n",
    "beta = Beta.readlines()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "27f1b39e",
   "metadata": {},
   "outputs": [],
   "source": [
    "#print the alpha file\n",
    "#alpha"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "88bc862d",
   "metadata": {},
   "outputs": [],
   "source": [
    "#print the beta file\n",
    "#beta "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "bde6510a",
   "metadata": {},
   "source": [
    "# Finding the lines to split at and constructing the header"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "732d085a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "26"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# find where the Euler data starts (actually where the other stuff ends)\n",
    "alphadataindex = alpha.index('# Column names: phi1, Phi, phi2, x, y, image_quality, confidence_index, phase_id, detector_signal, pattern_fit\\n')\n",
    "alphadataindex"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "bf0dfb20",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "26"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# find where the Euler data starts (actually where the other stuff ends)\n",
    "betadataindex = beta.index('# Column names: phi1, Phi, phi2, x, y, image_quality, confidence_index, phase_id, detector_signal, pattern_fit\\n')\n",
    "betadataindex"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "09231993",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "7"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#find where the beta phase information starts\n",
    "alphaphaseindex = alpha.index('# MaterialName    Ti\\n')\n",
    "alphaphaseindex"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "158509cc-6efd-4acc-8082-15e9bd0dcd92",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "7"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#find where the beta phase information starts\n",
    "betaphaseindex = beta.index('# MaterialName    Ti\\n')\n",
    "betaphaseindex"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "a3258dba",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "13"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#find where the beta phase information ends\n",
    "betaphaseend = beta.index('# GRID: SqrGrid\\n')\n",
    "betaphaseend"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "03424ccc",
   "metadata": {},
   "outputs": [],
   "source": [
    "blank_line = ['# \\n']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "43413538",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "13"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#find where the beta phase information ends\n",
    "alphaphaseend = alpha.index('# GRID: SqrGrid\\n')\n",
    "alphaphaseend"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "21f371cc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['# TEM_PIXperUM           1.000000\\n',\n",
       " '# x-star                 0.000000\\n',\n",
       " '# y-star                 0.000000\\n',\n",
       " '# z-star                 0.000000\\n',\n",
       " '# WorkingDistance        0.000000\\n',\n",
       " '# \\n',\n",
       " '# Phase 1\\n',\n",
       " '# MaterialName    Alpha Titanium\\n',\n",
       " '# Formula    Ti\\n',\n",
       " '# Info\\n',\n",
       " '# Symmetry    622\\n',\n",
       " '# LatticeConstants    2.951 2.951 4.681 90.000 90.000 120.000\\n',\n",
       " '# NumberFamilies    0\\n',\n",
       " '# \\n',\n",
       " '# Phase 2\\n',\n",
       " '# MaterialName    Beta Titanium\\n',\n",
       " '# Formula    Ti\\n',\n",
       " '# Info\\n',\n",
       " '# Symmetry    43\\n',\n",
       " '# LatticeConstants    3.232 3.232 3.232 90.000 90.000 90.000\\n',\n",
       " '# NumberFamilies    0\\n',\n",
       " '# \\n',\n",
       " '# GRID: SqrGrid\\n',\n",
       " '# XSTEP: 3.000000\\n',\n",
       " '# YSTEP: 3.000000\\n',\n",
       " '# NCOLS_ODD: 191\\n',\n",
       " '# NCOLS_EVEN: 191\\n',\n",
       " '# NROWS: 100\\n',\n",
       " '# \\n',\n",
       " '# OPERATOR: orix_v0.10.2\\n',\n",
       " '# \\n',\n",
       " '# SAMPLEID:\\n',\n",
       " '# \\n',\n",
       " '# SCANID:\\n',\n",
       " '# \\n',\n",
       " '# Column names: phi1, Phi, phi2, x, y, image_quality, confidence_index, phase_id, detector_signal, pattern_fit\\n',\n",
       " '# \\n']"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Make the header\n",
    "composite_header = alpha[:alphaphaseindex] + ['# MaterialName    Alpha Titanium\\n'] + alpha[alphaphaseindex+1:alphaphaseend] + \\\n",
    "blank_line + ['# Phase 2\\n'] + ['# MaterialName    Beta Titanium\\n'] + beta[betaphaseindex+1:betaphaseend] \\\n",
    "+ blank_line + alpha[alphaphaseend:alphadataindex+2]\n",
    "composite_header"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1a8f9e2d",
   "metadata": {},
   "source": [
    "# Making the composite map"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "ed8068ff",
   "metadata": {},
   "outputs": [],
   "source": [
    "#extracting the two sets of Euler angle data\n",
    "alphadata = alpha[alphadataindex+2:]\n",
    "betadata = beta[betadataindex+2:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "fa05ea3d",
   "metadata": {},
   "outputs": [],
   "source": [
    "#alphadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "fb62085e",
   "metadata": {},
   "outputs": [],
   "source": [
    "#betadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "e750d955",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Run the comparison\n",
    "# Make a file of alpha data as the starting point\n",
    "alphabetadata=alphadata.copy()\n",
    "\n",
    "# Bias factor: If we think that the normalisation of CI is fine, leave as 1.  \n",
    "# If you feel it is too likely to identify something as beta, increase this above 1.\n",
    "# If you think it is too likely to identify something as alpha, decrease this below 1.\n",
    "BF = 1\n",
    "\n",
    "# Run line by line through alphadata\n",
    "for i in range(len(alphadata)):\n",
    "    #Extract confidence index for Alpha and Beta\n",
    "    CI_A = float(alphadata[i].split()[6])\n",
    "    CI_B = float(betadata[i].split()[6])\n",
    "    #Compare the two confidence indices\n",
    "    if CI_B > BF*CI_A:\n",
    "        # Split the beta line into strings\n",
    "        betaline = betadata[i].split()\n",
    "        # Set the phase indicator to 2\n",
    "        betaline[7] = '2'\n",
    "        # Join the line back together correctly and replace the data in that line of alphabetadata\n",
    "        alphabetadata[i] = ' '+'   '.join(betaline)+'\\n'\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "9d44f5e6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[' 1.82743   1.53570   1.59162   270.00000     0.00000   11.89182   11.89182   1   0.00000   0.00000\\n',\n",
       " ' 1.82780   1.53570   1.59162   273.00000     0.00000   11.78143   11.78143   1   0.00000   0.00000\\n',\n",
       " ' 1.82849   1.53570   1.59162   276.00000     0.00000   11.93061   11.93061   1   0.00000   0.00000\\n',\n",
       " ' 1.82940   1.53570   1.59162   279.00000     0.00000   11.86319   11.86319   1   0.00000   0.00000\\n',\n",
       " ' 1.82911   1.53570   1.59162   282.00000     0.00000   11.61911   11.61911   1   0.00000   0.00000\\n',\n",
       " ' 1.83199   1.53573   1.58865   285.00000     0.00000   11.37479   11.37479   1   0.00000   0.00000\\n',\n",
       " ' 1.83635   1.52699   1.58576   288.00000     0.00000   10.68811   10.68811   1   0.00000   0.00000\\n',\n",
       " ' 0.29381   2.20030   5.52832   291.00000   0.00000   10.64900   10.64900   2   0.00000   0.00000\\n',\n",
       " ' 1.30546   0.93854   2.39290   294.00000   0.00000   10.66416   10.66416   2   0.00000   0.00000\\n',\n",
       " ' 1.31302   0.94129   2.38672   297.00000   0.00000   10.66286   10.66286   2   0.00000   0.00000\\n',\n",
       " ' 1.31895   0.94406   2.38057   300.00000   0.00000   10.55324   10.55324   2   0.00000   0.00000\\n',\n",
       " ' 1.32514   0.93796   2.37458   303.00000   0.00000   10.44095   10.44095   2   0.00000   0.00000\\n',\n",
       " ' 2.38294   0.91704   2.36244   306.00000   0.00000   10.27592   10.27592   2   0.00000   0.00000\\n',\n",
       " ' 2.38583   0.91704   2.36244   309.00000   0.00000   10.22210   10.22210   2   0.00000   0.00000\\n',\n",
       " ' 2.38972   0.91109   2.35619   312.00000   0.00000   10.13424   10.13424   2   0.00000   0.00000\\n',\n",
       " ' 2.39012   0.91109   2.35619   315.00000   0.00000   9.93420   9.93420   2   0.00000   0.00000\\n',\n",
       " ' 2.39031   0.91109   2.35619   318.00000   0.00000   9.62532   9.62532   2   0.00000   0.00000\\n',\n",
       " ' 5.53596   2.22456   5.50403   321.00000   0.00000   9.35055   9.35055   2   0.00000   0.00000\\n',\n",
       " ' 5.53667   2.22456   5.50403   324.00000   0.00000   8.99224   8.99224   2   0.00000   0.00000\\n',\n",
       " ' 1.33957   0.90818   2.36249   327.00000   0.00000   8.32013   8.32013   2   0.00000   0.00000\\n',\n",
       " ' 1.34167   0.90818   2.36249   330.00000   0.00000   8.33235   8.33235   2   0.00000   0.00000\\n',\n",
       " ' 1.34367   0.90818   2.36249   333.00000   0.00000   8.42492   8.42492   2   0.00000   0.00000\\n',\n",
       " ' 4.49609   2.22456   5.50403   336.00000   0.00000   8.55372   8.55372   2   0.00000   0.00000\\n',\n",
       " ' 5.55074   2.22141   5.51645   339.00000   0.00000   8.89710   8.89710   2   0.00000   0.00000\\n',\n",
       " ' 5.54986   2.22141   5.51645   342.00000   0.00000   8.99535   8.99535   2   0.00000   0.00000\\n',\n",
       " ' 5.55099   2.22141   5.51645   345.00000   0.00000   9.14738   9.14738   2   0.00000   0.00000\\n',\n",
       " ' 5.54979   2.22141   5.51645   348.00000   0.00000   9.28130   9.28130   2   0.00000   0.00000\\n',\n",
       " ' 5.54526   2.22743   5.51030   351.00000   0.00000   9.38007   9.38007   2   0.00000   0.00000\\n',\n",
       " ' 5.54512   2.22743   5.51030   354.00000   0.00000   9.30817   9.30817   2   0.00000   0.00000\\n',\n",
       " ' 5.54429   2.22743   5.51030   357.00000   0.00000   9.42545   9.42545   2   0.00000   0.00000\\n',\n",
       " ' 5.54358   2.22743   5.51030   360.00000   0.00000   9.44359   9.44359   2   0.00000   0.00000\\n',\n",
       " ' 5.53856   2.22456   5.50403   363.00000   0.00000   9.55574   9.55574   2   0.00000   0.00000\\n',\n",
       " ' 5.53675   2.23342   5.50408   366.00000   0.00000   9.64593   9.64593   2   0.00000   0.00000\\n',\n",
       " ' 2.39061   0.91109   2.35619   369.00000   0.00000   9.79296   9.79296   2   0.00000   0.00000\\n',\n",
       " ' 2.38881   0.91109   2.35619   372.00000   0.00000   9.98786   9.98786   2   0.00000   0.00000\\n',\n",
       " ' 2.38289   0.91704   2.36244   375.00000   0.00000   10.06671   10.06671   2   0.00000   0.00000\\n',\n",
       " ' 1.32504   0.93796   2.37458   378.00000   0.00000   10.38160   10.38160   2   0.00000   0.00000\\n',\n",
       " ' 1.31864   0.94406   2.38057   381.00000   0.00000   10.49459   10.49459   2   0.00000   0.00000\\n',\n",
       " ' 0.27462   0.94685   2.37444   384.00000   0.00000   10.58022   10.58022   2   0.00000   0.00000\\n',\n",
       " ' 5.50192   0.94129   2.38672   387.00000   0.00000   10.61702   10.61702   2   0.00000   0.00000\\n',\n",
       " ' 1.31175   0.94129   2.38672   390.00000   0.00000   10.60729   10.60729   2   0.00000   0.00000\\n',\n",
       " ' 5.49543   0.93854   2.39290   393.00000   0.00000   10.64144   10.64144   2   0.00000   0.00000\\n',\n",
       " ' 1.30903   0.94129   2.38672   396.00000   0.00000   10.61710   10.61710   2   0.00000   0.00000\\n',\n",
       " ' 1.30889   0.94129   2.38672   399.00000   0.00000   10.62192   10.62192   2   0.00000   0.00000\\n',\n",
       " ' 0.29554   2.20030   5.52832   402.00000   0.00000   10.68720   10.68720   2   0.00000   0.00000\\n',\n",
       " ' 0.29479   2.20030   5.52832   405.00000   0.00000   10.71487   10.71487   2   0.00000   0.00000\\n',\n",
       " ' 0.29414   2.20030   5.52832   408.00000   0.00000   10.76245   10.76245   2   0.00000   0.00000\\n',\n",
       " ' 5.52034   2.19475   5.51603   411.00000   0.00000   10.68074   10.68074   2   0.00000   0.00000\\n',\n",
       " ' 0.29359   2.20030   5.52832   414.00000   0.00000   10.77877   10.77877   2   0.00000   0.00000\\n',\n",
       " ' 5.51996   2.19475   5.51603   417.00000   0.00000   10.61849   10.61849   2   0.00000   0.00000\\n',\n",
       " ' 0.29285   2.20030   5.52832   420.00000   0.00000   10.75257   10.75257   2   0.00000   0.00000\\n',\n",
       " ' 0.29699   2.20306   5.53450   423.00000   0.00000   10.69516   10.69516   2   0.00000   0.00000\\n',\n",
       " ' 0.29742   2.20306   5.53450   426.00000   0.00000   10.70029   10.70029   2   0.00000   0.00000\\n',\n",
       " ' 0.29656   2.20306   5.53450   429.00000   0.00000   10.72019   10.72019   2   0.00000   0.00000\\n',\n",
       " ' 0.29211   2.20030   5.52832   432.00000   0.00000   10.74478   10.74478   2   0.00000   0.00000\\n',\n",
       " ' 0.29586   2.20306   5.53450   435.00000   0.00000   10.76740   10.76740   2   0.00000   0.00000\\n',\n",
       " ' 5.52290   2.19753   5.52216   438.00000   0.00000   10.84468   10.84468   2   0.00000   0.00000\\n',\n",
       " ' 0.29243   2.20030   5.52832   441.00000   0.00000   10.72756   10.72756   2   0.00000   0.00000\\n',\n",
       " ' 5.52282   2.19753   5.52216   444.00000   0.00000   11.03135   11.03135   2   0.00000   0.00000\\n',\n",
       " ' 5.52353   2.19753   5.52216   447.00000   0.00000   10.66147   10.66147   2   0.00000   0.00000\\n',\n",
       " ' 0.29266   2.20030   5.52832   450.00000   0.00000   10.67681   10.67681   2   0.00000   0.00000\\n',\n",
       " ' 0.29301   2.20030   5.52832   453.00000   0.00000   10.65449   10.65449   2   0.00000   0.00000\\n',\n",
       " ' 0.29310   2.20030   5.52832   456.00000   0.00000   10.60518   10.60518   2   0.00000   0.00000\\n',\n",
       " ' 0.29816   2.20306   5.53450   459.00000   0.00000   10.59342   10.59342   2   0.00000   0.00000\\n',\n",
       " ' 0.30021   2.20306   5.53450   462.00000   0.00000   10.64521   10.64521   2   0.00000   0.00000\\n',\n",
       " ' 1.30930   0.94129   2.38672   465.00000   0.00000   10.72509   10.72509   2   0.00000   0.00000\\n',\n",
       " ' 5.49574   0.93854   2.39290   468.00000   0.00000   10.92491   10.92491   2   0.00000   0.00000\\n',\n",
       " ' 5.50046   0.94129   2.38672   471.00000   0.00000   11.03021   11.03021   2   0.00000   0.00000\\n',\n",
       " ' 5.50067   0.94129   2.38672   474.00000   0.00000   11.11326   11.11326   2   0.00000   0.00000\\n',\n",
       " ' 5.50107   0.94129   2.38672   477.00000   0.00000   11.04480   11.04480   2   0.00000   0.00000\\n',\n",
       " ' 5.50049   0.94129   2.38672   480.00000   0.00000   11.02664   11.02664   2   0.00000   0.00000\\n',\n",
       " ' 4.99384   1.58840   4.74769   483.00000     0.00000   11.60028   11.60028   1   0.00000   0.00000\\n',\n",
       " ' 4.99427   1.59721   4.74789   486.00000     0.00000   11.86731   11.86731   1   0.00000   0.00000\\n',\n",
       " ' 4.99708   1.59702   4.71831   489.00000     0.00000   12.44671   12.44671   1   0.00000   0.00000\\n',\n",
       " ' 4.99612   1.59702   4.71831   492.00000     0.00000   12.78045   12.78045   1   0.00000   0.00000\\n',\n",
       " ' 4.99639   1.59702   4.71831   495.00000     0.00000   12.77042   12.77042   1   0.00000   0.00000\\n',\n",
       " ' 4.99602   1.59702   4.71831   498.00000     0.00000   13.23601   13.23601   1   0.00000   0.00000\\n',\n",
       " ' 4.99524   1.59702   4.71831   501.00000     0.00000   13.11329   13.11329   1   0.00000   0.00000\\n',\n",
       " ' 4.99373   1.59700   4.71535   504.00000     0.00000   13.10161   13.10161   1   0.00000   0.00000\\n',\n",
       " ' 4.99279   1.59700   4.71535   507.00000     0.00000   13.02653   13.02653   1   0.00000   0.00000\\n',\n",
       " ' 4.99285   1.59700   4.71535   510.00000     0.00000   12.95266   12.95266   1   0.00000   0.00000\\n',\n",
       " ' 4.99319   1.59700   4.71535   513.00000     0.00000   12.80791   12.80791   1   0.00000   0.00000\\n',\n",
       " ' 4.99347   1.59700   4.71535   516.00000     0.00000   12.57389   12.57389   1   0.00000   0.00000\\n',\n",
       " ' 4.99366   1.59700   4.71535   519.00000     0.00000   12.41868   12.41868   1   0.00000   0.00000\\n',\n",
       " ' 4.99457   1.59702   4.71831   522.00000     0.00000   12.07283   12.07283   1   0.00000   0.00000\\n',\n",
       " ' 4.99454   1.60576   4.71834   525.00000     0.00000   11.56360   11.56360   1   0.00000   0.00000\\n',\n",
       " ' 4.99243   1.61446   4.71538   528.00000     0.00000   10.99982   10.99982   1   0.00000   0.00000\\n',\n",
       " ' 1.31159   0.93237   2.38696   531.00000   0.00000   10.29984   10.29984   2   0.00000   0.00000\\n',\n",
       " ' 1.31083   0.92346   2.38719   534.00000   0.00000   10.22130   10.22130   2   0.00000   0.00000\\n',\n",
       " ' 1.31600   0.91736   2.38113   537.00000   0.00000   10.14884   10.14884   2   0.00000   0.00000\\n',\n",
       " ' 1.31849   0.91736   2.38113   540.00000   0.00000   9.94435   9.94435   2   0.00000   0.00000\\n',\n",
       " ' 1.32374   0.91130   2.37501   543.00000   0.00000   9.71736   9.71736   2   0.00000   0.00000\\n',\n",
       " ' 1.32578   0.91130   2.37501   546.00000   0.00000   9.55610   9.55610   2   0.00000   0.00000\\n',\n",
       " ' 1.33006   0.90528   2.36881   549.00000   0.00000   9.39480   9.39480   2   0.00000   0.00000\\n',\n",
       " ' 1.33113   0.90528   2.36881   552.00000   0.00000   9.30608   9.30608   2   0.00000   0.00000\\n',\n",
       " ' 1.33240   0.90528   2.36881   555.00000   0.00000   9.09106   9.09106   2   0.00000   0.00000\\n',\n",
       " ' 1.33257   0.91416   2.36871   558.00000   0.00000   9.12064   9.12064   2   0.00000   0.00000\\n',\n",
       " ' 0.28040   0.93796   2.37458   561.00000   0.00000   9.86061   9.86061   2   0.00000   0.00000\\n',\n",
       " ' 0.27803   0.92907   2.37472   564.00000   0.00000   10.13195   10.13195   2   0.00000   0.00000\\n',\n",
       " ' 0.27631   0.92907   2.37472   567.00000   0.00000   10.40498   10.40498   2   0.00000   0.00000\\n']"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "start =90\n",
    "alphabetadata[start:start+100]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cd024b7e",
   "metadata": {},
   "source": [
    "# Construct final file and write"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "c0ffc725",
   "metadata": {},
   "outputs": [],
   "source": [
    "# concatenate the lists\n",
    "listforoutput = composite_header + alphabetadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "894cd424",
   "metadata": {},
   "outputs": [],
   "source": [
    "alphabetaFN = alphaFN.replace('_alpha.ang','_alphabeta.ang')\n",
    "output = open(filepath+alphabetaFN,\"w\")\n",
    "  \n",
    "# \\n is placed to indicate EOL (End of Line)\n",
    "output.writelines(listforoutput)\n",
    "output.close() #to change file access modes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d9976cc9",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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