Kinase similarity demo mode

.github/workflows/ci.yml

@@ -5,10 +5,12 @@ on:
     branches:
       - "master"
       - "maintenance/.+"
+      - "livecoms-review"
   pull_request:
     branches:
       - "master"
       - "maintenance/.+"
+      - "livecoms-review"
   schedule:
     # Run a cron job once weekly on Monday
     - cron: "0 3 * * 1"

.github/workflows/docs.yml

@@ -5,10 +5,12 @@ on:
     branches:
       - "master"
       - "maintenance/.+"
+      - "livecoms-review"
   pull_request:
     branches:
       - "master"
       - "maintenance/.+"
+      - "livecoms-review"
   schedule:
     # Run a cron job once weekly on Monday
     - cron: "0 3 * * 1"

README.md

@@ -192,7 +192,7 @@ It will help measure the impact of the TeachOpenCADD platform and future funding
 - Web services clients:
   [`pypdb`](https://github.com/williamgilpin/pypdb),
   [`chembl_webresource_client`](https://github.com/chembl/chembl_webresource_client),
-  [`requests`](https://docs.python-requests.org/en/master/),
+  [`requests`](https://requests.readthedocs.io/en/latest/),
   [`bravado`](https://bravado.readthedocs.io/en/stable/),
   [`beautifulsoup4`](https://www.crummy.com/software/BeautifulSoup/bs4/doc/)
 - Utilities:

devtools/test_env.yml

@@ -42,6 +42,7 @@ dependencies:
   - pdbfixer
   - tqdm
   - lxml
+  - kissim
   ## CI tests
   # Workaround for https://github.com/computationalmodelling/nbval/issues/153
   - pytest 5.*

teachopencadd/talktorials/T023_what_is_a_kinase/data/kinase_selection_xiong.csv

@@ -0,0 +1,9 @@
+kinase,kinase_klifs,uniprot_id,group
+RET,RET,P07949,TK
+BRAF,BRAF,P15056,TKL
+SRC,SRC,P12931,TK
+S6K,p70S6K,P23443,AGC
+MKNK1,MNK1,Q9BUB5,CAMK
+TTK,TTK,P33981,Other
+PDK,PDK1,O15530,AGC
+PAK3,PAK3,O75914,STE

teachopencadd/talktorials/T023_what_is_a_kinase/data/pipeline_configs.csv

@@ -0,0 +1,4 @@
+variable,default_value,description
+DEMO,1,"Run the notebooks exactly as displayed online (default: 1) or set to 0 and run your own kinase set (as defined in `kinase_selection.csv`)"
+N_STRUCTURES_PER_KINASE,-1,"Run structure-based notebooks on all structures per kinase (default: -1) or a subset of structures (replace -1 with e.g. 3)"
+N_CORES,1,"Run T025 on one (default: 1) or more cores"

teachopencadd/talktorials/T023_what_is_a_kinase/talktorial.ipynb

@@ -326,7 +326,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We have collected information about these nine kinases in the CSV file `kinase_selection.csv`:\n",
+    "We have collected information about these nine kinases in the CSV file `T023_what_is_a_kinase/data/kinase_selection.csv`:\n",
     "\n",
     "- `kinase`: Kinase name as used in [<i>Molecules</i> (2021), <b>26(3)</b>, 629](https://www.mdpi.com/1420-3049/26/3/629)\n",
     "- `kinase_klifs`: Kinase name as used in the KLIFS database\n",
@@ -335,13 +335,6 @@
     "- `full_kinase_name`: Full kinase name as used in [<i>Molecules</i> (2021), <b>26(3)</b>, 629](https://www.mdpi.com/1420-3049/26/3/629)"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "_Note_: You can run the kinase similarity __Talktorials T024-T028__ with your own set of kinases. To do so, please update the CSV file with your kinases; the only mandatory columns are `kinase_klifs` and `uniprot_id`."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 3,
@@ -494,6 +487,98 @@
     "We will load this dataset in all downstream talktorials to assess kinase similarity from different perspectives."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "_Note_: You can run the kinase similarity __Talktorials T024-T028__ with your own set of kinases. To do so, please update the following files:\n",
+    "\n",
+    "- Update the `T023_what_is_a_kinase/data/kinase_selection.csv` file with your kinases; the only mandatory columns are `kinase_klifs` and `uniprot_id`.\n",
+    "- Update the `T023_what_is_a_kinase/data/pipeline_configs.csv` file with your configurations:\n",
+    "  - Set \"DEMO\" to 0.\n",
+    "  - Choose the number of structures per kinases to be used in T025 (KiSSim) and T026 (IFP). If \"N_STRUCTURES_PER_KINASE\" is set to -1, all structures are used; if set to a number (X), the best X structures are being used for the encoding and comparison (w.r.t. resolution and KLIFS quality score). The latter makes sense for a test run of your data (running the T025 on all structures is time-consuming).\n",
+    "  - If you run the notebooks on all structures (see \"N_STRUCTURES_PER_KINASE\"), we recommend to increase the number of cores to be used in T025 (KiSSim) by redefining \"N_CORES\".\n",
+    "  \n",
+    "Let's take a look at the currently set configurations:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>variable</th>\n",
+       "      <th>default_value</th>\n",
+       "      <th>description</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>DEMO</td>\n",
+       "      <td>1</td>\n",
+       "      <td>Run the notebooks exactly as displayed online (default: 1) or set to 0 and run your own kinase set (as defined in `kinase_selection.csv`)</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>N_STRUCTURES_PER_KINASE</td>\n",
+       "      <td>-1</td>\n",
+       "      <td>Run structure-based notebooks on all structures per kinase (default: -1) or a subset of structures (replace -1 with e.g. 3)</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>N_CORES</td>\n",
+       "      <td>1</td>\n",
+       "      <td>Run T025 on one (default: 1) or more cores</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                  variable  default_value  \\\n",
+       "0                     DEMO              1   \n",
+       "1  N_STRUCTURES_PER_KINASE             -1   \n",
+       "2                  N_CORES              1   \n",
+       "\n",
+       "                                                                                                                                 description  \n",
+       "0  Run the notebooks exactly as displayed online (default: 1) or set to 0 and run your own kinase set (as defined in `kinase_selection.csv`)  \n",
+       "1                Run structure-based notebooks on all structures per kinase (default: -1) or a subset of structures (replace -1 with e.g. 3)  \n",
+       "2                                                                                                 Run T025 on one (default: 1) or more cores  "
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pd.options.display.max_colwidth = None\n",
+    "configs = pd.read_csv(DATA / \"pipeline_configs.csv\")\n",
+    "configs"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -519,7 +604,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -565,7 +650,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -600,7 +685,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -609,7 +694,7 @@
        "('CDK2', 426)"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -638,7 +723,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -700,15 +785,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {
     "tags": []
    },
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "8951db9308d84e54adceabdb750d2439",
+       "model_id": "27a4173bf7504c9a9f529823f56ec466",
        "version_major": 2,
        "version_minor": 0
       },
@@ -747,7 +832,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -756,7 +841,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {
     "tags": [
      "nbsphinx-thumbnail"
@@ -770,7 +855,7 @@
        "<IPython.core.display.Image object>"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 11,
      "metadata": {},
      "output_type": "execute_result"
     }