Merge pull request #23 from ccdc-opensource/csd544_updates

Csd544 updates

Author: jasonccole

notebooks/Discovery/01_CSD_Search/01_Substructure_searching_the_CSD.ipynb

@@ -1,6 +1,7 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -17,6 +18,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -33,14 +35,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
     "import logging\n",
     "from pathlib import Path\n",
-    "from platform import platform\n",
     "import sys\n",
+    "\n",
     "import os\n",
     "from time import time\n",
     "\n",
@@ -49,7 +51,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -60,7 +62,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -72,7 +74,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -83,12 +85,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "sys.path.append('../..')\n",
+    "from ccdc_notebook_utilities import run_hermes, create_logger"
+   ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -97,48 +103,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
-    "logger = logging.getLogger(__name__)\n",
-    "\n",
-    "if not logger.hasHandlers():\n",
-    "    handler = logging.StreamHandler()\n",
-    "    handler.setFormatter(logging.Formatter('[%(asctime)s %(levelname)-7s] %(message)s', datefmt='%y-%m-%d %H:%M:%S'))\n",
-    "    logger.addHandler(handler)\n",
-    "    logger.setLevel(logging.INFO)"
+    "logger = create_logger()"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "logger.info(f\"\"\"\n",
-    "Platform:                     {platform()}\n",
-    "\n",
-    "Python exe:                   {sys.executable}\n",
-    "Python version:               {'.'.join(str(x) for x in sys.version_info[:3])}\n",
-    "\n",
-    "CSD version:                  {ccdc.io.csd_version()}\n",
-    "CSD directory:                {ccdc.io.csd_directory()}\n",
-    "API version:                  {ccdc.__version__}\n",
-    "\n",
-    "CSDHOME:                      {os.environ.get('CSDHOME', 'Not set')}\n",
-    "CCDC_LICENSING_CONFIGURATION: {os.environ.get('CCDC_LICENSING_CONFIGURATION', 'Not set')}\n",
-    "\"\"\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -149,7 +122,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -159,6 +132,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -167,7 +141,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -184,6 +158,7 @@
    "source": []
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -209,6 +184,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -230,6 +206,7 @@
    "source": []
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -238,7 +215,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -253,6 +230,7 @@
    "source": []
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -272,7 +250,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -284,6 +262,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -292,14 +271,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
     "guanidino = query.add_substructure(guanidino_ss)"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -310,14 +290,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
     "query.add_centroid('CENT1', (guanidino, 3), (guanidino, 4))"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -326,7 +307,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -341,6 +322,7 @@
    "source": []
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -349,7 +331,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -362,7 +344,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -371,7 +353,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -388,6 +370,7 @@
    "source": []
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -398,7 +381,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -415,6 +398,7 @@
    "source": []
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -452,6 +436,7 @@
    "source": []
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -482,6 +467,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -496,6 +482,7 @@
    "source": []
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -519,6 +506,7 @@
    "source": []
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -547,6 +535,7 @@
    "source": []
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -585,6 +574,7 @@
    "source": []
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -610,15 +600,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.7 (XPython)",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "xpython"
+   "name": "python3"
   },
   "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
-   "version": "3.7.12"
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.16"
   }
  },
  "nbformat": 4,