Move macrocycle functions to its own directory

molSimplify/Informatics/GeoFreeRAC.ipynb → workflows/NandyJACSAu2022/GeoFreeRAC.ipynb

@@ -8,16 +8,9 @@
    "source": [
     "%matplotlib inline \n",
     "import sys\n",
-    "import os,shutil,datetime\n",
     "import numpy as np\n",
-    "import math\n",
-    "import random\n",
-    "import string\n",
-    "import subprocess\n",
-    "import pickle\n",
+    "import pandas as pd\n",
     "import matplotlib.pylab as plt\n",
-    "import scipy.sparse as sps\n",
-    "from molSimplify.Classes import globalvars\n",
     "from molSimplify.Classes.mol3D import mol3D, atom3D\n",
     "from molSimplify.Classes.ligand import ligand, ligand_breakdown, ligand_assign_consistent\n",
     "from molSimplify.Scripts.io import lig_load\n",
@@ -215,56 +208,6 @@
     "    return RAC_dict"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 19,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "['misc-dent-ax', 'misc-charge-ax', 'misc-dent-eq', 'misc-charge-eq', 'f-chi-0-all', 'f-chi-1-all', 'f-chi-2-all', 'f-chi-3-all', 'f-Z-0-all', 'f-Z-1-all', 'f-Z-2-all', 'f-Z-3-all', 'f-I-0-all', 'f-I-1-all', 'f-I-2-all', 'f-I-3-all', 'f-T-0-all', 'f-T-1-all', 'f-T-2-all', 'f-T-3-all', 'f-S-0-all', 'f-S-1-all', 'f-S-2-all', 'f-S-3-all', 'f-chi-0-ax', 'f-chi-1-ax', 'f-chi-2-ax', 'f-chi-3-ax', 'f-Z-0-ax', 'f-Z-1-ax', 'f-Z-2-ax', 'f-Z-3-ax', 'f-I-0-ax', 'f-I-1-ax', 'f-I-2-ax', 'f-I-3-ax', 'f-T-0-ax', 'f-T-1-ax', 'f-T-2-ax', 'f-T-3-ax', 'f-S-0-ax', 'f-S-1-ax', 'f-S-2-ax', 'f-S-3-ax', 'f-chi-0-eq', 'f-chi-1-eq', 'f-chi-2-eq', 'f-chi-3-eq', 'f-Z-0-eq', 'f-Z-1-eq', 'f-Z-2-eq', 'f-Z-3-eq', 'f-I-0-eq', 'f-I-1-eq', 'f-I-2-eq', 'f-I-3-eq', 'f-T-0-eq', 'f-T-1-eq', 'f-T-2-eq', 'f-T-3-eq', 'f-S-0-eq', 'f-S-1-eq', 'f-S-2-eq', 'f-S-3-eq', 'lc-chi-0-ax', 'lc-chi-1-ax', 'lc-chi-2-ax', 'lc-chi-3-ax', 'lc-Z-0-ax', 'lc-Z-1-ax', 'lc-Z-2-ax', 'lc-Z-3-ax', 'lc-I-0-ax', 'lc-I-1-ax', 'lc-I-2-ax', 'lc-I-3-ax', 'lc-T-0-ax', 'lc-T-1-ax', 'lc-T-2-ax', 'lc-T-3-ax', 'lc-S-0-ax', 'lc-S-1-ax', 'lc-S-2-ax', 'lc-S-3-ax', 'lc-chi-0-eq', 'lc-chi-1-eq', 'lc-chi-2-eq', 'lc-chi-3-eq', 'lc-Z-0-eq', 'lc-Z-1-eq', 'lc-Z-2-eq', 'lc-Z-3-eq', 'lc-I-0-eq', 'lc-I-1-eq', 'lc-I-2-eq', 'lc-I-3-eq', 'lc-T-0-eq', 'lc-T-1-eq', 'lc-T-2-eq', 'lc-T-3-eq', 'lc-S-0-eq', 'lc-S-1-eq', 'lc-S-2-eq', 'lc-S-3-eq', 'D_lc-chi-0-ax', 'D_lc-chi-1-ax', 'D_lc-chi-2-ax', 'D_lc-chi-3-ax', 'D_lc-Z-0-ax', 'D_lc-Z-1-ax', 'D_lc-Z-2-ax', 'D_lc-Z-3-ax', 'D_lc-I-0-ax', 'D_lc-I-1-ax', 'D_lc-I-2-ax', 'D_lc-I-3-ax', 'D_lc-T-0-ax', 'D_lc-T-1-ax', 'D_lc-T-2-ax', 'D_lc-T-3-ax', 'D_lc-S-0-ax', 'D_lc-S-1-ax', 'D_lc-S-2-ax', 'D_lc-S-3-ax', 'D_lc-chi-0-eq', 'D_lc-chi-1-eq', 'D_lc-chi-2-eq', 'D_lc-chi-3-eq', 'D_lc-Z-0-eq', 'D_lc-Z-1-eq', 'D_lc-Z-2-eq', 'D_lc-Z-3-eq', 'D_lc-I-0-eq', 'D_lc-I-1-eq', 'D_lc-I-2-eq', 'D_lc-I-3-eq', 'D_lc-T-0-eq', 'D_lc-T-1-eq', 'D_lc-T-2-eq', 'D_lc-T-3-eq', 'D_lc-S-0-eq', 'D_lc-S-1-eq', 'D_lc-S-2-eq', 'D_lc-S-3-eq', 'mc-chi-0-all', 'mc-chi-1-all', 'mc-chi-2-all', 'mc-chi-3-all', 'mc-Z-0-all', 'mc-Z-1-all', 'mc-Z-2-all', 'mc-Z-3-all', 'mc-I-0-all', 'mc-I-1-all', 'mc-I-2-all', 'mc-I-3-all', 'mc-T-0-all', 'mc-T-1-all', 'mc-T-2-all', 'mc-T-3-all', 'mc-S-0-all', 'mc-S-1-all', 'mc-S-2-all', 'mc-S-3-all', 'D_mc-chi-0-all', 'D_mc-chi-1-all', 'D_mc-chi-2-all', 'D_mc-chi-3-all', 'D_mc-Z-0-all', 'D_mc-Z-1-all', 'D_mc-Z-2-all', 'D_mc-Z-3-all', 'D_mc-I-0-all', 'D_mc-I-1-all', 'D_mc-I-2-all', 'D_mc-I-3-all', 'D_mc-T-0-all', 'D_mc-T-1-all', 'D_mc-T-2-all', 'D_mc-T-3-all', 'D_mc-S-0-all', 'D_mc-S-1-all', 'D_mc-S-2-all', 'D_mc-S-3-all']\n"
-     ]
-    }
-   ],
-   "source": [
-    "print(list(f1.keys()))\n",
-    "for i, row in enumerate(list(f1.keys())):\n",
-    "    if round(f1[row], 4) != round(f2[row], 4):\n",
-    "        print(row)\n",
-    "        if row == \"f-I-0-all\":\n",
-    "            print(f1[\"f-I-0-all\"], f2[\"f-I-0-all\"], temp_mol.natoms)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 20,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "{'misc-dent-ax': 3.0, 'misc-charge-ax': 0.0, 'misc-dent-eq': 5.0, 'misc-charge-eq': 0.0, 'f-chi-0-all': 390.4742999999993, 'f-chi-1-all': 919.9488000000002, 'f-chi-2-all': 1935.0001999999977, 'f-chi-3-all': 3016.9269999999988, 'f-Z-0-all': 1956.0, 'f-Z-1-all': 5172.0, 'f-Z-2-all': 10352.0, 'f-Z-3-all': 12110.0, 'f-I-0-all': 67.0, 'f-I-1-all': 146.0, 'f-I-2-all': 304.0, 'f-I-3-all': 484.0, 'f-T-0-all': 450.0, 'f-T-1-all': 1304.0, 'f-T-2-all': 2528.0, 'f-T-3-all': 3728.0, 'f-S-0-all': 23.51070000000003, 'f-S-1-all': 66.99219999999997, 'f-S-2-all': 130.26399999999984, 'f-S-3-all': 204.5820000000002, 'f-chi-0-ax': 193.41309999999976, 'f-chi-1-ax': 425.13600000000014, 'f-chi-2-ax': 755.8185999999994, 'f-chi-3-ax': 916.9196, 'f-Z-0-ax': 586.0, 'f-Z-1-ax': 1410.0, 'f-Z-2-ax': 1921.0, 'f-Z-3-ax': 2114.0, 'f-I-0-ax': 33.0, 'f-I-1-ax': 67.0, 'f-I-2-ax': 122.0, 'f-I-3-ax': 151.0, 'f-T-0-ax': 189.0, 'f-T-1-ax': 470.0, 'f-T-2-ax': 667.0, 'f-T-3-ax': 821.0, 'f-S-0-ax': 11.023300000000013, 'f-S-1-ax': 28.051100000000012, 'f-S-2-ax': 42.718999999999966, 'f-S-3-ax': 51.775499999999994, 'f-chi-0-eq': 350.05959999999953, 'f-chi-1-eq': 788.1030000000003, 'f-chi-2-eq': 1433.4331999999988, 'f-chi-3-eq': 1793.7112, 'f-Z-0-eq': 1048.0, 'f-Z-1-eq': 2628.0, 'f-Z-2-eq': 3716.0, 'f-Z-3-eq': 4186.0, 'f-I-0-eq': 60.0, 'f-I-1-eq': 124.0, 'f-I-2-eq': 230.0, 'f-I-3-eq': 296.0, 'f-T-0-eq': 354.0, 'f-T-1-eq': 896.0, 'f-T-2-eq': 1308.0, 'f-T-3-eq': 1636.0, 'f-S-0-eq': 19.887600000000027, 'f-S-1-eq': 52.05200000000003, 'f-S-2-eq': 81.75219999999993, 'f-S-3-eq': 101.88599999999998, 'lc-chi-0-ax': 9.2416, 'lc-chi-1-ax': 15.504, 'lc-chi-2-ax': 35.568000000000005, 'lc-chi-3-ax': 43.9584, 'lc-Z-0-ax': 49.0, 'lc-Z-1-ax': 84.0, 'lc-Z-2-ax': 105.0, 'lc-Z-3-ax': 105.0, 'lc-I-0-ax': 1.0, 'lc-I-1-ax': 2.0, 'lc-I-2-ax': 5.0, 'lc-I-3-ax': 6.0, 'lc-T-0-ax': 5.0, 'lc-T-1-ax': 19.0, 'lc-T-2-ax': 29.0, 'lc-T-3-ax': 24.0, 'lc-S-0-ax': 0.5625, 'lc-S-1-ax': 1.155, 'lc-S-2-ax': 1.9875, 'lc-S-3-ax': 2.0924999999999994, 'lc-chi-0-eq': 9.2416, 'lc-chi-1-eq': 21.318, 'lc-chi-2-eq': 54.86440000000001, 'lc-chi-3-eq': 46.03320000000001, 'lc-Z-0-eq': 49.0, 'lc-Z-1-eq': 115.5, 'lc-Z-2-eq': 143.5, 'lc-Z-3-eq': 152.25, 'lc-I-0-eq': 1.0, 'lc-I-1-eq': 2.75, 'lc-I-2-eq': 7.75, 'lc-I-3-eq': 6.0, 'lc-T-0-eq': 7.75, 'lc-T-1-eq': 30.0, 'lc-T-2-eq': 39.5, 'lc-T-3-eq': 30.5, 'lc-S-0-eq': 0.5625, 'lc-S-1-eq': 1.588125, 'lc-S-2-eq': 2.8968749999999996, 'lc-S-3-eq': 2.46, 'D_lc-chi-0-ax': 0.0, 'D_lc-chi-1-ax': 0.9800000000000004, 'D_lc-chi-2-ax': 3.5, 'D_lc-chi-3-ax': 3.7799999999999994, 'D_lc-Z-0-ax': 0.0, 'D_lc-Z-1-ax': 2.0, 'D_lc-Z-2-ax': 20.0, 'D_lc-Z-3-ax': 27.0, 'D_lc-I-0-ax': 0.0, 'D_lc-I-1-ax': 0.0, 'D_lc-I-2-ax': 0.0, 'D_lc-I-3-ax': 0.0, 'D_lc-T-0-ax': 0.0, 'D_lc-T-1-ax': -2.0, 'D_lc-T-2-ax': 3.0, 'D_lc-T-3-ax': 6.0, 'D_lc-S-0-ax': 0.0, 'D_lc-S-1-ax': -0.040000000000000036, 'D_lc-S-2-ax': 1.0999999999999999, 'D_lc-S-3-ax': 1.71, 'D_lc-chi-0-eq': 0.0, 'D_lc-chi-1-eq': 1.3475000000000006, 'D_lc-chi-2-eq': 5.512499999999999, 'D_lc-chi-3-eq': 3.0974999999999997, 'D_lc-Z-0-eq': 0.0, 'D_lc-Z-1-eq': 2.75, 'D_lc-Z-2-eq': 33.75, 'D_lc-Z-3-eq': 20.25, 'D_lc-I-0-eq': 0.0, 'D_lc-I-1-eq': 0.0, 'D_lc-I-2-eq': 0.0, 'D_lc-I-3-eq': 0.0, 'D_lc-T-0-eq': 0.0, 'D_lc-T-1-eq': -2.75, 'D_lc-T-2-eq': 8.0, 'D_lc-T-3-eq': 4.75, 'D_lc-S-0-eq': 0.0, 'D_lc-S-1-eq': -0.05500000000000005, 'D_lc-S-2-eq': 1.9499999999999997, 'D_lc-S-3-eq': 1.22, 'mc-chi-0-all': 3.6481, 'mc-chi-1-all': 34.8384, 'mc-chi-2-all': 73.0575, 'mc-chi-3-all': 133.87189999999995, 'mc-Z-0-all': 784.0, 'mc-Z-1-all': 1176.0, 'mc-Z-2-all': 2520.0, 'mc-Z-3-all': 1456.0, 'mc-I-0-all': 1.0, 'mc-I-1-all': 6.0, 'mc-I-2-all': 15.0, 'mc-I-3-all': 31.0, 'mc-T-0-all': 36.0, 'mc-T-1-all': 126.0, 'mc-T-2-all': 336.0, 'mc-T-3-all': 240.0, 'mc-S-0-all': 1.4641, 'mc-S-1-all': 5.444999999999999, 'mc-S-2-all': 13.975499999999997, 'mc-S-3-all': 15.79049999999999, 'D_mc-chi-0-all': 0.0, 'D_mc-chi-1-all': -6.78, 'D_mc-chi-2-all': -9.599999999999998, 'D_mc-chi-3-all': -10.88000000000001, 'D_mc-Z-0-all': 0.0, 'D_mc-Z-1-all': 126.0, 'D_mc-Z-2-all': 330.0, 'D_mc-Z-3-all': 816.0, 'D_mc-I-0-all': 0.0, 'D_mc-I-1-all': 0.0, 'D_mc-I-2-all': 0.0, 'D_mc-I-3-all': 0.0, 'D_mc-T-0-all': 0.0, 'D_mc-T-1-all': 15.0, 'D_mc-T-2-all': 34.0, 'D_mc-T-3-all': 146.0, 'D_mc-S-0-all': 0.0, 'D_mc-S-1-all': 2.76, 'D_mc-S-2-all': 6.599999999999998, 'D_mc-S-3-all': 24.459999999999997}\n"
-     ]
-    }
-   ],
-   "source": [
-    "from molSimplify.Informatics.lacRACAssemble import get_descriptor_vector\n",
-    "\n",
-    "features, values = get_descriptor_vector(temp_mol)\n",
-    "feat_dict = dict(zip(features, values))\n",
-    "print(feat_dict)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 21,
@@ -7691,7 +7634,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.8.13"
   }
  },
  "nbformat": 4,