diff --git a/docs/other/20201013_opencadd_new_features_slides.ipynb b/docs/other/20201013_opencadd_new_features_slides.ipynb
index db431a83..70598822 100644
--- a/docs/other/20201013_opencadd_new_features_slides.ipynb
+++ b/docs/other/20201013_opencadd_new_features_slides.ipynb
@@ -108,13 +108,17 @@
"Some of the class method options:\n",
"\n",
"| | kinases | ligands | structures | bioactivities | interactions | pockets |\n",
- "|:--------------------------| - | - | - | - | - | - |\n",
- "| __by_kinase_klifs_id__ | x | x | x | x | x | | \n",
- "| __by_kinase_name__ | x | x | x | | | |\n",
- "| __by_ligand_klifs_id__ | | x | x | x | x | |\n",
- "| __by_ligand_expo_id__ | | x | x | | | |\n",
- "| __by_structure_klifs_id__ | | | x | | x | x |\n",
- "| __by_structure_pdb_id__ | | | x | | | |"
+ "|:--------------------------| - | - | - | - | - | - |\n",
+ "| __by_kinase_klifs_id__ | x* | x* | x* | | x | | \n",
+ "| __by_kinase_name__ | x* | x | x | | | |\n",
+ "| __by_ligand_klifs_id__ | | x* | x | x\\* \\** | x | |\n",
+ "| __by_ligand_expo_id__ | | x | x | x\\* \\** | | |\n",
+ "| __by_structure_klifs_id__ | | | x* | | x* | x* |\n",
+ "| __by_structure_pdb_id__ | | | x* | | | |\n",
+ "\n",
+ " \\* Direct use of KLIFS Swagger API.\n",
+ " \n",
+ " \\** KLIFS Swagger API allows only ONE input value.\n"
]
},
{
diff --git a/docs/other/klifs_kinase_names.ipynb b/docs/other/klifs_kinase_names.ipynb
deleted file mode 100644
index 594994db..00000000
--- a/docs/other/klifs_kinase_names.ipynb
+++ /dev/null
@@ -1,2036 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# KLIFS kinase names\n",
- "\n",
- "Explore different kinase name columns."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 1,
- "metadata": {},
- "outputs": [],
- "source": [
- "%load_ext autoreload\n",
- "%autoreload 2"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 2,
- "metadata": {},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "INFO:opencadd.databases.klifs.api:If you want to see an non-truncated version of the DataFrames in this module, use `pd.set_option('display.max_columns', 50)` in your notebook.\n"
- ]
- }
- ],
- "source": [
- "import pandas as pd\n",
- "\n",
- "from opencadd.databases.klifs import setup_remote, setup_local"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 3,
- "metadata": {},
- "outputs": [],
- "source": [
- "pd.set_option('display.max_columns', 50)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 4,
- "metadata": {},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "INFO:opencadd.databases.klifs.api:Set up remote session...\n",
- "INFO:opencadd.databases.klifs.api:Remote session is ready!\n"
- ]
- }
- ],
- "source": [
- "remote = setup_remote()"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Kinase details 1 (short version)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 5,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "
\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.id | \n",
- " kinase.hgnc_name | \n",
- " kinase.full_name | \n",
- " species.klifs | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " 0 | \n",
- " 1 | \n",
- " AKT1 | \n",
- " None | \n",
- " Human | \n",
- "
\n",
- " \n",
- " 1 | \n",
- " 2 | \n",
- " AKT2 | \n",
- " None | \n",
- " Human | \n",
- "
\n",
- " \n",
- " 2 | \n",
- " 3 | \n",
- " AKT3 | \n",
- " None | \n",
- " Human | \n",
- "
\n",
- " \n",
- " 3 | \n",
- " 4 | \n",
- " CIT | \n",
- " None | \n",
- " Human | \n",
- "
\n",
- " \n",
- " 4 | \n",
- " 5 | \n",
- " DMPK | \n",
- " None | \n",
- " Human | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " kinase.id kinase.hgnc_name kinase.full_name species.klifs\n",
- "0 1 AKT1 None Human\n",
- "1 2 AKT2 None Human\n",
- "2 3 AKT3 None Human\n",
- "3 4 CIT None Human\n",
- "4 5 DMPK None Human"
- ]
- },
- "execution_count": 5,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "kinases1 = remote.kinases.all_kinases()\n",
- "kinases1.sort_values(\"kinase.id\", inplace=True)\n",
- "kinases1.reset_index(drop=True, inplace=True)\n",
- "kinases1.head()"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Kinase details 2 (long details)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Number of IDs: 1127\n"
- ]
- }
- ],
- "source": [
- "kinase_ids = kinases1[\"kinase.id\"].to_list()\n",
- "print(f\"Number of IDs: {len(kinase_ids)}\")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 7,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Number of kinases: 1127\n"
- ]
- },
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.id | \n",
- " kinase.klifs_name | \n",
- " kinase.hgnc_name | \n",
- " kinase.family | \n",
- " kinase.group | \n",
- " kinase.class | \n",
- " species.klifs | \n",
- " kinase.full_name | \n",
- " kinase.uniprot | \n",
- " kinase.iuphar | \n",
- " kinase.pocket | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " 0 | \n",
- " 1 | \n",
- " AKT1 | \n",
- " AKT1 | \n",
- " Akt | \n",
- " AGC | \n",
- " | \n",
- " Human | \n",
- " None | \n",
- " P31749 | \n",
- " 1479 | \n",
- " KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... | \n",
- "
\n",
- " \n",
- " 1 | \n",
- " 2 | \n",
- " AKT2 | \n",
- " AKT2 | \n",
- " Akt | \n",
- " AGC | \n",
- " | \n",
- " Human | \n",
- " None | \n",
- " P31751 | \n",
- " 1480 | \n",
- " KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVME... | \n",
- "
\n",
- " \n",
- " 2 | \n",
- " 3 | \n",
- " AKT3 | \n",
- " AKT3 | \n",
- " Akt | \n",
- " AGC | \n",
- " | \n",
- " Human | \n",
- " None | \n",
- " Q9Y243 | \n",
- " 2286 | \n",
- " KLLGKGTFGKVILYAMKILHTLTESRVLKNTRPFLTSLKYSCFVME... | \n",
- "
\n",
- " \n",
- " 3 | \n",
- " 4 | \n",
- " CRIK | \n",
- " CIT | \n",
- " DMPK | \n",
- " AGC | \n",
- " CRIK | \n",
- " Human | \n",
- " None | \n",
- " O14578 | \n",
- " 1509 | \n",
- " SLVGCGHFAEVQVYAMKVMFFEEERNILSRSTPWIPQLQYAYLVME... | \n",
- "
\n",
- " \n",
- " 4 | \n",
- " 5 | \n",
- " DMPK1 | \n",
- " DMPK | \n",
- " DMPK | \n",
- " AGC | \n",
- " GEK | \n",
- " Human | \n",
- " None | \n",
- " Q09013 | \n",
- " 1505 | \n",
- " KVIGRGAFSEVAVYAMKIMCFREERDVLVNGDRWITQLHFAYLVME... | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " kinase.id kinase.klifs_name kinase.hgnc_name kinase.family kinase.group \\\n",
- "0 1 AKT1 AKT1 Akt AGC \n",
- "1 2 AKT2 AKT2 Akt AGC \n",
- "2 3 AKT3 AKT3 Akt AGC \n",
- "3 4 CRIK CIT DMPK AGC \n",
- "4 5 DMPK1 DMPK DMPK AGC \n",
- "\n",
- " kinase.class species.klifs kinase.full_name kinase.uniprot kinase.iuphar \\\n",
- "0 Human None P31749 1479 \n",
- "1 Human None P31751 1480 \n",
- "2 Human None Q9Y243 2286 \n",
- "3 CRIK Human None O14578 1509 \n",
- "4 GEK Human None Q09013 1505 \n",
- "\n",
- " kinase.pocket \n",
- "0 KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... \n",
- "1 KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVME... \n",
- "2 KLLGKGTFGKVILYAMKILHTLTESRVLKNTRPFLTSLKYSCFVME... \n",
- "3 SLVGCGHFAEVQVYAMKVMFFEEERNILSRSTPWIPQLQYAYLVME... \n",
- "4 KVIGRGAFSEVAVYAMKIMCFREERDVLVNGDRWITQLHFAYLVME... "
- ]
- },
- "execution_count": 7,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "kinases2 = remote.kinases.by_kinase_ids(kinase_ids)\n",
- "print(f\"Number of kinases: {kinases2.shape[0]}\")\n",
- "kinases2.sort_values(\"kinase.id\", inplace=True)\n",
- "kinases2.reset_index(drop=True, inplace=True)\n",
- "kinases2.head()"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### How many kinases have unambiguous name?"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 9,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "(817, 11)"
- ]
- },
- "execution_count": 9,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "kinases2[kinases2.apply(lambda x: x[\"kinase.klifs_name\"] != x[\"kinase.hgnc_name\"], axis=1)].shape"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### Which columns are matched for kinase name?"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 10,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "application/vnd.jupyter.widget-view+json": {
- "model_id": "fc50536f196b44d9a34b40c5eda54d51",
- "version_major": 2,
- "version_minor": 0
- },
- "text/plain": [
- "HBox(children=(HTML(value='Processing...'), FloatProgress(value=0.0, max=1.0), HTML(value='')))"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "\n"
- ]
- },
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.id | \n",
- " kinase.klifs_name | \n",
- " kinase.hgnc_name | \n",
- " kinase.family | \n",
- " kinase.group | \n",
- " kinase.class | \n",
- " species.klifs | \n",
- " kinase.full_name | \n",
- " kinase.uniprot | \n",
- " kinase.iuphar | \n",
- " kinase.pocket | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " 0 | \n",
- " 4 | \n",
- " CRIK | \n",
- " CIT | \n",
- " DMPK | \n",
- " AGC | \n",
- " CRIK | \n",
- " Human | \n",
- " None | \n",
- " O14578 | \n",
- " 1509 | \n",
- " SLVGCGHFAEVQVYAMKVMFFEEERNILSRSTPWIPQLQYAYLVME... | \n",
- "
\n",
- " \n",
- " 1 | \n",
- " 637 | \n",
- " CRIK | \n",
- " Cit | \n",
- " DMPK | \n",
- " AGC | \n",
- " | \n",
- " Mouse | \n",
- " None | \n",
- " P49025 | \n",
- " 0 | \n",
- " SLVGCGHFAEVQVYAMKIMFFEEERNILSRSTPWIPQLQYAYLVME... | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " kinase.id kinase.klifs_name kinase.hgnc_name kinase.family kinase.group \\\n",
- "0 4 CRIK CIT DMPK AGC \n",
- "1 637 CRIK Cit DMPK AGC \n",
- "\n",
- " kinase.class species.klifs kinase.full_name kinase.uniprot kinase.iuphar \\\n",
- "0 CRIK Human None O14578 1509 \n",
- "1 Mouse None P49025 0 \n",
- "\n",
- " kinase.pocket \n",
- "0 SLVGCGHFAEVQVYAMKVMFFEEERNILSRSTPWIPQLQYAYLVME... \n",
- "1 SLVGCGHFAEVQVYAMKIMFFEEERNILSRSTPWIPQLQYAYLVME... "
- ]
- },
- "execution_count": 10,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "remote.kinases.by_kinase_names(kinase_names='CRIK')"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 11,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "application/vnd.jupyter.widget-view+json": {
- "model_id": "0c212fdd7ad9455293e7bfee644d5c0e",
- "version_major": 2,
- "version_minor": 0
- },
- "text/plain": [
- "HBox(children=(HTML(value='Processing...'), FloatProgress(value=0.0, max=1.0), HTML(value='')))"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "\n"
- ]
- },
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.id | \n",
- " kinase.klifs_name | \n",
- " kinase.hgnc_name | \n",
- " kinase.family | \n",
- " kinase.group | \n",
- " kinase.class | \n",
- " species.klifs | \n",
- " kinase.full_name | \n",
- " kinase.uniprot | \n",
- " kinase.iuphar | \n",
- " kinase.pocket | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " 0 | \n",
- " 4 | \n",
- " CRIK | \n",
- " CIT | \n",
- " DMPK | \n",
- " AGC | \n",
- " CRIK | \n",
- " Human | \n",
- " None | \n",
- " O14578 | \n",
- " 1509 | \n",
- " SLVGCGHFAEVQVYAMKVMFFEEERNILSRSTPWIPQLQYAYLVME... | \n",
- "
\n",
- " \n",
- " 1 | \n",
- " 637 | \n",
- " CRIK | \n",
- " Cit | \n",
- " DMPK | \n",
- " AGC | \n",
- " | \n",
- " Mouse | \n",
- " None | \n",
- " P49025 | \n",
- " 0 | \n",
- " SLVGCGHFAEVQVYAMKIMFFEEERNILSRSTPWIPQLQYAYLVME... | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " kinase.id kinase.klifs_name kinase.hgnc_name kinase.family kinase.group \\\n",
- "0 4 CRIK CIT DMPK AGC \n",
- "1 637 CRIK Cit DMPK AGC \n",
- "\n",
- " kinase.class species.klifs kinase.full_name kinase.uniprot kinase.iuphar \\\n",
- "0 CRIK Human None O14578 1509 \n",
- "1 Mouse None P49025 0 \n",
- "\n",
- " kinase.pocket \n",
- "0 SLVGCGHFAEVQVYAMKVMFFEEERNILSRSTPWIPQLQYAYLVME... \n",
- "1 SLVGCGHFAEVQVYAMKIMFFEEERNILSRSTPWIPQLQYAYLVME... "
- ]
- },
- "execution_count": 11,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "remote.kinases.by_kinase_names(kinase_names='CIT')"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "__Note__: Apparently, the kinase name is matched for `kinase.name` and `kinase.hgnc`."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### Differing `kinases.name` and `kinases.hgnc`?"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 14,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Number of differing names/HGNC: 817\n"
- ]
- },
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.klifs_name | \n",
- " kinase.hgnc_name | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " 3 | \n",
- " CRIK | \n",
- " CIT | \n",
- "
\n",
- " \n",
- " 4 | \n",
- " DMPK1 | \n",
- " DMPK | \n",
- "
\n",
- " \n",
- " 5 | \n",
- " MRCKa | \n",
- " CDC42BPA | \n",
- "
\n",
- " \n",
- " 6 | \n",
- " MRCKb | \n",
- " CDC42BPB | \n",
- "
\n",
- " \n",
- " 7 | \n",
- " DMPK2 | \n",
- " CDC42BPG | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " kinase.klifs_name kinase.hgnc_name\n",
- "3 CRIK CIT\n",
- "4 DMPK1 DMPK\n",
- "5 MRCKa CDC42BPA\n",
- "6 MRCKb CDC42BPB\n",
- "7 DMPK2 CDC42BPG"
- ]
- },
- "execution_count": 14,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "diff2 = kinases2[kinases2.apply(lambda x: x[\"kinase.klifs_name\"] != x[\"kinase.hgnc_name\"], axis=1)]\n",
- "print(f\"Number of differing names/HGNC: {diff2.shape[0]}\")\n",
- "diff2[[\"kinase.klifs_name\", \"kinase.hgnc_name\"]].head()"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Merge details for kinases 1 and 2"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 16,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.id | \n",
- " kinase.hgnc_name_x | \n",
- " kinase.full_name_x | \n",
- " kinase.klifs_name | \n",
- " kinase.hgnc_name_y | \n",
- " kinase.full_name_y | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " 0 | \n",
- " 1 | \n",
- " AKT1 | \n",
- " None | \n",
- " AKT1 | \n",
- " AKT1 | \n",
- " None | \n",
- "
\n",
- " \n",
- " 1 | \n",
- " 2 | \n",
- " AKT2 | \n",
- " None | \n",
- " AKT2 | \n",
- " AKT2 | \n",
- " None | \n",
- "
\n",
- " \n",
- " 2 | \n",
- " 3 | \n",
- " AKT3 | \n",
- " None | \n",
- " AKT3 | \n",
- " AKT3 | \n",
- " None | \n",
- "
\n",
- " \n",
- " 3 | \n",
- " 4 | \n",
- " CIT | \n",
- " None | \n",
- " CRIK | \n",
- " CIT | \n",
- " None | \n",
- "
\n",
- " \n",
- " 4 | \n",
- " 5 | \n",
- " DMPK | \n",
- " None | \n",
- " DMPK1 | \n",
- " DMPK | \n",
- " None | \n",
- "
\n",
- " \n",
- " ... | \n",
- " ... | \n",
- " ... | \n",
- " ... | \n",
- " ... | \n",
- " ... | \n",
- " ... | \n",
- "
\n",
- " \n",
- " 1122 | \n",
- " 1123 | \n",
- " Pip5k1a | \n",
- " None | \n",
- " Pip5k1a | \n",
- " Pip5k1a | \n",
- " None | \n",
- "
\n",
- " \n",
- " 1123 | \n",
- " 1124 | \n",
- " Map4k2 | \n",
- " None | \n",
- " Map4k2 | \n",
- " Map4k2 | \n",
- " None | \n",
- "
\n",
- " \n",
- " 1124 | \n",
- " 1125 | \n",
- " Pan3 | \n",
- " None | \n",
- " Pan3 | \n",
- " Pan3 | \n",
- " None | \n",
- "
\n",
- " \n",
- " 1125 | \n",
- " 1126 | \n",
- " Plk5 | \n",
- " None | \n",
- " Plk5 | \n",
- " Plk5 | \n",
- " None | \n",
- "
\n",
- " \n",
- " 1126 | \n",
- " 1127 | \n",
- " Efna2 | \n",
- " None | \n",
- " Efna2 | \n",
- " Efna2 | \n",
- " None | \n",
- "
\n",
- " \n",
- "
\n",
- "
1127 rows × 6 columns
\n",
- "
"
- ],
- "text/plain": [
- " kinase.id kinase.hgnc_name_x kinase.full_name_x kinase.klifs_name \\\n",
- "0 1 AKT1 None AKT1 \n",
- "1 2 AKT2 None AKT2 \n",
- "2 3 AKT3 None AKT3 \n",
- "3 4 CIT None CRIK \n",
- "4 5 DMPK None DMPK1 \n",
- "... ... ... ... ... \n",
- "1122 1123 Pip5k1a None Pip5k1a \n",
- "1123 1124 Map4k2 None Map4k2 \n",
- "1124 1125 Pan3 None Pan3 \n",
- "1125 1126 Plk5 None Plk5 \n",
- "1126 1127 Efna2 None Efna2 \n",
- "\n",
- " kinase.hgnc_name_y kinase.full_name_y \n",
- "0 AKT1 None \n",
- "1 AKT2 None \n",
- "2 AKT3 None \n",
- "3 CIT None \n",
- "4 DMPK None \n",
- "... ... ... \n",
- "1122 Pip5k1a None \n",
- "1123 Map4k2 None \n",
- "1124 Pan3 None \n",
- "1125 Plk5 None \n",
- "1126 Efna2 None \n",
- "\n",
- "[1127 rows x 6 columns]"
- ]
- },
- "execution_count": 16,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "kinases = kinases1.merge(kinases2, on=\"kinase.id\", how=\"left\")\n",
- "kinases = kinases.iloc[:, [0, 1, 2, 4, 5, 10]]\n",
- "kinases"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 17,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.id | \n",
- " kinase.hgnc_name_x | \n",
- " kinase.full_name_x | \n",
- " kinase.klifs_name | \n",
- " kinase.hgnc_name_y | \n",
- " kinase.full_name_y | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " 248 | \n",
- " 249 | \n",
- " MAPK14 | \n",
- " None | \n",
- " p38a | \n",
- " MAPK14 | \n",
- " None | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " kinase.id kinase.hgnc_name_x kinase.full_name_x kinase.klifs_name \\\n",
- "248 249 MAPK14 None p38a \n",
- "\n",
- " kinase.hgnc_name_y kinase.full_name_y \n",
- "248 MAPK14 None "
- ]
- },
- "execution_count": 17,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "kinases[kinases[\"kinase.hgnc_name_x\"] == \"MAPK14\"]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 18,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.id | \n",
- " kinase.hgnc_name_x | \n",
- " kinase.full_name_x | \n",
- " kinase.klifs_name | \n",
- " kinase.hgnc_name_y | \n",
- " kinase.full_name_y | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- "Empty DataFrame\n",
- "Columns: [kinase.id, kinase.hgnc_name_x, kinase.full_name_x, kinase.klifs_name, kinase.hgnc_name_y, kinase.full_name_y]\n",
- "Index: []"
- ]
- },
- "execution_count": 18,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "kinases[kinases[\"kinase.klifs_name\"].isin([\"\", \" \", 0, \"0\", None])]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 19,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.id | \n",
- " kinase.hgnc_name_x | \n",
- " kinase.full_name_x | \n",
- " kinase.klifs_name | \n",
- " kinase.hgnc_name_y | \n",
- " kinase.full_name_y | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- "Empty DataFrame\n",
- "Columns: [kinase.id, kinase.hgnc_name_x, kinase.full_name_x, kinase.klifs_name, kinase.hgnc_name_y, kinase.full_name_y]\n",
- "Index: []"
- ]
- },
- "execution_count": 19,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "kinases[kinases[\"kinase.hgnc_name_x\"].isin([\"\", \" \", 0, \"0\", None])]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 20,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.id | \n",
- " kinase.hgnc_name_x | \n",
- " kinase.full_name_x | \n",
- " kinase.klifs_name | \n",
- " kinase.hgnc_name_y | \n",
- " kinase.full_name_y | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " 528 | \n",
- " 529 | \n",
- " A6 | \n",
- " None | \n",
- " A6 | \n",
- " | \n",
- " None | \n",
- "
\n",
- " \n",
- " 529 | \n",
- " 530 | \n",
- " A6r | \n",
- " None | \n",
- " A6r | \n",
- " | \n",
- " None | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " kinase.id kinase.hgnc_name_x kinase.full_name_x kinase.klifs_name \\\n",
- "528 529 A6 None A6 \n",
- "529 530 A6r None A6r \n",
- "\n",
- " kinase.hgnc_name_y kinase.full_name_y \n",
- "528 None \n",
- "529 None "
- ]
- },
- "execution_count": 20,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "kinases[kinases[\"kinase.hgnc_name_y\"].isin([\"\", \" \", 0, \"0\", None])]"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### Differing `kinase.name_full`?"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 21,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Number of differing full names: 0\n"
- ]
- }
- ],
- "source": [
- "diff1 = kinases[kinases.apply(lambda x: x[\"kinase.full_name_x\"] != x[\"kinase.full_name_y\"], axis=1)]\n",
- "print(f\"Number of differing full names: {diff1.shape[0]}\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### Differing `kinase.hgnc`?"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 22,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Number of differing HGNC names: 2\n"
- ]
- },
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.id | \n",
- " kinase.hgnc_name_x | \n",
- " kinase.full_name_x | \n",
- " kinase.klifs_name | \n",
- " kinase.hgnc_name_y | \n",
- " kinase.full_name_y | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " 528 | \n",
- " 529 | \n",
- " A6 | \n",
- " None | \n",
- " A6 | \n",
- " | \n",
- " None | \n",
- "
\n",
- " \n",
- " 529 | \n",
- " 530 | \n",
- " A6r | \n",
- " None | \n",
- " A6r | \n",
- " | \n",
- " None | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " kinase.id kinase.hgnc_name_x kinase.full_name_x kinase.klifs_name \\\n",
- "528 529 A6 None A6 \n",
- "529 530 A6r None A6r \n",
- "\n",
- " kinase.hgnc_name_y kinase.full_name_y \n",
- "528 None \n",
- "529 None "
- ]
- },
- "execution_count": 22,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "diff3 = kinases[kinases.apply(lambda x: x[\"kinase.hgnc_name_x\"] != x[\"kinase.hgnc_name_y\"], axis=1)]\n",
- "print(f\"Number of differing HGNC names: {diff3.shape[0]}\")\n",
- "diff3.head()"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "__Note__: In case of kinases A6 and A6r, the HGNC column from `all_kinases` got non-HGNC entries?"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Local kinase details"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 23,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "(11592, 15) (11592, 27)\n"
- ]
- }
- ],
- "source": [
- "from opencadd.databases.klifs.local import _LocalDatabaseGenerator\n",
- "local = _LocalDatabaseGenerator()\n",
- "klifs_export_path = \"data/KLIFS_export.20201020.csv.zip\"\n",
- "klifs_export = local._from_klifs_export_file(klifs_export_path)\n",
- "klifs_overview_path = \"data/overview.20201020.csv.zip\"\n",
- "klifs_overview = local._from_klifs_overview_file(klifs_overview_path)\n",
- "print(klifs_export.shape, klifs_overview.shape)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 24,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.names | \n",
- " kinase.family | \n",
- " kinase.group | \n",
- " structure.pdb | \n",
- " structure.chain | \n",
- " structure.alternate_model | \n",
- " species.klifs | \n",
- " ligand.name | \n",
- " ligand.pdb | \n",
- " ligand_allosteric.name | \n",
- " ligand_allosteric.pdb | \n",
- " structure.dfg | \n",
- " structure.ac_helix | \n",
- " kinase.hgnc_name | \n",
- " kinase.klifs_name | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " 0 | \n",
- " [MAPK14, p38a] | \n",
- " MAPK | \n",
- " CMGC | \n",
- " 1a9u | \n",
- " A | \n",
- " - | \n",
- " Human | \n",
- " 4-[5-(4-FLUORO-PHENYL)-2-(4-METHANESULFINYL-PH... | \n",
- " SB2 | \n",
- " - | \n",
- " - | \n",
- " in | \n",
- " out-like | \n",
- " MAPK14 | \n",
- " p38a | \n",
- "
\n",
- " \n",
- " 1 | \n",
- " [HCK] | \n",
- " Src | \n",
- " TK | \n",
- " 1ad5 | \n",
- " A | \n",
- " - | \n",
- " Human | \n",
- " PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER | \n",
- " ANP | \n",
- " - | \n",
- " - | \n",
- " in | \n",
- " out | \n",
- " HCK | \n",
- " HCK | \n",
- "
\n",
- " \n",
- " 2 | \n",
- " [HCK] | \n",
- " Src | \n",
- " TK | \n",
- " 1ad5 | \n",
- " B | \n",
- " - | \n",
- " Human | \n",
- " PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER | \n",
- " ANP | \n",
- " - | \n",
- " - | \n",
- " in | \n",
- " out-like | \n",
- " HCK | \n",
- " HCK | \n",
- "
\n",
- " \n",
- " 3 | \n",
- " [FGFR1] | \n",
- " FGFR | \n",
- " TK | \n",
- " 1agw | \n",
- " A | \n",
- " A | \n",
- " Human | \n",
- " 3-[4-(1-FORMYLPIPERAZIN-4-YL)-BENZYLIDENYL]-2-... | \n",
- " SU2 | \n",
- " - | \n",
- " - | \n",
- " in | \n",
- " out-like | \n",
- " FGFR1 | \n",
- " FGFR1 | \n",
- "
\n",
- " \n",
- " 4 | \n",
- " [FGFR1] | \n",
- " FGFR | \n",
- " TK | \n",
- " 1agw | \n",
- " A | \n",
- " B | \n",
- " Human | \n",
- " 3-[4-(1-FORMYLPIPERAZIN-4-YL)-BENZYLIDENYL]-2-... | \n",
- " SU2 | \n",
- " - | \n",
- " - | \n",
- " in | \n",
- " out-like | \n",
- " FGFR1 | \n",
- " FGFR1 | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " kinase.names kinase.family kinase.group structure.pdb structure.chain \\\n",
- "0 [MAPK14, p38a] MAPK CMGC 1a9u A \n",
- "1 [HCK] Src TK 1ad5 A \n",
- "2 [HCK] Src TK 1ad5 B \n",
- "3 [FGFR1] FGFR TK 1agw A \n",
- "4 [FGFR1] FGFR TK 1agw A \n",
- "\n",
- " structure.alternate_model species.klifs \\\n",
- "0 - Human \n",
- "1 - Human \n",
- "2 - Human \n",
- "3 A Human \n",
- "4 B Human \n",
- "\n",
- " ligand.name ligand.pdb \\\n",
- "0 4-[5-(4-FLUORO-PHENYL)-2-(4-METHANESULFINYL-PH... SB2 \n",
- "1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER ANP \n",
- "2 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER ANP \n",
- "3 3-[4-(1-FORMYLPIPERAZIN-4-YL)-BENZYLIDENYL]-2-... SU2 \n",
- "4 3-[4-(1-FORMYLPIPERAZIN-4-YL)-BENZYLIDENYL]-2-... SU2 \n",
- "\n",
- " ligand_allosteric.name ligand_allosteric.pdb structure.dfg \\\n",
- "0 - - in \n",
- "1 - - in \n",
- "2 - - in \n",
- "3 - - in \n",
- "4 - - in \n",
- "\n",
- " structure.ac_helix kinase.hgnc_name kinase.klifs_name \n",
- "0 out-like MAPK14 p38a \n",
- "1 out HCK HCK \n",
- "2 out-like HCK HCK \n",
- "3 out-like FGFR1 FGFR1 \n",
- "4 out-like FGFR1 FGFR1 "
- ]
- },
- "execution_count": 24,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "klifs_export.sort_values([\"structure.pdb\", \"structure.chain\", \"structure.alternate_model\"], inplace=True, ignore_index=True)\n",
- "klifs_export.head()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 26,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "(4867, 15)"
- ]
- },
- "execution_count": 26,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "klifs_export[klifs_export[\"kinase.names\"].apply(len) == 2].shape"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 27,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " species.klifs | \n",
- " kinase.klifs_name | \n",
- " structure.pdb | \n",
- " structure.alternate_model | \n",
- " structure.chain | \n",
- " ligand.pdb | \n",
- " ligand_allosteric.pdb | \n",
- " structure.rmsd1 | \n",
- " structure.rmsd2 | \n",
- " structure.qualityscore | \n",
- " structure.pocket | \n",
- " structure.resolution | \n",
- " structure.missing_residues | \n",
- " structure.missing_atoms | \n",
- " interaction.fingerprint | \n",
- " structure.fp_i | \n",
- " structure.fp_ii | \n",
- " structure.bp_i_a | \n",
- " structure.bp_i_b | \n",
- " structure.bp_ii_in | \n",
- " structure.bp_ii_a_in | \n",
- " structure.bp_ii_b_in | \n",
- " structure.bp_ii_out | \n",
- " structure.bp_ii_b | \n",
- " structure.bp_iii | \n",
- " structure.bp_iv | \n",
- " structure.bp_v | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " 0 | \n",
- " Human | \n",
- " p38a | \n",
- " 1a9u | \n",
- " - | \n",
- " A | \n",
- " SB2 | \n",
- " - | \n",
- " 0.828 | \n",
- " 2.186 | \n",
- " 8.0 | \n",
- " SPVGSGAYGSVCAVAVKKLRTYRELRLLKHMKENVIGLLDVYLVTH... | \n",
- " 2.5 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0000000000000000000000000000000000000000000000... | \n",
- " 0.0 | \n",
- " 1.0 | \n",
- " 1.0 | \n",
- " 1.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- "
\n",
- " \n",
- " 1 | \n",
- " Human | \n",
- " HCK | \n",
- " 1ad5 | \n",
- " - | \n",
- " A | \n",
- " ANP | \n",
- " - | \n",
- " 0.816 | \n",
- " 2.141 | \n",
- " 9.6 | \n",
- " KKLGAGQFGEVWMVAVKTMAFLAEANVMKTLQDKLVKLHAVYIITE... | \n",
- " 2.6 | \n",
- " 0 | \n",
- " 4 | \n",
- " 0000000000000010000000000000000000000000000000... | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- "
\n",
- " \n",
- " 2 | \n",
- " Human | \n",
- " HCK | \n",
- " 1ad5 | \n",
- " - | \n",
- " B | \n",
- " ANP | \n",
- " - | \n",
- " 0.817 | \n",
- " 2.141 | \n",
- " 9.6 | \n",
- " KKLGAGQFGEVWMVAVKTMAFLAEANVMKTLQDKLVKLHAVYIITE... | \n",
- " 2.6 | \n",
- " 0 | \n",
- " 4 | \n",
- " 0000000000000010000001000000000000000000000000... | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- "
\n",
- " \n",
- " 3 | \n",
- " Human | \n",
- " FGFR1 | \n",
- " 1agw | \n",
- " A | \n",
- " A | \n",
- " SU2 | \n",
- " - | \n",
- " 0.831 | \n",
- " 2.001 | \n",
- " 7.6 | \n",
- " KPLG_____QVVLVAVKMLDLISEMEMMKMIGKNIINLLGAYVIVE... | \n",
- " 2.4 | \n",
- " 5 | \n",
- " 4 | \n",
- " 0000000000000010000000000000000000000000000000... | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- "
\n",
- " \n",
- " 4 | \n",
- " Human | \n",
- " FGFR1 | \n",
- " 1agw | \n",
- " B | \n",
- " A | \n",
- " SU2 | \n",
- " - | \n",
- " 0.831 | \n",
- " 2.001 | \n",
- " 7.6 | \n",
- " KPLG_____QVVLVAVKMLDLISEMEMMKMIGKNIINLLGAYVIVE... | \n",
- " 2.4 | \n",
- " 5 | \n",
- " 4 | \n",
- " 0000000000000010000000000000000000000000000000... | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- " 0.0 | \n",
- "
\n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- " species.klifs kinase.klifs_name structure.pdb structure.alternate_model \\\n",
- "0 Human p38a 1a9u - \n",
- "1 Human HCK 1ad5 - \n",
- "2 Human HCK 1ad5 - \n",
- "3 Human FGFR1 1agw A \n",
- "4 Human FGFR1 1agw B \n",
- "\n",
- " structure.chain ligand.pdb ligand_allosteric.pdb structure.rmsd1 \\\n",
- "0 A SB2 - 0.828 \n",
- "1 A ANP - 0.816 \n",
- "2 B ANP - 0.817 \n",
- "3 A SU2 - 0.831 \n",
- "4 A SU2 - 0.831 \n",
- "\n",
- " structure.rmsd2 structure.qualityscore \\\n",
- "0 2.186 8.0 \n",
- "1 2.141 9.6 \n",
- "2 2.141 9.6 \n",
- "3 2.001 7.6 \n",
- "4 2.001 7.6 \n",
- "\n",
- " structure.pocket structure.resolution \\\n",
- "0 SPVGSGAYGSVCAVAVKKLRTYRELRLLKHMKENVIGLLDVYLVTH... 2.5 \n",
- "1 KKLGAGQFGEVWMVAVKTMAFLAEANVMKTLQDKLVKLHAVYIITE... 2.6 \n",
- "2 KKLGAGQFGEVWMVAVKTMAFLAEANVMKTLQDKLVKLHAVYIITE... 2.6 \n",
- "3 KPLG_____QVVLVAVKMLDLISEMEMMKMIGKNIINLLGAYVIVE... 2.4 \n",
- "4 KPLG_____QVVLVAVKMLDLISEMEMMKMIGKNIINLLGAYVIVE... 2.4 \n",
- "\n",
- " structure.missing_residues structure.missing_atoms \\\n",
- "0 0 0 \n",
- "1 0 4 \n",
- "2 0 4 \n",
- "3 5 4 \n",
- "4 5 4 \n",
- "\n",
- " interaction.fingerprint structure.fp_i \\\n",
- "0 0000000000000000000000000000000000000000000000... 0.0 \n",
- "1 0000000000000010000000000000000000000000000000... 0.0 \n",
- "2 0000000000000010000001000000000000000000000000... 0.0 \n",
- "3 0000000000000010000000000000000000000000000000... 0.0 \n",
- "4 0000000000000010000000000000000000000000000000... 0.0 \n",
- "\n",
- " structure.fp_ii structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
- "0 1.0 1.0 1.0 0.0 \n",
- "1 0.0 0.0 0.0 0.0 \n",
- "2 0.0 0.0 0.0 0.0 \n",
- "3 0.0 0.0 0.0 0.0 \n",
- "4 0.0 0.0 0.0 0.0 \n",
- "\n",
- " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
- "0 0.0 0.0 0.0 \n",
- "1 0.0 0.0 0.0 \n",
- "2 0.0 0.0 0.0 \n",
- "3 0.0 0.0 0.0 \n",
- "4 0.0 0.0 0.0 \n",
- "\n",
- " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \n",
- "0 0.0 0.0 0.0 0.0 \n",
- "1 0.0 0.0 0.0 0.0 \n",
- "2 0.0 0.0 0.0 0.0 \n",
- "3 0.0 0.0 0.0 0.0 \n",
- "4 0.0 0.0 0.0 0.0 "
- ]
- },
- "execution_count": 27,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "klifs_overview.sort_values([\"structure.pdb\", \"structure.chain\", \"structure.alternate_model\"], inplace=True, ignore_index=True)\n",
- "klifs_overview.head()"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### Kinase name mismatches in local overview and export files?"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 28,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.names | \n",
- " kinase.family | \n",
- " kinase.group | \n",
- " structure.pdb | \n",
- " structure.chain | \n",
- " structure.alternate_model | \n",
- " species.klifs | \n",
- " ligand.name | \n",
- " ligand.pdb | \n",
- " ligand_allosteric.name | \n",
- " ligand_allosteric.pdb | \n",
- " structure.dfg | \n",
- " structure.ac_helix | \n",
- " kinase.hgnc_name | \n",
- " kinase.klifs_name | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- "Empty DataFrame\n",
- "Columns: [kinase.names, kinase.family, kinase.group, structure.pdb, structure.chain, structure.alternate_model, species.klifs, ligand.name, ligand.pdb, ligand_allosteric.name, ligand_allosteric.pdb, structure.dfg, structure.ac_helix, kinase.hgnc_name, kinase.klifs_name]\n",
- "Index: []"
- ]
- },
- "execution_count": 28,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "klifs_export[klifs_export[\"kinase.klifs_name\"] != klifs_overview[\"kinase.klifs_name\"]]"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### Kinase name mismatches locally and remotely?"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 29,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.names | \n",
- " kinase.family | \n",
- " kinase.group | \n",
- " structure.pdb | \n",
- " structure.chain | \n",
- " structure.alternate_model | \n",
- " species.klifs | \n",
- " ligand.name | \n",
- " ligand.pdb | \n",
- " ligand_allosteric.name | \n",
- " ligand_allosteric.pdb | \n",
- " structure.dfg | \n",
- " structure.ac_helix | \n",
- " kinase.hgnc_name | \n",
- " kinase.klifs_name | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- "Empty DataFrame\n",
- "Columns: [kinase.names, kinase.family, kinase.group, structure.pdb, structure.chain, structure.alternate_model, species.klifs, ligand.name, ligand.pdb, ligand_allosteric.name, ligand_allosteric.pdb, structure.dfg, structure.ac_helix, kinase.hgnc_name, kinase.klifs_name]\n",
- "Index: []"
- ]
- },
- "execution_count": 29,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "klifs_export[~klifs_export[\"kinase.klifs_name\"].isin(kinases[\"kinase.klifs_name\"].to_list())]"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### Kinase HGNC name mismatches locally and remotely?"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 30,
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
- "\n",
- "\n",
- "
\n",
- " \n",
- " \n",
- " | \n",
- " kinase.names | \n",
- " kinase.family | \n",
- " kinase.group | \n",
- " structure.pdb | \n",
- " structure.chain | \n",
- " structure.alternate_model | \n",
- " species.klifs | \n",
- " ligand.name | \n",
- " ligand.pdb | \n",
- " ligand_allosteric.name | \n",
- " ligand_allosteric.pdb | \n",
- " structure.dfg | \n",
- " structure.ac_helix | \n",
- " kinase.hgnc_name | \n",
- " kinase.klifs_name | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- "
\n",
- "
"
- ],
- "text/plain": [
- "Empty DataFrame\n",
- "Columns: [kinase.names, kinase.family, kinase.group, structure.pdb, structure.chain, structure.alternate_model, species.klifs, ligand.name, ligand.pdb, ligand_allosteric.name, ligand_allosteric.pdb, structure.dfg, structure.ac_helix, kinase.hgnc_name, kinase.klifs_name]\n",
- "Index: []"
- ]
- },
- "execution_count": 30,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "klifs_export[~klifs_export[\"kinase.hgnc_name\"].isin(kinases[\"kinase.hgnc_name_x\"].to_list())]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.8.6"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}
diff --git a/docs/tutorials/databases_klifs.ipynb b/docs/tutorials/databases_klifs.ipynb
index 80262aa7..0dfb7ff6 100644
--- a/docs/tutorials/databases_klifs.ipynb
+++ b/docs/tutorials/databases_klifs.ipynb
@@ -8,8 +8,8 @@
"\n",
"The `opencadd.databases.klifs` module offers to interact with KLIFS data \n",
"\n",
- "- __locally__ ([KLIFS data download](https://klifs.vu-compmedchem.nl/search.php)) and\n",
- "- __remote__ ([KLIFS swagger API](https://klifs.vu-compmedchem.nl/swagger/)) \n",
+ "- __locally__ ([KLIFS data download](https://klifs.net/search.php)) and\n",
+ "- __remote__ ([KLIFS swagger API (beta)](https://klifs.net/swagger_v2/)) \n",
"\n",
"following the same API in its `local` and `remote` modules.\n",
"\n",
@@ -102,16 +102,7 @@
"cell_type": "code",
"execution_count": 5,
"metadata": {},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "INFO:opencadd.databases.klifs.api:Set up remote session...\n",
- "INFO:opencadd.databases.klifs.api:Remote session is ready!\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"remote = setup_remote()"
]
@@ -124,7 +115,7 @@
{
"data": {
"text/plain": [
- "SwaggerClient(https://klifs.net/api)"
+ "SwaggerClient(https://dev.klifs.net/api_v2)"
]
},
"execution_count": 6,
@@ -154,21 +145,7 @@
"cell_type": "code",
"execution_count": 7,
"metadata": {},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "INFO:opencadd.databases.klifs.api:Set up local session...\n",
- "INFO:opencadd.databases.klifs.local:Load overview.csv...\n",
- "INFO:opencadd.databases.klifs.local:Load KLIFS_export.csv...\n",
- "INFO:opencadd.databases.klifs.local:Merge both csv files...\n",
- "INFO:opencadd.databases.klifs.local:Add paths to coordinate folders to structures...\n",
- "INFO:opencadd.databases.klifs.local:Add KLIFS IDs to structures (uses remote since not available locally!)...\n",
- "INFO:opencadd.databases.klifs.api:Local session is ready!\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"local = setup_local(\"../../opencadd/tests/data/klifs\")"
]
@@ -233,7 +210,7 @@
" structure.bp_iv | \n",
" structure.bp_v | \n",
" kinase.names | \n",
- " kinase.hgnc_name | \n",
+ " kinase.gene_name | \n",
" kinase.klifs_name | \n",
" kinase.family | \n",
" kinase.group | \n",
@@ -263,18 +240,18 @@
" 4 | \n",
" 0 | \n",
" 0000000000000010000001000000000000000000000000... | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 1.0 | \n",
+ " 1.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
" [BMX] | \n",
" BMX | \n",
" BMX | \n",
@@ -304,18 +281,18 @@
" 7 | \n",
" 61 | \n",
" 0000000000000000000000000000000000000000000000... | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 1.0 | \n",
+ " 1.0 | \n",
+ " 1.0 | \n",
+ " 1.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
+ " 0.0 | \n",
" [BRAF] | \n",
" BRAF | \n",
" BRAF | \n",
@@ -330,163 +307,219 @@
" 509 | \n",
" \n",
" \n",
- " 2 | \n",
- " Mouse | \n",
- " 1fpu | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ "
\n",
+ " \n",
+ " 4 | \n",
+ " Human | \n",
+ " 7lht | \n",
" - | \n",
" A | \n",
- " PRC | \n",
" - | \n",
- " 0.925 | \n",
- " 2.319 | \n",
- " 8.8 | \n",
- " HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... | \n",
- " 2.40 | \n",
- " 0 | \n",
- " 8 | \n",
- " 0000000000000010000000000000000000000000000000... | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 1 | \n",
- " 0 | \n",
+ " ATP | \n",
+ " 10.267 | \n",
+ " 15.045 | \n",
+ " 4.0 | \n",
+ " KALGKGLFSMVIRITLKVVGLRILNLPHLILEYCKAKDIIRFLQQK... | \n",
+ " 3.50 | \n",
" 0 | \n",
" 0 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " [Abl1, ABL1] | \n",
- " Abl1 | \n",
- " ABL1 | \n",
- " Abl | \n",
- " TK | \n",
- " N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " [LRRK2] | \n",
+ " LRRK2 | \n",
+ " LRRK2 | \n",
+ " LRRK | \n",
+ " TKL | \n",
" - | \n",
+ " ADENOSINE-5'-TRIPHOSPHATE | \n",
" out | \n",
" out | \n",
- " MOUSE/ABL1/1fpu_chainA | \n",
- " 5728 | \n",
- " 532 | \n",
+ " HUMAN/LRRK2/7lht_chainA | \n",
+ " 13623 | \n",
+ " 495 | \n",
"
\n",
" \n",
- " 3 | \n",
- " Mouse | \n",
- " 1fpu | \n",
+ " 5 | \n",
+ " Human | \n",
+ " 2ogv | \n",
" - | \n",
- " B | \n",
- " PRC | \n",
+ " A | \n",
" - | \n",
- " 0.925 | \n",
- " 2.329 | \n",
- " 9.2 | \n",
- " HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... | \n",
- " 2.40 | \n",
- " 0 | \n",
- " 4 | \n",
- " 0000000000000010000000000000000000000000000000... | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
- " 1 | \n",
- " 0 | \n",
- " 0 | \n",
- " 0 | \n",
+ " - | \n",
+ " 1.043 | \n",
+ " 2.362 | \n",
+ " 6.4 | \n",
+ " KTLGAGAFGKVVEVAVKMLALMSELKIMSHLGENIVNLLGALVITE... | \n",
+ " 2.70 | \n",
+ " 2 | \n",
" 0 | \n",
- " [Abl1, ABL1] | \n",
- " Abl1 | \n",
- " ABL1 | \n",
- " Abl | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " NaN | \n",
+ " [CSF1R, FMS] | \n",
+ " CSF1R | \n",
+ " FMS | \n",
+ " PDGFR | \n",
" TK | \n",
- " N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... | \n",
+ " - | \n",
" - | \n",
" out | \n",
- " out | \n",
- " MOUSE/ABL1/1fpu_chainB | \n",
- " 5705 | \n",
- " 532 | \n",
+ " in | \n",
+ " HUMAN/FMS/2ogv_chainA | \n",
+ " 1243 | \n",
+ " 449 | \n",
"
\n",
" \n",
"\n",
+ "6 rows × 38 columns
\n",
""
],
"text/plain": [
- " species.klifs structure.pdb_id structure.alternate_model structure.chain \\\n",
- "0 Human 3sxr - A \n",
- "1 Human 6uuo - A \n",
- "2 Mouse 1fpu - A \n",
- "3 Mouse 1fpu - B \n",
- "\n",
- " ligand.expo_id ligand_allosteric.expo_id structure.rmsd1 structure.rmsd2 \\\n",
- "0 1N1 - 0.839 1.967 \n",
- "1 QH1 - 0.806 2.028 \n",
- "2 PRC - 0.925 2.319 \n",
- "3 PRC - 0.925 2.329 \n",
- "\n",
- " structure.qualityscore structure.pocket \\\n",
- "0 6.4 KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... \n",
- "1 5.2 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... \n",
- "2 8.8 HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... \n",
- "3 9.2 HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... \n",
- "\n",
- " structure.resolution structure.missing_residues structure.missing_atoms \\\n",
- "0 2.40 4 0 \n",
- "1 3.29 7 61 \n",
- "2 2.40 0 8 \n",
- "3 2.40 0 4 \n",
- "\n",
- " interaction.fingerprint structure.fp_i \\\n",
- "0 0000000000000010000001000000000000000000000000... 0 \n",
- "1 0000000000000000000000000000000000000000000000... 0 \n",
- "2 0000000000000010000000000000000000000000000000... 0 \n",
- "3 0000000000000010000000000000000000000000000000... 0 \n",
- "\n",
- " structure.fp_ii structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
- "0 0 1 1 0 \n",
- "1 0 1 1 1 \n",
- "2 0 1 1 0 \n",
- "3 0 0 1 0 \n",
- "\n",
- " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
- "0 0 0 0 \n",
- "1 1 0 0 \n",
- "2 0 0 1 \n",
- "3 0 0 1 \n",
- "\n",
- " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
- "0 0 0 0 0 \n",
- "1 0 0 0 0 \n",
- "2 0 0 0 0 \n",
- "3 0 0 0 0 \n",
- "\n",
- " kinase.names kinase.hgnc_name kinase.klifs_name kinase.family kinase.group \\\n",
- "0 [BMX] BMX BMX Tec TK \n",
- "1 [BRAF] BRAF BRAF RAF TKL \n",
- "2 [Abl1, ABL1] Abl1 ABL1 Abl TK \n",
- "3 [Abl1, ABL1] Abl1 ABL1 Abl TK \n",
- "\n",
- " ligand.name ligand_allosteric.name \\\n",
- "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... - \n",
- "1 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... - \n",
- "2 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... - \n",
- "3 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... - \n",
- "\n",
- " structure.dfg structure.ac_helix structure.filepath \\\n",
- "0 out-like in HUMAN/BMX/3sxr_chainA \n",
- "1 in out-like HUMAN/BRAF/6uuo_chainA \n",
- "2 out out MOUSE/ABL1/1fpu_chainA \n",
- "3 out out MOUSE/ABL1/1fpu_chainB \n",
- "\n",
- " structure.klifs_id kinase.klifs_id \n",
- "0 3482 472 \n",
- "1 12347 509 \n",
- "2 5728 532 \n",
- "3 5705 532 "
+ " species.klifs structure.pdb_id structure.alternate_model structure.chain \\\n",
+ "0 Human 3sxr - A \n",
+ "1 Human 6uuo - A \n",
+ ".. ... ... ... ... \n",
+ "4 Human 7lht - A \n",
+ "5 Human 2ogv - A \n",
+ "\n",
+ " ligand.expo_id ligand_allosteric.expo_id structure.rmsd1 structure.rmsd2 \\\n",
+ "0 1N1 - 0.839 1.967 \n",
+ "1 QH1 - 0.806 2.028 \n",
+ ".. ... ... ... ... \n",
+ "4 - ATP 10.267 15.045 \n",
+ "5 - - 1.043 2.362 \n",
+ "\n",
+ " structure.qualityscore structure.pocket \\\n",
+ "0 6.4 KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... \n",
+ "1 5.2 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... \n",
+ ".. ... ... \n",
+ "4 4.0 KALGKGLFSMVIRITLKVVGLRILNLPHLILEYCKAKDIIRFLQQK... \n",
+ "5 6.4 KTLGAGAFGKVVEVAVKMLALMSELKIMSHLGENIVNLLGALVITE... \n",
+ "\n",
+ " structure.resolution structure.missing_residues structure.missing_atoms \\\n",
+ "0 2.40 4 0 \n",
+ "1 3.29 7 61 \n",
+ ".. ... ... ... \n",
+ "4 3.50 0 0 \n",
+ "5 2.70 2 0 \n",
+ "\n",
+ " interaction.fingerprint structure.fp_i \\\n",
+ "0 0000000000000010000001000000000000000000000000... 0.0 \n",
+ "1 0000000000000000000000000000000000000000000000... 0.0 \n",
+ ".. ... ... \n",
+ "4 NaN NaN \n",
+ "5 NaN NaN \n",
+ "\n",
+ " structure.fp_ii structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
+ "0 0.0 1.0 1.0 0.0 \n",
+ "1 0.0 1.0 1.0 1.0 \n",
+ ".. ... ... ... ... \n",
+ "4 NaN NaN NaN NaN \n",
+ "5 NaN NaN NaN NaN \n",
+ "\n",
+ " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
+ "0 0.0 0.0 0.0 \n",
+ "1 1.0 0.0 0.0 \n",
+ ".. ... ... ... \n",
+ "4 NaN NaN NaN \n",
+ "5 NaN NaN NaN \n",
+ "\n",
+ " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
+ "0 0.0 0.0 0.0 0.0 \n",
+ "1 0.0 0.0 0.0 0.0 \n",
+ ".. ... ... ... ... \n",
+ "4 NaN NaN NaN NaN \n",
+ "5 NaN NaN NaN NaN \n",
+ "\n",
+ " kinase.names kinase.gene_name kinase.klifs_name kinase.family \\\n",
+ "0 [BMX] BMX BMX Tec \n",
+ "1 [BRAF] BRAF BRAF RAF \n",
+ ".. ... ... ... ... \n",
+ "4 [LRRK2] LRRK2 LRRK2 LRRK \n",
+ "5 [CSF1R, FMS] CSF1R FMS PDGFR \n",
+ "\n",
+ " kinase.group ligand.name \\\n",
+ "0 TK N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... \n",
+ "1 TKL 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... \n",
+ ".. ... ... \n",
+ "4 TKL - \n",
+ "5 TK - \n",
+ "\n",
+ " ligand_allosteric.name structure.dfg structure.ac_helix \\\n",
+ "0 - out-like in \n",
+ "1 - in out-like \n",
+ ".. ... ... ... \n",
+ "4 ADENOSINE-5'-TRIPHOSPHATE out out \n",
+ "5 - out in \n",
+ "\n",
+ " structure.filepath structure.klifs_id kinase.klifs_id \n",
+ "0 HUMAN/BMX/3sxr_chainA 3482 472 \n",
+ "1 HUMAN/BRAF/6uuo_chainA 12347 509 \n",
+ ".. ... ... ... \n",
+ "4 HUMAN/LRRK2/7lht_chainA 13623 495 \n",
+ "5 HUMAN/FMS/2ogv_chainA 1243 449 \n",
+ "\n",
+ "[6 rows x 38 columns]"
]
},
"execution_count": 8,
@@ -525,13 +558,15 @@
"metadata": {},
"source": [
"| | kinases | ligands | structures | bioactivities | interactions | pockets |\n",
- "|:--------------------------| - | - | - | - | - | - |\n",
- "| __by_kinase_klifs_id__ | x | x | x | x | x | | \n",
- "| __by_kinase_name__ | x | x | x | | | |\n",
- "| __by_ligand_klifs_id__ | | x | x | x | x | |\n",
- "| __by_ligand_expo_id__ | | x | x | x | | |\n",
- "| __by_structure_klifs_id__ | | | x | | x | x |\n",
- "| __by_structure_pdb_id__ | | | x | | | |"
+ "|:--------------------------| - | - | - | - | - | - |\n",
+ "| __by_kinase_klifs_id__ | x* | x* | x* | | x | | \n",
+ "| __by_kinase_name__ | x* | x | x | | | |\n",
+ "| __by_ligand_klifs_id__ | | x* | x | x* | x | |\n",
+ "| __by_ligand_expo_id__ | | x | x | x* | | |\n",
+ "| __by_structure_klifs_id__ | | | x* | | x* | x* |\n",
+ "| __by_structure_pdb_id__ | | | x* | | | |\n",
+ "\n",
+ " \\* Direct use of KLIFS Swagger API."
]
},
{
@@ -859,7 +894,7 @@
}
],
"source": [
- "remote.kinases.all_kinase_families(group=\"TK\")"
+ "remote.kinases.all_kinase_families(groups=\"TK\")"
]
},
{
@@ -877,7 +912,7 @@
],
"source": [
"try:\n",
- " remote.kinases.all_kinase_families(group=\"XXX\")\n",
+ " remote.kinases.all_kinase_families(groups=\"XXX\")\n",
"except SwaggerMappingError as e:\n",
" print(e)"
]
@@ -933,6 +968,14 @@
" 2 | \n",
" Abl | \n",
" \n",
+ " \n",
+ " 3 | \n",
+ " LRRK | \n",
+ "
\n",
+ " \n",
+ " 4 | \n",
+ " PDGFR | \n",
+ "
\n",
" \n",
"\n",
""
@@ -941,7 +984,9 @@
" kinase.family\n",
"0 Tec\n",
"1 RAF\n",
- "2 Abl"
+ "2 Abl\n",
+ "3 LRRK\n",
+ "4 PDGFR"
]
},
"execution_count": 14,
@@ -991,6 +1036,10 @@
" 1 | \n",
" Abl | \n",
" \n",
+ " \n",
+ " 2 | \n",
+ " PDGFR | \n",
+ "
\n",
" \n",
"\n",
""
@@ -998,7 +1047,8 @@
"text/plain": [
" kinase.family\n",
"0 Tec\n",
- "1 Abl"
+ "1 Abl\n",
+ "2 PDGFR"
]
},
"execution_count": 15,
@@ -1007,7 +1057,7 @@
}
],
"source": [
- "local.kinases.all_kinase_families(group=\"TK\")"
+ "local.kinases.all_kinase_families(groups=\"TK\")"
]
},
{
@@ -1071,24 +1121,30 @@
" \n",
" | \n",
" kinase.klifs_id | \n",
- " kinase.hgnc_name | \n",
+ " kinase.klifs_name | \n",
" kinase.full_name | \n",
+ " kinase.gene_name | \n",
+ " kinase.uniprot | \n",
" species.klifs | \n",
"
\n",
" \n",
" \n",
" \n",
" 0 | \n",
- " 813 | \n",
- " 4921509C19Rik | \n",
- " RIKEN cDNA 4921509C19 gene | \n",
+ " 529 | \n",
+ " A6 | \n",
+ " 0 | \n",
+ " | \n",
+ " 0 | \n",
" Mouse | \n",
"
\n",
" \n",
" 1 | \n",
- " 815 | \n",
- " 4921509C19Rik | \n",
- " RIKEN cDNA 4921509C19 gene | \n",
+ " 530 | \n",
+ " A6r | \n",
+ " 0 | \n",
+ " | \n",
+ " 0 | \n",
" Mouse | \n",
"
\n",
" \n",
@@ -1097,42 +1153,55 @@
" ... | \n",
" ... | \n",
" ... | \n",
+ " ... | \n",
+ " ... | \n",
"
\n",
" \n",
" 1125 | \n",
- " 529 | \n",
- " A6 | \n",
- " 0 | \n",
+ " 1062 | \n",
+ " ZAP70 | \n",
+ " zeta-chain (TCR) associated protein kinase | \n",
+ " Zap70 | \n",
+ " P43404 | \n",
" Mouse | \n",
"
\n",
" \n",
" 1126 | \n",
- " 530 | \n",
- " A6r | \n",
- " 0 | \n",
- " Mouse | \n",
+ " 471 | \n",
+ " ZAP70 | \n",
+ " zeta chain of T cell receptor associated prote... | \n",
+ " ZAP70 | \n",
+ " P43403 | \n",
+ " Human | \n",
"
\n",
" \n",
"\n",
- "1127 rows × 4 columns
\n",
+ "1127 rows × 6 columns
\n",
""
],
"text/plain": [
- " kinase.klifs_id kinase.hgnc_name kinase.full_name \\\n",
- "0 813 4921509C19Rik RIKEN cDNA 4921509C19 gene \n",
- "1 815 4921509C19Rik RIKEN cDNA 4921509C19 gene \n",
- "... ... ... ... \n",
- "1125 529 A6 0 \n",
- "1126 530 A6r 0 \n",
- "\n",
- " species.klifs \n",
- "0 Mouse \n",
- "1 Mouse \n",
- "... ... \n",
- "1125 Mouse \n",
- "1126 Mouse \n",
- "\n",
- "[1127 rows x 4 columns]"
+ " kinase.klifs_id kinase.klifs_name \\\n",
+ "0 529 A6 \n",
+ "1 530 A6r \n",
+ "... ... ... \n",
+ "1125 1062 ZAP70 \n",
+ "1126 471 ZAP70 \n",
+ "\n",
+ " kinase.full_name kinase.gene_name \\\n",
+ "0 0 \n",
+ "1 0 \n",
+ "... ... ... \n",
+ "1125 zeta-chain (TCR) associated protein kinase Zap70 \n",
+ "1126 zeta chain of T cell receptor associated prote... ZAP70 \n",
+ "\n",
+ " kinase.uniprot species.klifs \n",
+ "0 0 Mouse \n",
+ "1 0 Mouse \n",
+ "... ... ... \n",
+ "1125 P43404 Mouse \n",
+ "1126 P43403 Human \n",
+ "\n",
+ "[1127 rows x 6 columns]"
]
},
"execution_count": 17,
@@ -1171,8 +1240,10 @@
" \n",
" | \n",
" kinase.klifs_id | \n",
- " kinase.hgnc_name | \n",
+ " kinase.klifs_name | \n",
" kinase.full_name | \n",
+ " kinase.gene_name | \n",
+ " kinase.uniprot | \n",
" species.klifs | \n",
"
\n",
" \n",
@@ -1180,36 +1251,46 @@
" \n",
" 0 | \n",
" 574 | \n",
- " Bmx | \n",
+ " BMX | \n",
" BMX non-receptor tyrosine kinase | \n",
+ " Bmx | \n",
+ " P97504 | \n",
" Mouse | \n",
"
\n",
" \n",
" 1 | \n",
" 583 | \n",
- " Btk | \n",
+ " BTK | \n",
" Bruton agammaglobulinemia tyrosine kinase | \n",
+ " Btk | \n",
+ " P35991 | \n",
" Mouse | \n",
"
\n",
" \n",
" 2 | \n",
" 739 | \n",
- " Itk | \n",
+ " ITK | \n",
" IL2 inducible T cell kinase | \n",
+ " Itk | \n",
+ " Q03526 | \n",
" Mouse | \n",
"
\n",
" \n",
" 3 | \n",
" 1008 | \n",
- " Tec | \n",
+ " TEC | \n",
" tec protein tyrosine kinase | \n",
+ " Tec | \n",
+ " P24604 | \n",
" Mouse | \n",
"
\n",
" \n",
" 4 | \n",
" 1039 | \n",
- " Txk | \n",
+ " TXK | \n",
" TXK tyrosine kinase | \n",
+ " Txk | \n",
+ " P42682 | \n",
" Mouse | \n",
"
\n",
" \n",
@@ -1217,19 +1298,26 @@
""
],
"text/plain": [
- " kinase.klifs_id kinase.hgnc_name \\\n",
- "0 574 Bmx \n",
- "1 583 Btk \n",
- "2 739 Itk \n",
- "3 1008 Tec \n",
- "4 1039 Txk \n",
- "\n",
- " kinase.full_name species.klifs \n",
- "0 BMX non-receptor tyrosine kinase Mouse \n",
- "1 Bruton agammaglobulinemia tyrosine kinase Mouse \n",
- "2 IL2 inducible T cell kinase Mouse \n",
- "3 tec protein tyrosine kinase Mouse \n",
- "4 TXK tyrosine kinase Mouse "
+ " kinase.klifs_id kinase.klifs_name \\\n",
+ "0 574 BMX \n",
+ "1 583 BTK \n",
+ "2 739 ITK \n",
+ "3 1008 TEC \n",
+ "4 1039 TXK \n",
+ "\n",
+ " kinase.full_name kinase.gene_name kinase.uniprot \\\n",
+ "0 BMX non-receptor tyrosine kinase Bmx P97504 \n",
+ "1 Bruton agammaglobulinemia tyrosine kinase Btk P35991 \n",
+ "2 IL2 inducible T cell kinase Itk Q03526 \n",
+ "3 tec protein tyrosine kinase Tec P24604 \n",
+ "4 TXK tyrosine kinase Txk P42682 \n",
+ "\n",
+ " species.klifs \n",
+ "0 Mouse \n",
+ "1 Mouse \n",
+ "2 Mouse \n",
+ "3 Mouse \n",
+ "4 Mouse "
]
},
"execution_count": 18,
@@ -1238,7 +1326,7 @@
}
],
"source": [
- "remote.kinases.all_kinases(group=\"TK\", family=\"Tec\", species=\"Mouse\")"
+ "remote.kinases.all_kinases(groups=\"TK\", families=\"Tec\", species=\"Mouse\")"
]
},
{
@@ -1256,7 +1344,7 @@
],
"source": [
"try:\n",
- " remote.kinases.all_kinases(group=\"XXX\")\n",
+ " remote.kinases.all_kinases(groups=\"XXX\")\n",
"except SwaggerMappingError as e:\n",
" print(e)"
]
@@ -1297,8 +1385,10 @@
" \n",
" | \n",
" kinase.klifs_id | \n",
- " kinase.hgnc_name | \n",
+ " kinase.klifs_name | \n",
" kinase.full_name | \n",
+ " kinase.gene_name | \n",
+ " kinase.uniprot | \n",
" species.klifs | \n",
"
\n",
" \n",
@@ -1308,6 +1398,8 @@
" 472 | \n",
" BMX | \n",
" <NA> | \n",
+ " BMX | \n",
+ " <NA> | \n",
" Human | \n",
" \n",
" \n",
@@ -1315,8 +1407,11 @@
""
],
"text/plain": [
- " kinase.klifs_id kinase.hgnc_name kinase.full_name species.klifs\n",
- "0 472 BMX Human"
+ " kinase.klifs_id kinase.klifs_name kinase.full_name kinase.gene_name \\\n",
+ "0 472 BMX BMX \n",
+ "\n",
+ " kinase.uniprot species.klifs \n",
+ "0 Human "
]
},
"execution_count": 20,
@@ -1325,7 +1420,7 @@
}
],
"source": [
- "local.kinases.all_kinases(family=\"Tec\")"
+ "local.kinases.all_kinases(families=\"Tec\")"
]
},
{
@@ -1355,8 +1450,10 @@
" \n",
" | \n",
" kinase.klifs_id | \n",
- " kinase.hgnc_name | \n",
+ " kinase.klifs_name | \n",
" kinase.full_name | \n",
+ " kinase.gene_name | \n",
+ " kinase.uniprot | \n",
" species.klifs | \n",
"
\n",
" \n",
@@ -1364,6 +1461,8 @@
" \n",
" 0 | \n",
" 532 | \n",
+ " ABL1 | \n",
+ " <NA> | \n",
" Abl1 | \n",
" <NA> | \n",
" Mouse | \n",
@@ -1373,8 +1472,11 @@
""
],
"text/plain": [
- " kinase.klifs_id kinase.hgnc_name kinase.full_name species.klifs\n",
- "0 532 Abl1 Mouse"
+ " kinase.klifs_id kinase.klifs_name kinase.full_name kinase.gene_name \\\n",
+ "0 532 ABL1 Abl1 \n",
+ "\n",
+ " kinase.uniprot species.klifs \n",
+ "0 Mouse "
]
},
"execution_count": 21,
@@ -1383,7 +1485,7 @@
}
],
"source": [
- "local.kinases.all_kinases(family=\"Abl\", species=\"Mouse\")"
+ "local.kinases.all_kinases(families=\"Abl\", species=\"Mouse\")"
]
},
{
@@ -1401,7 +1503,7 @@
],
"source": [
"try:\n",
- " local.kinases.all_kinases(group=\"XXX\")\n",
+ " local.kinases.all_kinases(groups=\"XXX\")\n",
"except ValueError as e:\n",
" print(e)"
]
@@ -1448,12 +1550,12 @@
" | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
- " kinase.hgnc_name | \n",
+ " kinase.full_name | \n",
+ " kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
- " kinase.class | \n",
+ " kinase.subfamily | \n",
" species.klifs | \n",
- " kinase.full_name | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
" kinase.pocket | \n",
@@ -1464,12 +1566,12 @@
" 0 | \n",
" 1 | \n",
" AKT1 | \n",
+ " v-akt murine thymoma viral oncogene homolog 1 | \n",
" AKT1 | \n",
" Akt | \n",
" AGC | \n",
" | \n",
" Human | \n",
- " v-akt murine thymoma viral oncogene homolog 1 | \n",
" P31749 | \n",
" 1479 | \n",
" KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... | \n",
@@ -1479,17 +1581,17 @@
""
],
"text/plain": [
- " kinase.klifs_id kinase.klifs_name kinase.hgnc_name kinase.family \\\n",
- "0 1 AKT1 AKT1 Akt \n",
+ " kinase.klifs_id kinase.klifs_name \\\n",
+ "0 1 AKT1 \n",
"\n",
- " kinase.group kinase.class species.klifs \\\n",
- "0 AGC Human \n",
+ " kinase.full_name kinase.gene_name \\\n",
+ "0 v-akt murine thymoma viral oncogene homolog 1 AKT1 \n",
"\n",
- " kinase.full_name kinase.uniprot kinase.iuphar \\\n",
- "0 v-akt murine thymoma viral oncogene homolog 1 P31749 1479 \n",
+ " kinase.family kinase.group kinase.subfamily species.klifs kinase.uniprot \\\n",
+ "0 Akt AGC Human P31749 \n",
"\n",
- " kinase.pocket \n",
- "0 KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... "
+ " kinase.iuphar kinase.pocket \n",
+ "0 1479 KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... "
]
},
"execution_count": 23,
@@ -1529,12 +1631,12 @@
" | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
- " kinase.hgnc_name | \n",
+ " kinase.full_name | \n",
+ " kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
- " kinase.class | \n",
+ " kinase.subfamily | \n",
" species.klifs | \n",
- " kinase.full_name | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
" kinase.pocket | \n",
@@ -1545,12 +1647,12 @@
" 0 | \n",
" 1 | \n",
" AKT1 | \n",
+ " v-akt murine thymoma viral oncogene homolog 1 | \n",
" AKT1 | \n",
" Akt | \n",
" AGC | \n",
" | \n",
" Human | \n",
- " v-akt murine thymoma viral oncogene homolog 1 | \n",
" P31749 | \n",
" 1479 | \n",
" KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... | \n",
@@ -1559,12 +1661,12 @@
" 1 | \n",
" 2 | \n",
" AKT2 | \n",
+ " v-akt murine thymoma viral oncogene homolog 2 | \n",
" AKT2 | \n",
" Akt | \n",
" AGC | \n",
" | \n",
" Human | \n",
- " v-akt murine thymoma viral oncogene homolog 2 | \n",
" P31751 | \n",
" 1480 | \n",
" KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVME... | \n",
@@ -1574,21 +1676,21 @@
""
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- "0 1 AKT1 AKT1 Akt \n",
- "1 2 AKT2 AKT2 Akt \n",
+ " kinase.klifs_id kinase.klifs_name \\\n",
+ "0 1 AKT1 \n",
+ "1 2 AKT2 \n",
"\n",
- " kinase.group kinase.class species.klifs \\\n",
- "0 AGC Human \n",
- "1 AGC Human \n",
+ " kinase.full_name kinase.gene_name \\\n",
+ "0 v-akt murine thymoma viral oncogene homolog 1 AKT1 \n",
+ "1 v-akt murine thymoma viral oncogene homolog 2 AKT2 \n",
"\n",
- " kinase.full_name kinase.uniprot kinase.iuphar \\\n",
- "0 v-akt murine thymoma viral oncogene homolog 1 P31749 1479 \n",
- "1 v-akt murine thymoma viral oncogene homolog 2 P31751 1480 \n",
+ " kinase.family kinase.group kinase.subfamily species.klifs kinase.uniprot \\\n",
+ "0 Akt AGC Human P31749 \n",
+ "1 Akt AGC Human P31751 \n",
"\n",
- " kinase.pocket \n",
- "0 KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... \n",
- "1 KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVME... "
+ " kinase.iuphar kinase.pocket \n",
+ "0 1479 KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... \n",
+ "1 1480 KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVME... "
]
},
"execution_count": 24,
@@ -1632,26 +1734,6 @@
"execution_count": 26,
"metadata": {},
"outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Index(['species.klifs', 'structure.pdb_id', 'structure.alternate_model',\n",
- " 'structure.chain', 'ligand.expo_id', 'ligand_allosteric.expo_id',\n",
- " 'structure.rmsd1', 'structure.rmsd2', 'structure.qualityscore',\n",
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" kinase.pocket | \n",
@@ -1691,6 +1773,7 @@
" 0 | \n",
" 472 | \n",
" BMX | \n",
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@@ -1699,18 +1782,17 @@
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@@ -1730,26 +1812,6 @@
"execution_count": 27,
"metadata": {},
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- "Index(['species.klifs', 'structure.pdb_id', 'structure.alternate_model',\n",
- " 'structure.chain', 'ligand.expo_id', 'ligand_allosteric.expo_id',\n",
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- " 'ligand_allosteric.name', 'structure.dfg', 'structure.ac_helix',\n",
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" 0 | \n",
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+ " kinase.klifs_id kinase.klifs_name kinase.full_name kinase.gene_name \\\n",
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"\n",
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@@ -1849,20 +1911,6 @@
"name": "stdout",
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- "Index(['species.klifs', 'structure.pdb_id', 'structure.alternate_model',\n",
- " 'structure.chain', 'ligand.expo_id', 'ligand_allosteric.expo_id',\n",
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- " dtype='object')\n",
"Input values yield no results.\n"
]
}
@@ -1893,27 +1941,6 @@
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@@ -1937,12 +1964,12 @@
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+ " kinase.full_name | \n",
+ " kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
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" kinase.iuphar | \n",
" kinase.pocket | \n",
@@ -1953,12 +1980,12 @@
" 0 | \n",
" 574 | \n",
" BMX | \n",
+ " BMX non-receptor tyrosine kinase | \n",
" Bmx | \n",
" Tec | \n",
" TK | \n",
" | \n",
" Mouse | \n",
- " BMX non-receptor tyrosine kinase | \n",
" P97504 | \n",
" 0 | \n",
" KELGNGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... | \n",
@@ -1967,12 +1994,12 @@
" 1 | \n",
" 472 | \n",
" BMX | \n",
+ " BMX non-receptor tyrosine kinase | \n",
" BMX | \n",
" Tec | \n",
" TK | \n",
" | \n",
" Human | \n",
- " BMX non-receptor tyrosine kinase | \n",
" P51813 | \n",
" 1942 | \n",
" KELGSGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... | \n",
@@ -1982,13 +2009,13 @@
""
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+ " kinase.klifs_id kinase.klifs_name kinase.full_name \\\n",
+ "0 574 BMX BMX non-receptor tyrosine kinase \n",
+ "1 472 BMX BMX non-receptor tyrosine kinase \n",
"\n",
- " kinase.group kinase.class species.klifs kinase.full_name \\\n",
- "0 TK Mouse BMX non-receptor tyrosine kinase \n",
- "1 TK Human BMX non-receptor tyrosine kinase \n",
+ " kinase.gene_name kinase.family kinase.group kinase.subfamily species.klifs \\\n",
+ "0 Bmx Tec TK Mouse \n",
+ "1 BMX Tec TK Human \n",
"\n",
" kinase.uniprot kinase.iuphar \\\n",
"0 P97504 0 \n",
@@ -2013,27 +2040,6 @@
"execution_count": 30,
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@@ -2057,12 +2063,12 @@
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+ " kinase.full_name | \n",
+ " kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
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@@ -2073,12 +2079,12 @@
" 0 | \n",
" 574 | \n",
" BMX | \n",
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" | \n",
" Mouse | \n",
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@@ -2087,12 +2093,12 @@
" 1 | \n",
" 472 | \n",
" BMX | \n",
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" BMX | \n",
" Tec | \n",
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" | \n",
" Human | \n",
- " BMX non-receptor tyrosine kinase | \n",
" P51813 | \n",
" 1942 | \n",
" KELGSGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... | \n",
@@ -2102,13 +2108,13 @@
""
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+ " kinase.klifs_id kinase.klifs_name kinase.full_name \\\n",
+ "0 574 BMX BMX non-receptor tyrosine kinase \n",
+ "1 472 BMX BMX non-receptor tyrosine kinase \n",
"\n",
- " kinase.group kinase.class species.klifs kinase.full_name \\\n",
- "0 TK Mouse BMX non-receptor tyrosine kinase \n",
- "1 TK Human BMX non-receptor tyrosine kinase \n",
+ " kinase.gene_name kinase.family kinase.group kinase.subfamily species.klifs \\\n",
+ "0 Bmx Tec TK Mouse \n",
+ "1 BMX Tec TK Human \n",
"\n",
" kinase.uniprot kinase.iuphar \\\n",
"0 P97504 0 \n",
@@ -2133,35 +2139,11 @@
"execution_count": 31,
"metadata": {},
"outputs": [
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- "output_type": "stream",
- "text": [
- "ERROR:opencadd.databases.klifs.core:There was (were) 1/1 failed request(s).\n",
- "Show error messages (up to 5 messages only):\n",
- "ERROR:opencadd.databases.klifs.core:Error for BMX: Expected type to be dict for value [400, 'KLIFS error: The provided species does not exist. '] to unmarshal to a .Was instead.\n"
- ]
- },
{
"name": "stdout",
"output_type": "stream",
"text": [
- "\n",
- "Input values yield no results.\n"
+ "Expected type to be dict for value [400, 'KLIFS error: The provided species does not exist. '] to unmarshal to a .Was instead.\n"
]
}
],
@@ -2177,36 +2159,6 @@
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- "ERROR:opencadd.databases.klifs.core:Error for XXX: Expected type to be dict for value [400, 'KLIFS error: An unknown kinase name was provided'] to unmarshal to a .Was instead.\n"
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@@ -2230,12 +2182,12 @@
" | \n",
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@@ -2244,52 +2196,52 @@
" \n",
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- "
\n",
- " \n",
- " 1 | \n",
" 509 | \n",
" BRAF | \n",
+ " B-Raf proto-oncogene, serine/threonine kinase | \n",
" BRAF | \n",
" RAF | \n",
" TKL | \n",
" RAF | \n",
" Human | \n",
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" 1943 | \n",
" QRIGSGSFGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... | \n",
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+ " Tec | \n",
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+ " | \n",
+ " Human | \n",
+ " P51813 | \n",
+ " 1942 | \n",
+ " KELGSGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... | \n",
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- "0 472 BMX BMX Tec \n",
- "1 509 BRAF BRAF RAF \n",
+ " kinase.klifs_id kinase.klifs_name \\\n",
+ "0 509 BRAF \n",
+ "1 472 BMX \n",
"\n",
- " kinase.group kinase.class species.klifs \\\n",
- "0 TK Human \n",
- "1 TKL RAF Human \n",
+ " kinase.full_name kinase.gene_name \\\n",
+ "0 B-Raf proto-oncogene, serine/threonine kinase BRAF \n",
+ "1 BMX non-receptor tyrosine kinase BMX \n",
"\n",
- " kinase.full_name kinase.uniprot kinase.iuphar \\\n",
- "0 BMX non-receptor tyrosine kinase P51813 1942 \n",
- "1 B-Raf proto-oncogene, serine/threonine kinase P15056 1943 \n",
+ " kinase.family kinase.group kinase.subfamily species.klifs kinase.uniprot \\\n",
+ "0 RAF TKL RAF Human P15056 \n",
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"\n",
- " kinase.pocket \n",
- "0 KELGSGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... \n",
- "1 QRIGSGSFGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... "
+ " kinase.iuphar kinase.pocket \n",
+ "0 1943 QRIGSGSFGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... \n",
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},
"execution_count": 32,
@@ -2336,12 +2288,12 @@
" | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
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+ " kinase.full_name | \n",
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" kinase.family | \n",
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- " kinase.full_name | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
" kinase.pocket | \n",
@@ -2352,6 +2304,7 @@
" 0 | \n",
" 472 | \n",
" BMX | \n",
+ " <NA> | \n",
" BMX | \n",
" Tec | \n",
" TK | \n",
@@ -2360,18 +2313,17 @@
" <NA> | \n",
" <NA> | \n",
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- " kinase.klifs_id kinase.klifs_name kinase.hgnc_name kinase.family \\\n",
- "0 472 BMX BMX Tec \n",
+ " kinase.klifs_id kinase.klifs_name kinase.full_name kinase.gene_name \\\n",
+ "0 472 BMX BMX \n",
"\n",
- " kinase.group kinase.class species.klifs kinase.full_name kinase.uniprot \\\n",
- "0 TK Human \n",
+ " kinase.family kinase.group kinase.subfamily species.klifs kinase.uniprot \\\n",
+ "0 Tec TK Human \n",
"\n",
" kinase.iuphar kinase.pocket \n",
"0 "
@@ -2434,12 +2386,12 @@
" | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
- " kinase.hgnc_name | \n",
+ " kinase.full_name | \n",
+ " kinase.gene_name | \n",
" kinase.family | \n",
" kinase.group | \n",
- " kinase.class | \n",
+ " kinase.subfamily | \n",
" species.klifs | \n",
- " kinase.full_name | \n",
" kinase.uniprot | \n",
" kinase.iuphar | \n",
" kinase.pocket | \n",
@@ -2450,6 +2402,7 @@
" 0 | \n",
" 472 | \n",
" BMX | \n",
+ " <NA> | \n",
" BMX | \n",
" Tec | \n",
" TK | \n",
@@ -2458,12 +2411,12 @@
" <NA> | \n",
" <NA> | \n",
" <NA> | \n",
- " <NA> | \n",
" \n",
" \n",
" 1 | \n",
" 509 | \n",
" BRAF | \n",
+ " <NA> | \n",
" BRAF | \n",
" RAF | \n",
" TKL | \n",
@@ -2472,20 +2425,19 @@
" <NA> | \n",
" <NA> | \n",
" <NA> | \n",
- " <NA> | \n",
"
\n",
" \n",
"\n",
""
],
"text/plain": [
- " kinase.klifs_id kinase.klifs_name kinase.hgnc_name kinase.family \\\n",
- "0 472 BMX BMX Tec \n",
- "1 509 BRAF BRAF RAF \n",
+ " kinase.klifs_id kinase.klifs_name kinase.full_name kinase.gene_name \\\n",
+ "0 472 BMX BMX \n",
+ "1 509 BRAF BRAF \n",
"\n",
- " kinase.group kinase.class species.klifs kinase.full_name kinase.uniprot \\\n",
- "0 TK Human \n",
- "1 TKL Human \n",
+ " kinase.family kinase.group kinase.subfamily species.klifs kinase.uniprot \\\n",
+ "0 Tec TK Human \n",
+ "1 RAF TKL Human \n",
"\n",
" kinase.iuphar kinase.pocket \n",
"0 \n",
@@ -2583,24 +2535,24 @@
" ... | \n",
" \n",
" \n",
- " 3580 | \n",
- " 3871 | \n",
- " Q6G | \n",
- " Selpercatinib | \n",
- " O(c1ncc(cc1)CN2[C@H]3CN(c4ncc(cc4)C=5C=6N(N=CC... | \n",
- " InChI not available | \n",
+ " 3791 | \n",
+ " 4083 | \n",
+ " GC6 | \n",
+ " [(3R)-3-azanylpiperidin-1-yl]-[1-(2-azanylpyri... | \n",
+ " c1cc2c(cc1C#CC3(CCCCC3)O)n(cc2C(=O)N4CCC[C@H](... | \n",
+ " DADSGHOHYQROCR-LJQANCHMSA-N | \n",
"
\n",
" \n",
- " 3581 | \n",
- " 3872 | \n",
- " Q4J | \n",
- " Pralsetinib | \n",
- " FC=1C=NN(c2ncc(cc2)[C@@H](NC(=O)C3(OC)CCC(c4nc... | \n",
- " InChI not available | \n",
+ " 3792 | \n",
+ " 4082 | \n",
+ " ON6 | \n",
+ " (2~{Z})-6-[[2,6-bis(chloranyl)phenyl]methylsul... | \n",
+ " c1cc(c(c(c1)Cl)CS(=O)(=O)c2ccc3c(c2)NC(=O)/C(=... | \n",
+ " VUSCGLBHGBXFCC-NKVSQWTQSA-N | \n",
"
\n",
" \n",
"\n",
- "3582 rows × 5 columns
\n",
+ "3793 rows × 5 columns
\n",
""
],
"text/plain": [
@@ -2608,31 +2560,31 @@
"0 1 IHZ \n",
"1 2 477 \n",
"... ... ... \n",
- "3580 3871 Q6G \n",
- "3581 3872 Q4J \n",
+ "3791 4083 GC6 \n",
+ "3792 4082 ON6 \n",
"\n",
" ligand.name \\\n",
"0 5-[(2-methyl-5-{[3-(trifluoromethyl)phenyl]car... \n",
"1 3-{2-[5-(difluoromethyl)-2H-thieno[3,2-c]pyraz... \n",
"... ... \n",
- "3580 Selpercatinib \n",
- "3581 Pralsetinib \n",
+ "3791 [(3R)-3-azanylpiperidin-1-yl]-[1-(2-azanylpyri... \n",
+ "3792 (2~{Z})-6-[[2,6-bis(chloranyl)phenyl]methylsul... \n",
"\n",
" ligand.smiles \\\n",
"0 FC(F)(F)c1cc(NC(=O)c2cc(Nc3cncc(c3)C(=O)N)c(cc... \n",
"1 S1C=2C(=NNC2C=C1C(F)F)C=3Nc4c(ccc(c4)C(O)(CC)C... \n",
"... ... \n",
- "3580 O(c1ncc(cc1)CN2[C@H]3CN(c4ncc(cc4)C=5C=6N(N=CC... \n",
- "3581 FC=1C=NN(c2ncc(cc2)[C@@H](NC(=O)C3(OC)CCC(c4nc... \n",
+ "3791 c1cc2c(cc1C#CC3(CCCCC3)O)n(cc2C(=O)N4CCC[C@H](... \n",
+ "3792 c1cc(c(c(c1)Cl)CS(=O)(=O)c2ccc3c(c2)NC(=O)/C(=... \n",
"\n",
" ligand.inchikey \n",
"0 SAAYRHKJHDIDPH-UHFFFAOYSA-N \n",
"1 CQZZZUNOWZUNNG-UHFFFAOYSA-N \n",
"... ... \n",
- "3580 InChI not available \n",
- "3581 InChI not available \n",
+ "3791 DADSGHOHYQROCR-LJQANCHMSA-N \n",
+ "3792 VUSCGLBHGBXFCC-NKVSQWTQSA-N \n",
"\n",
- "[3582 rows x 5 columns]"
+ "[3793 rows x 5 columns]"
]
},
"execution_count": 36,
@@ -2711,6 +2663,14 @@
" <NA> | \n",
" <NA> | \n",
" \n",
+ " \n",
+ " 3 | \n",
+ " <NA> | \n",
+ " - | \n",
+ " - | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ "
\n",
" \n",
"\n",
""
@@ -2720,16 +2680,19 @@
"0 1N1 \n",
"1 QH1 \n",
"2 PRC \n",
+ "3 - \n",
"\n",
" ligand.name ligand.smiles \\\n",
"0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... \n",
"1 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... \n",
"2 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... \n",
+ "3 - \n",
"\n",
" ligand.inchikey \n",
"0 \n",
"1 \n",
- "2 "
+ "2 \n",
+ "3 "
]
},
"execution_count": 37,
@@ -2770,24 +2733,17 @@
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"version_minor": 0
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"text/plain": [
- "HBox(children=(HTML(value='Processing...'), FloatProgress(value=0.0, max=1.0), HTML(value='')))"
+ "Processing...: 0%| | 0/1 [00:00, ?it/s]"
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@@ -2888,12 +2844,12 @@
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- "HBox(children=(HTML(value='Processing...'), FloatProgress(value=0.0, max=3.0), HTML(value='')))"
+ "Processing...: 0%| | 0/3 [00:00, ?it/s]"
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@@ -2903,16 +2859,9 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "ERROR:opencadd.databases.klifs.core:There was (were) 1/3 failed request(s).\n",
+ "There was (were) 1/3 failed request(s).\n",
"Show error messages (up to 5 messages only):\n",
- "ERROR:opencadd.databases.klifs.core:Error for 10000: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a .Was instead.\n"
- ]
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "\n"
+ "Error for 10000: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a .Was instead.\n"
]
},
{
@@ -2973,26 +2922,26 @@
" ... | \n",
" \n",
" \n",
- " 64 | \n",
- " 3715 | \n",
- " QH1 | \n",
- " 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... | \n",
- " S(O)(O)(Nc1c(F)c(N2c3c(nc(N(C4C=CN(C(=O)C)C=C4... | \n",
+ " 68 | \n",
+ " 4028 | \n",
+ " VQP | \n",
+ " N-(3,3-dimethylbutyl)-N'-{2-fluoro-5-[(5-... | \n",
+ " Fc1c(Nc2c(cc(F)c(NC(=O)NCCC(C)(C)C)c2)C)ccc3N=... | \n",
" InChI not available | \n",
" 509 | \n",
"
\n",
" \n",
- " 65 | \n",
- " 3829 | \n",
- " E7M | \n",
- " 3-[(imidazo[1,2-b]pyridazin-3-yl)ethynyl]-4-me... | \n",
- " FC(F)(F)c1c(ccc(NC(=O)c2cc(C#CC=3N4N=CC=CC4=NC... | \n",
+ " 69 | \n",
+ " 4029 | \n",
+ " V5J | \n",
+ " 3-(2-cyanopropan-2-yl)-N-[2-fluoro-4-methyl-5-... | \n",
+ " Fc1c(NC(=O)c2cc(ccc2)C(C#N)(C)C)cc(c3cnc4c(c3)... | \n",
" InChI not available | \n",
" 509 | \n",
"
\n",
" \n",
"\n",
- "66 rows × 6 columns
\n",
+ "70 rows × 6 columns
\n",
""
],
"text/plain": [
@@ -3000,31 +2949,31 @@
"0 281 1N1 \n",
"1 632 PP2 \n",
".. ... ... \n",
- "64 3715 QH1 \n",
- "65 3829 E7M \n",
+ "68 4028 VQP \n",
+ "69 4029 V5J \n",
"\n",
" ligand.name \\\n",
"0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... \n",
"1 1-TERT-BUTYL-3-(4-CHLORO-PHENYL)-1H-PYRAZOLO[3... \n",
".. ... \n",
- "64 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... \n",
- "65 3-[(imidazo[1,2-b]pyridazin-3-yl)ethynyl]-4-me... \n",
+ "68 N-(3,3-dimethylbutyl)-N'-{2-fluoro-5-[(5-... \n",
+ "69 3-(2-cyanopropan-2-yl)-N-[2-fluoro-4-methyl-5-... \n",
"\n",
" ligand.smiles \\\n",
"0 Clc1c(NC(=O)C=2SC(=NC2)Nc3nc(nc(N4CCN(CCO)CC4)... \n",
"1 Clc1ccc(cc1)C2=[NH+]N(c3ncnc(N)c32)C(C)(C)C \n",
".. ... \n",
- "64 S(O)(O)(Nc1c(F)c(N2c3c(nc(N(C4C=CN(C(=O)C)C=C4... \n",
- "65 FC(F)(F)c1c(ccc(NC(=O)c2cc(C#CC=3N4N=CC=CC4=NC... \n",
+ "68 Fc1c(Nc2c(cc(F)c(NC(=O)NCCC(C)(C)C)c2)C)ccc3N=... \n",
+ "69 Fc1c(NC(=O)c2cc(ccc2)C(C#N)(C)C)cc(c3cnc4c(c3)... \n",
"\n",
" ligand.inchikey kinase.klifs_id (query) \n",
"0 ZBNZXTGUTAYRHI-UHFFFAOYSA-N 472 \n",
"1 PBBRWFOVCUAONR-UHFFFAOYSA-O 472 \n",
".. ... ... \n",
- "64 InChI not available 509 \n",
- "65 InChI not available 509 \n",
+ "68 InChI not available 509 \n",
+ "69 InChI not available 509 \n",
"\n",
- "[66 rows x 6 columns]"
+ "[70 rows x 6 columns]"
]
},
"execution_count": 39,
@@ -3044,12 +2993,12 @@
{
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"version_minor": 0
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"text/plain": [
- "HBox(children=(HTML(value='Processing...'), FloatProgress(value=0.0, max=1.0), HTML(value='')))"
+ "Processing...: 0%| | 0/1 [00:00, ?it/s]"
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@@ -3059,16 +3008,15 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "ERROR:opencadd.databases.klifs.core:There was (were) 1/1 failed request(s).\n",
+ "There was (were) 1/1 failed request(s).\n",
"Show error messages (up to 5 messages only):\n",
- "ERROR:opencadd.databases.klifs.core:Error for 10000: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a .Was instead.\n"
+ "Error for 10000: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a .Was instead.\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
- "\n",
"Input values yield no results.\n"
]
}
@@ -3274,50 +3222,15 @@
"execution_count": 44,
"metadata": {},
"outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "INFO:opencadd.databases.klifs.remote:Fetch kinase KLIFS IDs for input kinase names...\n"
- ]
- },
- {
- "data": {
- "application/vnd.jupyter.widget-view+json": {
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- ]
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- "metadata": {},
- "output_type": "display_data"
- },
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "INFO:opencadd.databases.klifs.remote:Fetch ligands based on these KLIFS IDs...\n"
- ]
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "\n"
- ]
- },
{
"data": {
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"version_minor": 0
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"text/plain": [
- "HBox(children=(HTML(value='Processing...'), FloatProgress(value=0.0, max=4.0), HTML(value='')))"
+ "Processing...: 0%| | 0/4 [00:00, ?it/s]"
]
},
"metadata": {},
@@ -3327,16 +3240,9 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "ERROR:opencadd.databases.klifs.core:There was (were) 1/4 failed request(s).\n",
+ "There was (were) 1/4 failed request(s).\n",
"Show error messages (up to 5 messages only):\n",
- "ERROR:opencadd.databases.klifs.core:Error for 574: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a .Was instead.\n"
- ]
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "\n"
+ "Error for 574: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a .Was instead.\n"
]
},
{
@@ -3367,33 +3273,33 @@
" ligand.inchikey | \n",
" kinase.klifs_id (query) | \n",
" kinase.klifs_name (query) | \n",
- " kinase.hgnc_name (query) | \n",
+ " kinase.gene_name (query) | \n",
" species.klifs (query) | \n",
" \n",
" \n",
" \n",
" \n",
" 0 | \n",
- " 26 | \n",
- " ADP | \n",
- " ADENOSINE-5'-DIPHOSPHATE | \n",
- " P(=O)(OP(=O)(O)O)(OC[C@H]1O[C@@H](N2c3ncnc(N)c... | \n",
- " XTWYTFMLZFPYCI-KQYNXXCUSA-N | \n",
- " 392 | \n",
- " ABL1 | \n",
- " ABL1 | \n",
+ " 281 | \n",
+ " 1N1 | \n",
+ " N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... | \n",
+ " Clc1c(NC(=O)C=2SC(=NC2)Nc3nc(nc(N4CCN(CCO)CC4)... | \n",
+ " ZBNZXTGUTAYRHI-UHFFFAOYSA-N | \n",
+ " 472 | \n",
+ " BMX | \n",
+ " BMX | \n",
" Human | \n",
"
\n",
" \n",
" 1 | \n",
- " 38 | \n",
- " AGS | \n",
- " PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER | \n",
- " S=P(OP(=O)(OP(=O)(OC[C@H]1O[C@@H](N2c3ncnc(N)c... | \n",
- " NLTUCYMLOPLUHL-KQYNXXCUSA-N | \n",
- " 392 | \n",
- " ABL1 | \n",
- " ABL1 | \n",
+ " 632 | \n",
+ " PP2 | \n",
+ " 1-TERT-BUTYL-3-(4-CHLORO-PHENYL)-1H-PYRAZOLO[3... | \n",
+ " Clc1ccc(cc1)C2=[NH+]N(c3ncnc(N)c32)C(C)(C)C | \n",
+ " PBBRWFOVCUAONR-UHFFFAOYSA-O | \n",
+ " 472 | \n",
+ " BMX | \n",
+ " BMX | \n",
" Human | \n",
"
\n",
" \n",
@@ -3409,71 +3315,71 @@
" ... | \n",
"
\n",
" \n",
- " 43 | \n",
- " 632 | \n",
- " PP2 | \n",
- " 1-TERT-BUTYL-3-(4-CHLORO-PHENYL)-1H-PYRAZOLO[3... | \n",
- " Clc1ccc(cc1)C2=[NH+]N(c3ncnc(N)c32)C(C)(C)C | \n",
- " PBBRWFOVCUAONR-UHFFFAOYSA-O | \n",
- " 472 | \n",
- " BMX | \n",
- " BMX | \n",
- " Human | \n",
+ " 45 | \n",
+ " 3247 | \n",
+ " FYH | \n",
+ " 3-(morpholin-4-ylmethyl)-~{N}-[4-(trifluoromet... | \n",
+ " FC(F)(F)Oc1ccc(NC(=O)c2cc(ccc2)CN3CCOCC3)cc1 | \n",
+ " MYWULUKAXYAFSH-UHFFFAOYSA-N | \n",
+ " 532 | \n",
+ " ABL1 | \n",
+ " Abl1 | \n",
+ " Mouse | \n",
"
\n",
" \n",
- " 44 | \n",
- " 3716 | \n",
- " H88 | \n",
- " ~{N}-[2-methyl-5-[8-[4-(methylsulfonylamino)ph... | \n",
- " S(=O)(=O)(Nc1ccc(c2cc3ncc4c(N(c5cc(NC(=O)CCO)c... | \n",
- " InChI not available | \n",
- " 472 | \n",
- " BMX | \n",
- " BMX | \n",
- " Human | \n",
+ " 46 | \n",
+ " 3255 | \n",
+ " FYW | \n",
+ " 6-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-5-pyrimi... | \n",
+ " c1cc(ccc1NC(=O)c2cc(c(nc2)N3CC[C@H](C3)O)c4cnc... | \n",
+ " LARFZNXVNANWFD-MRXNPFEDSA-N | \n",
+ " 532 | \n",
+ " ABL1 | \n",
+ " Abl1 | \n",
+ " Mouse | \n",
"
\n",
" \n",
"\n",
- "45 rows × 9 columns
\n",
+ "47 rows × 9 columns
\n",
""
],
"text/plain": [
" ligand.klifs_id ligand.expo_id \\\n",
- "0 26 ADP \n",
- "1 38 AGS \n",
+ "0 281 1N1 \n",
+ "1 632 PP2 \n",
".. ... ... \n",
- "43 632 PP2 \n",
- "44 3716 H88 \n",
+ "45 3247 FYH \n",
+ "46 3255 FYW \n",
"\n",
" ligand.name \\\n",
- "0 ADENOSINE-5'-DIPHOSPHATE \n",
- "1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER \n",
+ "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... \n",
+ "1 1-TERT-BUTYL-3-(4-CHLORO-PHENYL)-1H-PYRAZOLO[3... \n",
".. ... \n",
- "43 1-TERT-BUTYL-3-(4-CHLORO-PHENYL)-1H-PYRAZOLO[3... \n",
- "44 ~{N}-[2-methyl-5-[8-[4-(methylsulfonylamino)ph... \n",
+ "45 3-(morpholin-4-ylmethyl)-~{N}-[4-(trifluoromet... \n",
+ "46 6-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-5-pyrimi... \n",
"\n",
" ligand.smiles \\\n",
- "0 P(=O)(OP(=O)(O)O)(OC[C@H]1O[C@@H](N2c3ncnc(N)c... \n",
- "1 S=P(OP(=O)(OP(=O)(OC[C@H]1O[C@@H](N2c3ncnc(N)c... \n",
+ "0 Clc1c(NC(=O)C=2SC(=NC2)Nc3nc(nc(N4CCN(CCO)CC4)... \n",
+ "1 Clc1ccc(cc1)C2=[NH+]N(c3ncnc(N)c32)C(C)(C)C \n",
".. ... \n",
- "43 Clc1ccc(cc1)C2=[NH+]N(c3ncnc(N)c32)C(C)(C)C \n",
- "44 S(=O)(=O)(Nc1ccc(c2cc3ncc4c(N(c5cc(NC(=O)CCO)c... \n",
+ "45 FC(F)(F)Oc1ccc(NC(=O)c2cc(ccc2)CN3CCOCC3)cc1 \n",
+ "46 c1cc(ccc1NC(=O)c2cc(c(nc2)N3CC[C@H](C3)O)c4cnc... \n",
"\n",
" ligand.inchikey kinase.klifs_id (query) \\\n",
- "0 XTWYTFMLZFPYCI-KQYNXXCUSA-N 392 \n",
- "1 NLTUCYMLOPLUHL-KQYNXXCUSA-N 392 \n",
+ "0 ZBNZXTGUTAYRHI-UHFFFAOYSA-N 472 \n",
+ "1 PBBRWFOVCUAONR-UHFFFAOYSA-O 472 \n",
".. ... ... \n",
- "43 PBBRWFOVCUAONR-UHFFFAOYSA-O 472 \n",
- "44 InChI not available 472 \n",
+ "45 MYWULUKAXYAFSH-UHFFFAOYSA-N 532 \n",
+ "46 LARFZNXVNANWFD-MRXNPFEDSA-N 532 \n",
"\n",
- " kinase.klifs_name (query) kinase.hgnc_name (query) species.klifs (query) \n",
- "0 ABL1 ABL1 Human \n",
- "1 ABL1 ABL1 Human \n",
+ " kinase.klifs_name (query) kinase.gene_name (query) species.klifs (query) \n",
+ "0 BMX BMX Human \n",
+ "1 BMX BMX Human \n",
".. ... ... ... \n",
- "43 BMX BMX Human \n",
- "44 BMX BMX Human \n",
+ "45 ABL1 Abl1 Mouse \n",
+ "46 ABL1 Abl1 Mouse \n",
"\n",
- "[45 rows x 9 columns]"
+ "[47 rows x 9 columns]"
]
},
"execution_count": 44,
@@ -3490,42 +3396,11 @@
"execution_count": 45,
"metadata": {},
"outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "INFO:opencadd.databases.klifs.remote:Fetch kinase KLIFS IDs for input kinase names...\n"
- ]
- },
- {
- "data": {
- "application/vnd.jupyter.widget-view+json": {
- "model_id": "35833ed4ad6d4e24a95100311633c2e5",
- "version_major": 2,
- "version_minor": 0
- },
- "text/plain": [
- "HBox(children=(HTML(value='Processing...'), FloatProgress(value=0.0, max=1.0), HTML(value='')))"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- },
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "ERROR:opencadd.databases.klifs.core:There was (were) 1/1 failed request(s).\n",
- "Show error messages (up to 5 messages only):\n",
- "ERROR:opencadd.databases.klifs.core:Error for XXX: Expected type to be dict for value [400, 'KLIFS error: An unknown kinase name was provided'] to unmarshal to a .Was instead.\n"
- ]
- },
{
"name": "stdout",
"output_type": "stream",
"text": [
- "\n",
- "Input values yield no results.\n"
+ "Expected type to be dict for value [400, 'KLIFS error: An unknown kinase name was provided'] to unmarshal to a .Was instead.\n"
]
}
],
@@ -3575,7 +3450,7 @@
" ligand.smiles | \n",
" ligand.inchikey | \n",
" kinase.klifs_name (query) | \n",
- " kinase.hgnc_name (query) | \n",
+ " kinase.gene_name (query) | \n",
" species.klifs (query) | \n",
" \n",
" \n",
@@ -3615,7 +3490,7 @@
"0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... \n",
"1 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... \n",
"\n",
- " ligand.inchikey kinase.klifs_name (query) kinase.hgnc_name (query) \\\n",
+ " ligand.inchikey kinase.klifs_name (query) kinase.gene_name (query) \\\n",
"0 BMX BMX \n",
"1 ABL1 Abl1 \n",
"\n",
@@ -4041,11 +3916,14 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
" ligand.expo_id | \n",
" ligand_allosteric.expo_id | \n",
+ " ligand.klifs_id | \n",
+ " ligand_allosteric.klifs_id | \n",
" ligand.name | \n",
" ligand_allosteric.name | \n",
" structure.dfg | \n",
@@ -4056,6 +3934,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -4075,34 +3954,39 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
" \n",
" \n",
" \n",
" \n",
" 0 | \n",
- " 2542 | \n",
- " 4ejn | \n",
- " - | \n",
+ " 6765 | \n",
+ " 3cqw | \n",
+ " B | \n",
" A | \n",
" Human | \n",
" 1 | \n",
" AKT1 | \n",
" <NA> | \n",
" <NA> | \n",
- " KLLGKGTFGKVILYAMKIL_______VLQNSRPFLTALKYSCFVME... | \n",
+ " <NA> | \n",
+ " KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... | \n",
+ " CQW | \n",
" - | \n",
- " 0R4 | \n",
+ " 2147 | \n",
+ " 0 | \n",
" <NA> | \n",
" <NA> | \n",
- " out | \n",
- " na | \n",
- " 2.19 | \n",
- " 4.4 | \n",
- " 7 | \n",
- " 22 | \n",
- " 0.950 | \n",
- " 2.319 | \n",
- " False | \n",
+ " in | \n",
+ " in | \n",
+ " 2.0 | \n",
+ " 8.0 | \n",
+ " 0 | \n",
+ " 0 | \n",
+ " 0.779 | \n",
+ " 2.093 | \n",
+ " <NA> | \n",
+ " True | \n",
" False | \n",
" False | \n",
" False | \n",
@@ -4117,35 +4001,40 @@
" False | \n",
" False | \n",
" False | \n",
- " 18.979799 | \n",
- " 65.341499 | \n",
- " 56.192699 | \n",
+ " 17.943501 | \n",
+ " 58.283501 | \n",
+ " 52.774200 | \n",
" <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" 1 | \n",
- " 10881 | \n",
- " 6npz | \n",
- " A | \n",
+ " 10429 | \n",
+ " 6c0i | \n",
+ " C | \n",
" B | \n",
" Human | \n",
" 1 | \n",
" AKT1 | \n",
" <NA> | \n",
" <NA> | \n",
+ " <NA> | \n",
" KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... | \n",
" - | \n",
" - | \n",
+ " 0 | \n",
+ " 0 | \n",
" <NA> | \n",
" <NA> | \n",
" in | \n",
" in | \n",
- " 2.12 | \n",
+ " 2.4 | \n",
" 8.0 | \n",
" 0 | \n",
" 0 | \n",
" 0.776 | \n",
- " 2.092 | \n",
+ " 2.091 | \n",
+ " <NA> | \n",
" False | \n",
" False | \n",
" False | \n",
@@ -4161,10 +4050,11 @@
" False | \n",
" False | \n",
" False | \n",
- " 17.940701 | \n",
- " 60.261398 | \n",
- " 66.135399 | \n",
+ " 17.901100 | \n",
+ " 59.594799 | \n",
+ " 60.872501 | \n",
" <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" ... | \n",
@@ -4209,9 +4099,14 @@
" ... | \n",
" ... | \n",
" ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
"
\n",
" \n",
- " 11776 | \n",
+ " 12519 | \n",
" 9070 | \n",
" 6bq1 | \n",
" - | \n",
@@ -4221,12 +4116,15 @@
" PI4KA | \n",
" <NA> | \n",
" <NA> | \n",
+ " <NA> | \n",
" _PMQSAAKAPYLAAIFKVGDCRQDMLALQIIDLFVFPYRVVCGVIE... | \n",
" E4S | \n",
" - | \n",
+ " 2974 | \n",
+ " 0 | \n",
" <NA> | \n",
" <NA> | \n",
- " in | \n",
+ " out-like | \n",
" in | \n",
" NaN | \n",
" 6.8 | \n",
@@ -4234,6 +4132,7 @@
" 0 | \n",
" 1.704 | \n",
" 2.676 | \n",
+ " <NA> | \n",
" True | \n",
" False | \n",
" False | \n",
@@ -4253,9 +4152,10 @@
" 58.963501 | \n",
" 131.186996 | \n",
" <NA> | \n",
+ " False | \n",
"
\n",
" \n",
- " 11777 | \n",
+ " 12520 | \n",
" 9069 | \n",
" 6bq1 | \n",
" - | \n",
@@ -4265,12 +4165,15 @@
" PI4KA | \n",
" <NA> | \n",
" <NA> | \n",
+ " <NA> | \n",
" _PMQSAAKAPYLAAIFKVGDCRQDMLALQIIDLFVFPYRVVCGVIE... | \n",
" E4S | \n",
" - | \n",
+ " 2974 | \n",
+ " 0 | \n",
" <NA> | \n",
" <NA> | \n",
- " in | \n",
+ " out-like | \n",
" in | \n",
" NaN | \n",
" 6.8 | \n",
@@ -4278,6 +4181,7 @@
" 0 | \n",
" 1.699 | \n",
" 2.670 | \n",
+ " <NA> | \n",
" True | \n",
" True | \n",
" False | \n",
@@ -4297,112 +4201,120 @@
" 58.645401 | \n",
" 136.503006 | \n",
" <NA> | \n",
+ " False | \n",
"
\n",
" \n",
"\n",
- "11778 rows × 41 columns
\n",
+ "12521 rows × 46 columns
\n",
""
],
"text/plain": [
" structure.klifs_id structure.pdb_id structure.alternate_model \\\n",
- "0 2542 4ejn - \n",
- "1 10881 6npz A \n",
+ "0 6765 3cqw B \n",
+ "1 10429 6c0i C \n",
"... ... ... ... \n",
- "11776 9070 6bq1 - \n",
- "11777 9069 6bq1 - \n",
+ "12519 9070 6bq1 - \n",
+ "12520 9069 6bq1 - \n",
"\n",
" structure.chain species.klifs kinase.klifs_id kinase.klifs_name \\\n",
"0 A Human 1 AKT1 \n",
"1 B Human 1 AKT1 \n",
"... ... ... ... ... \n",
- "11776 A Human 1096 PI4KA \n",
- "11777 E Human 1096 PI4KA \n",
+ "12519 A Human 1096 PI4KA \n",
+ "12520 E Human 1096 PI4KA \n",
"\n",
- " kinase.family kinase.group \\\n",
- "0 \n",
- "1 \n",
- "... ... ... \n",
- "11776 \n",
- "11777 \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 \n",
+ "1 \n",
+ "... ... ... ... \n",
+ "12519 \n",
+ "12520 \n",
"\n",
" structure.pocket ligand.expo_id \\\n",
- "0 KLLGKGTFGKVILYAMKIL_______VLQNSRPFLTALKYSCFVME... - \n",
+ "0 KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... CQW \n",
"1 KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME... - \n",
"... ... ... \n",
- "11776 _PMQSAAKAPYLAAIFKVGDCRQDMLALQIIDLFVFPYRVVCGVIE... E4S \n",
- "11777 _PMQSAAKAPYLAAIFKVGDCRQDMLALQIIDLFVFPYRVVCGVIE... E4S \n",
- "\n",
- " ligand_allosteric.expo_id ligand.name ligand_allosteric.name \\\n",
- "0 0R4 \n",
- "1 - \n",
- "... ... ... ... \n",
- "11776 - \n",
- "11777 - \n",
- "\n",
- " structure.dfg structure.ac_helix structure.resolution \\\n",
- "0 out na 2.19 \n",
- "1 in in 2.12 \n",
- "... ... ... ... \n",
- "11776 in in NaN \n",
- "11777 in in NaN \n",
- "\n",
- " structure.qualityscore structure.missing_residues \\\n",
- "0 4.4 7 \n",
- "1 8.0 0 \n",
- "... ... ... \n",
- "11776 6.8 2 \n",
- "11777 6.8 2 \n",
- "\n",
- " structure.missing_atoms structure.rmsd1 structure.rmsd2 \\\n",
- "0 22 0.950 2.319 \n",
- "1 0 0.776 2.092 \n",
- "... ... ... ... \n",
- "11776 0 1.704 2.676 \n",
- "11777 0 1.699 2.670 \n",
- "\n",
- " structure.front structure.gate structure.back structure.fp_i \\\n",
- "0 False False False False \n",
- "1 False False False False \n",
- "... ... ... ... ... \n",
- "11776 True False False False \n",
- "11777 True True False False \n",
- "\n",
- " structure.fp_ii structure.bp_i_a structure.bp_i_b \\\n",
- "0 False False False \n",
- "1 False False False \n",
- "... ... ... ... \n",
- "11776 False False True \n",
- "11777 False True True \n",
- "\n",
- " structure.bp_ii_in structure.bp_ii_a_in structure.bp_ii_b_in \\\n",
- "0 False False False \n",
- "1 False False False \n",
- "... ... ... ... \n",
- "11776 False False False \n",
- "11777 False False False \n",
- "\n",
- " structure.bp_ii_out structure.bp_ii_b structure.bp_iii \\\n",
- "0 False False False \n",
- "1 False False False \n",
- "... ... ... ... \n",
- "11776 False False False \n",
- "11777 False False False \n",
- "\n",
- " structure.bp_iv structure.bp_v structure.grich_distance \\\n",
- "0 False False 18.979799 \n",
- "1 False False 17.940701 \n",
- "... ... ... ... \n",
- "11776 False False 18.324301 \n",
- "11777 False False 18.168600 \n",
- "\n",
- " structure.grich_angle structure.grich_rotation structure.filepath \n",
- "0 65.341499 56.192699 \n",
- "1 60.261398 66.135399 \n",
- "... ... ... ... \n",
- "11776 58.963501 131.186996 \n",
- "11777 58.645401 136.503006 \n",
- "\n",
- "[11778 rows x 41 columns]"
+ "12519 _PMQSAAKAPYLAAIFKVGDCRQDMLALQIIDLFVFPYRVVCGVIE... E4S \n",
+ "12520 _PMQSAAKAPYLAAIFKVGDCRQDMLALQIIDLFVFPYRVVCGVIE... E4S \n",
+ "\n",
+ " ligand_allosteric.expo_id ligand.klifs_id ligand_allosteric.klifs_id \\\n",
+ "0 - 2147 0 \n",
+ "1 - 0 0 \n",
+ "... ... ... ... \n",
+ "12519 - 2974 0 \n",
+ "12520 - 2974 0 \n",
+ "\n",
+ " ligand.name ligand_allosteric.name structure.dfg structure.ac_helix \\\n",
+ "0 in in \n",
+ "1 in in \n",
+ "... ... ... ... ... \n",
+ "12519 out-like in \n",
+ "12520 out-like in \n",
+ "\n",
+ " structure.resolution structure.qualityscore \\\n",
+ "0 2.0 8.0 \n",
+ "1 2.4 8.0 \n",
+ "... ... ... \n",
+ "12519 NaN 6.8 \n",
+ "12520 NaN 6.8 \n",
+ "\n",
+ " structure.missing_residues structure.missing_atoms structure.rmsd1 \\\n",
+ "0 0 0 0.779 \n",
+ "1 0 0 0.776 \n",
+ "... ... ... ... \n",
+ "12519 2 0 1.704 \n",
+ "12520 2 0 1.699 \n",
+ "\n",
+ " structure.rmsd2 interaction.fingerprint structure.front \\\n",
+ "0 2.093 True \n",
+ "1 2.091 False \n",
+ "... ... ... ... \n",
+ "12519 2.676 True \n",
+ "12520 2.670 True \n",
+ "\n",
+ " structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
+ "0 False False False False \n",
+ "1 False False False False \n",
+ "... ... ... ... ... \n",
+ "12519 False False False False \n",
+ "12520 True False False False \n",
+ "\n",
+ " structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
+ "0 False False False \n",
+ "1 False False False \n",
+ "... ... ... ... \n",
+ "12519 False True False \n",
+ "12520 True True False \n",
+ "\n",
+ " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
+ "0 False False False \n",
+ "1 False False False \n",
+ "... ... ... ... \n",
+ "12519 False False False \n",
+ "12520 False False False \n",
+ "\n",
+ " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
+ "0 False False False False \n",
+ "1 False False False False \n",
+ "... ... ... ... ... \n",
+ "12519 False False False False \n",
+ "12520 False False False False \n",
+ "\n",
+ " structure.grich_distance structure.grich_angle \\\n",
+ "0 17.943501 58.283501 \n",
+ "1 17.901100 59.594799 \n",
+ "... ... ... \n",
+ "12519 18.324301 58.963501 \n",
+ "12520 18.168600 58.645401 \n",
+ "\n",
+ " structure.grich_rotation structure.filepath structure.curation_flag \n",
+ "0 52.774200 False \n",
+ "1 60.872501 False \n",
+ "... ... ... ... \n",
+ "12519 131.186996 False \n",
+ "12520 136.503006 False \n",
+ "\n",
+ "[12521 rows x 46 columns]"
]
},
"execution_count": 54,
@@ -4456,11 +4368,14 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
" ligand.expo_id | \n",
" ligand_allosteric.expo_id | \n",
+ " ligand.klifs_id | \n",
+ " ligand_allosteric.klifs_id | \n",
" ligand.name | \n",
" ligand_allosteric.name | \n",
" structure.dfg | \n",
@@ -4471,6 +4386,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -4490,6 +4406,7 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
" \n",
" \n",
" \n",
@@ -4502,11 +4419,14 @@
" Human | \n",
" 472 | \n",
" BMX | \n",
+ " ['BMX'] | \n",
" Tec | \n",
" TK | \n",
" KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... | \n",
" 1N1 | \n",
" - | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... | \n",
" - | \n",
" out-like | \n",
@@ -4517,6 +4437,7 @@
" 0 | \n",
" 0.839 | \n",
" 1.967 | \n",
+ " 0000000000000010000001000000000000000000000000... | \n",
" <NA> | \n",
" <NA> | \n",
" <NA> | \n",
@@ -4536,6 +4457,7 @@
" NaN | \n",
" NaN | \n",
" HUMAN/BMX/3sxr_chainA | \n",
+ " <NA> | \n",
" \n",
" \n",
" 1 | \n",
@@ -4546,11 +4468,14 @@
" Human | \n",
" 509 | \n",
" BRAF | \n",
+ " ['BRAF'] | \n",
" RAF | \n",
" TKL | \n",
" QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... | \n",
" QH1 | \n",
" - | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... | \n",
" - | \n",
" in | \n",
@@ -4561,6 +4486,7 @@
" 61 | \n",
" 0.806 | \n",
" 2.028 | \n",
+ " 0000000000000000000000000000000000000000000000... | \n",
" <NA> | \n",
" <NA> | \n",
" <NA> | \n",
@@ -4580,189 +4506,274 @@
" NaN | \n",
" NaN | \n",
" HUMAN/BRAF/6uuo_chainA | \n",
+ " <NA> | \n",
"
\n",
" \n",
- " 2 | \n",
- " 5728 | \n",
- " 1fpu | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ "
\n",
+ " \n",
+ " 4 | \n",
+ " 13623 | \n",
+ " 7lht | \n",
" - | \n",
" A | \n",
- " Mouse | \n",
- " 532 | \n",
- " ABL1 | \n",
- " Abl | \n",
- " TK | \n",
- " HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... | \n",
- " PRC | \n",
+ " Human | \n",
+ " 495 | \n",
+ " LRRK2 | \n",
+ " ['LRRK2'] | \n",
+ " LRRK | \n",
+ " TKL | \n",
+ " KALGKGLFSMVIRITLKVVGLRILNLPHLILEYCKAKDIIRFLQQK... | \n",
" - | \n",
- " N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... | \n",
+ " ATP | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" - | \n",
+ " ADENOSINE-5'-TRIPHOSPHATE | \n",
" out | \n",
" out | \n",
- " 2.40 | \n",
- " 8.8 | \n",
+ " 3.50 | \n",
+ " 4.0 | \n",
" 0 | \n",
- " 8 | \n",
- " 0.925 | \n",
- " 2.319 | \n",
+ " 0 | \n",
+ " 10.267 | \n",
+ " 15.045 | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" <NA> | \n",
" <NA> | \n",
" <NA> | \n",
- " False | \n",
- " False | \n",
- " True | \n",
- " True | \n",
- " False | \n",
- " False | \n",
- " False | \n",
- " True | \n",
- " False | \n",
- " False | \n",
- " False | \n",
- " False | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
- " MOUSE/ABL1/1fpu_chainA | \n",
+ " HUMAN/LRRK2/7lht_chainA | \n",
+ " <NA> | \n",
"
\n",
" \n",
- " 3 | \n",
- " 5705 | \n",
- " 1fpu | \n",
+ " 5 | \n",
+ " 1243 | \n",
+ " 2ogv | \n",
" - | \n",
- " B | \n",
- " Mouse | \n",
- " 532 | \n",
- " ABL1 | \n",
- " Abl | \n",
+ " A | \n",
+ " Human | \n",
+ " 449 | \n",
+ " FMS | \n",
+ " ['CSF1R', 'FMS'] | \n",
+ " PDGFR | \n",
" TK | \n",
- " HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... | \n",
- " PRC | \n",
+ " KTLGAGAFGKVVEVAVKMLALMSELKIMSHLGENIVNLLGALVITE... | \n",
+ " - | \n",
+ " - | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" - | \n",
- " N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... | \n",
" - | \n",
" out | \n",
- " out | \n",
- " 2.40 | \n",
- " 9.2 | \n",
+ " in | \n",
+ " 2.70 | \n",
+ " 6.4 | \n",
+ " 2 | \n",
" 0 | \n",
- " 4 | \n",
- " 0.925 | \n",
- " 2.329 | \n",
+ " 1.043 | \n",
+ " 2.362 | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" <NA> | \n",
" <NA> | \n",
" <NA> | \n",
- " False | \n",
- " False | \n",
- " False | \n",
- " True | \n",
- " False | \n",
- " False | \n",
- " False | \n",
- " True | \n",
- " False | \n",
- " False | \n",
- " False | \n",
- " False | \n",
" NaN | \n",
" NaN | \n",
" NaN | \n",
- " MOUSE/ABL1/1fpu_chainB | \n",
+ " HUMAN/FMS/2ogv_chainA | \n",
+ " <NA> | \n",
"
\n",
" \n",
"\n",
+ "6 rows × 46 columns
\n",
""
],
"text/plain": [
- " structure.klifs_id structure.pdb_id structure.alternate_model \\\n",
- "0 3482 3sxr - \n",
- "1 12347 6uuo - \n",
- "2 5728 1fpu - \n",
- "3 5705 1fpu - \n",
- "\n",
- " structure.chain species.klifs kinase.klifs_id kinase.klifs_name \\\n",
- "0 A Human 472 BMX \n",
- "1 A Human 509 BRAF \n",
- "2 A Mouse 532 ABL1 \n",
- "3 B Mouse 532 ABL1 \n",
- "\n",
- " kinase.family kinase.group \\\n",
- "0 Tec TK \n",
- "1 RAF TKL \n",
- "2 Abl TK \n",
- "3 Abl TK \n",
- "\n",
- " structure.pocket ligand.expo_id \\\n",
- "0 KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... 1N1 \n",
- "1 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... QH1 \n",
- "2 HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... PRC \n",
- "3 HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... PRC \n",
- "\n",
- " ligand_allosteric.expo_id \\\n",
- "0 - \n",
- "1 - \n",
- "2 - \n",
- "3 - \n",
- "\n",
- " ligand.name ligand_allosteric.name \\\n",
- "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... - \n",
- "1 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... - \n",
- "2 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... - \n",
- "3 N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]... - \n",
- "\n",
- " structure.dfg structure.ac_helix structure.resolution \\\n",
- "0 out-like in 2.40 \n",
- "1 in out-like 3.29 \n",
- "2 out out 2.40 \n",
- "3 out out 2.40 \n",
- "\n",
- " structure.qualityscore structure.missing_residues \\\n",
- "0 6.4 4 \n",
- "1 5.2 7 \n",
- "2 8.8 0 \n",
- "3 9.2 0 \n",
- "\n",
- " structure.missing_atoms structure.rmsd1 structure.rmsd2 structure.front \\\n",
- "0 0 0.839 1.967 \n",
- "1 61 0.806 2.028 \n",
- "2 8 0.925 2.319 \n",
- "3 4 0.925 2.329 \n",
- "\n",
- " structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
- "0 False False \n",
- "1 False False \n",
- "2 False False \n",
- "3 False False \n",
+ " structure.klifs_id structure.pdb_id structure.alternate_model \\\n",
+ "0 3482 3sxr - \n",
+ "1 12347 6uuo - \n",
+ ".. ... ... ... \n",
+ "4 13623 7lht - \n",
+ "5 1243 2ogv - \n",
"\n",
- " structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
- "0 True True False \n",
- "1 True True True \n",
- "2 True True False \n",
- "3 False True False \n",
+ " structure.chain species.klifs kinase.klifs_id kinase.klifs_name \\\n",
+ "0 A Human 472 BMX \n",
+ "1 A Human 509 BRAF \n",
+ ".. ... ... ... ... \n",
+ "4 A Human 495 LRRK2 \n",
+ "5 A Human 449 FMS \n",
"\n",
- " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
- "0 False False False \n",
- "1 True False False \n",
- "2 False False True \n",
- "3 False False True \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 ['BMX'] Tec TK \n",
+ "1 ['BRAF'] RAF TKL \n",
+ ".. ... ... ... \n",
+ "4 ['LRRK2'] LRRK TKL \n",
+ "5 ['CSF1R', 'FMS'] PDGFR TK \n",
"\n",
- " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
- "0 False False False False \n",
- "1 False False False False \n",
- "2 False False False False \n",
- "3 False False False False \n",
+ " structure.pocket ligand.expo_id \\\n",
+ "0 KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE... 1N1 \n",
+ "1 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... QH1 \n",
+ ".. ... ... \n",
+ "4 KALGKGLFSMVIRITLKVVGLRILNLPHLILEYCKAKDIIRFLQQK... - \n",
+ "5 KTLGAGAFGKVVEVAVKMLALMSELKIMSHLGENIVNLLGALVITE... - \n",
"\n",
- " structure.grich_distance structure.grich_angle structure.grich_rotation \\\n",
- "0 NaN NaN NaN \n",
- "1 NaN NaN NaN \n",
- "2 NaN NaN NaN \n",
- "3 NaN NaN NaN \n",
+ " ligand_allosteric.expo_id ligand.klifs_id ligand_allosteric.klifs_id \\\n",
+ "0 - \n",
+ "1 - \n",
+ ".. ... ... ... \n",
+ "4 ATP \n",
+ "5 - \n",
"\n",
- " structure.filepath \n",
- "0 HUMAN/BMX/3sxr_chainA \n",
- "1 HUMAN/BRAF/6uuo_chainA \n",
- "2 MOUSE/ABL1/1fpu_chainA \n",
- "3 MOUSE/ABL1/1fpu_chainB "
+ " ligand.name \\\n",
+ "0 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX... \n",
+ "1 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... \n",
+ ".. ... \n",
+ "4 - \n",
+ "5 - \n",
+ "\n",
+ " ligand_allosteric.name structure.dfg structure.ac_helix \\\n",
+ "0 - out-like in \n",
+ "1 - in out-like \n",
+ ".. ... ... ... \n",
+ "4 ADENOSINE-5'-TRIPHOSPHATE out out \n",
+ "5 - out in \n",
+ "\n",
+ " structure.resolution structure.qualityscore structure.missing_residues \\\n",
+ "0 2.40 6.4 4 \n",
+ "1 3.29 5.2 7 \n",
+ ".. ... ... ... \n",
+ "4 3.50 4.0 0 \n",
+ "5 2.70 6.4 2 \n",
+ "\n",
+ " structure.missing_atoms structure.rmsd1 structure.rmsd2 \\\n",
+ "0 0 0.839 1.967 \n",
+ "1 61 0.806 2.028 \n",
+ ".. ... ... ... \n",
+ "4 0 10.267 15.045 \n",
+ "5 0 1.043 2.362 \n",
+ "\n",
+ " interaction.fingerprint structure.front \\\n",
+ "0 0000000000000010000001000000000000000000000000... \n",
+ "1 0000000000000000000000000000000000000000000000... \n",
+ ".. ... ... \n",
+ "4 \n",
+ "5 \n",
+ "\n",
+ " structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
+ "0 False False \n",
+ "1 False False \n",
+ ".. ... ... ... ... \n",
+ "4 \n",
+ "5 \n",
+ "\n",
+ " structure.bp_i_a structure.bp_i_b structure.bp_ii_in \\\n",
+ "0 True True False \n",
+ "1 True True True \n",
+ ".. ... ... ... \n",
+ "4 \n",
+ "5 \n",
+ "\n",
+ " structure.bp_ii_a_in structure.bp_ii_b_in structure.bp_ii_out \\\n",
+ "0 False False False \n",
+ "1 True False False \n",
+ ".. ... ... ... \n",
+ "4 \n",
+ "5 \n",
+ "\n",
+ " structure.bp_ii_b structure.bp_iii structure.bp_iv structure.bp_v \\\n",
+ "0 False False False False \n",
+ "1 False False False False \n",
+ ".. ... ... ... ... \n",
+ "4 \n",
+ "5 \n",
+ "\n",
+ " structure.grich_distance structure.grich_angle structure.grich_rotation \\\n",
+ "0 NaN NaN NaN \n",
+ "1 NaN NaN NaN \n",
+ ".. ... ... ... \n",
+ "4 NaN NaN NaN \n",
+ "5 NaN NaN NaN \n",
+ "\n",
+ " structure.filepath structure.curation_flag \n",
+ "0 HUMAN/BMX/3sxr_chainA \n",
+ "1 HUMAN/BRAF/6uuo_chainA \n",
+ ".. ... ... \n",
+ "4 HUMAN/LRRK2/7lht_chainA \n",
+ "5 HUMAN/FMS/2ogv_chainA \n",
+ "\n",
+ "[6 rows x 46 columns]"
]
},
"execution_count": 55,
@@ -4821,11 +4832,14 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
" ligand.expo_id | \n",
" ligand_allosteric.expo_id | \n",
+ " ligand.klifs_id | \n",
+ " ligand_allosteric.klifs_id | \n",
" ligand.name | \n",
" ligand_allosteric.name | \n",
" structure.dfg | \n",
@@ -4836,6 +4850,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -4855,6 +4870,7 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
" \n",
" \n",
" \n",
@@ -4869,19 +4885,23 @@
" BRAF | \n",
" <NA> | \n",
" <NA> | \n",
+ " <NA> | \n",
" QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... | \n",
" QH1 | \n",
" - | \n",
+ " 3715 | \n",
+ " 0 | \n",
" <NA> | \n",
" <NA> | \n",
" in | \n",
- " out-like | \n",
+ " out | \n",
" 3.29 | \n",
" 5.2 | \n",
" 7 | \n",
" 61 | \n",
" 0.806 | \n",
" 2.028 | \n",
+ " <NA> | \n",
" True | \n",
" True | \n",
" True | \n",
@@ -4901,6 +4921,7 @@
" 0.0 | \n",
" 0.0 | \n",
" <NA> | \n",
+ " False | \n",
" \n",
" \n",
"\n",
@@ -4913,23 +4934,26 @@
" structure.chain species.klifs kinase.klifs_id kinase.klifs_name \\\n",
"0 A Human 509 BRAF \n",
"\n",
- " kinase.family kinase.group \\\n",
- "0 \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 \n",
"\n",
" structure.pocket ligand.expo_id \\\n",
"0 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... QH1 \n",
"\n",
- " ligand_allosteric.expo_id ligand.name ligand_allosteric.name structure.dfg \\\n",
- "0 - in \n",
+ " ligand_allosteric.expo_id ligand.klifs_id ligand_allosteric.klifs_id \\\n",
+ "0 - 3715 0 \n",
"\n",
- " structure.ac_helix structure.resolution structure.qualityscore \\\n",
- "0 out-like 3.29 5.2 \n",
+ " ligand.name ligand_allosteric.name structure.dfg structure.ac_helix \\\n",
+ "0 in out \n",
"\n",
- " structure.missing_residues structure.missing_atoms structure.rmsd1 \\\n",
- "0 7 61 0.806 \n",
+ " structure.resolution structure.qualityscore structure.missing_residues \\\n",
+ "0 3.29 5.2 7 \n",
"\n",
- " structure.rmsd2 structure.front structure.gate structure.back \\\n",
- "0 2.028 True True True \n",
+ " structure.missing_atoms structure.rmsd1 structure.rmsd2 \\\n",
+ "0 61 0.806 2.028 \n",
+ "\n",
+ " interaction.fingerprint structure.front structure.gate structure.back \\\n",
+ "0 True True True \n",
"\n",
" structure.fp_i structure.fp_ii structure.bp_i_a structure.bp_i_b \\\n",
"0 False False True True \n",
@@ -4943,8 +4967,8 @@
" structure.bp_v structure.grich_distance structure.grich_angle \\\n",
"0 False 0.0 0.0 \n",
"\n",
- " structure.grich_rotation structure.filepath \n",
- "0 0.0 "
+ " structure.grich_rotation structure.filepath structure.curation_flag \n",
+ "0 0.0 False "
]
},
"execution_count": 56,
@@ -4965,7 +4989,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Expected type to be dict for value [400, 'KLIFS error: An unknown ligand ID was provided'] to unmarshal to a .Was instead.\n"
+ "Expected type to be dict for value [400, 'KLIFS error: An unknown structure ID was provided'] to unmarshal to a .Was instead.\n"
]
}
],
@@ -5016,11 +5040,14 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
" ligand.expo_id | \n",
" ligand_allosteric.expo_id | \n",
+ " ligand.klifs_id | \n",
+ " ligand_allosteric.klifs_id | \n",
" ligand.name | \n",
" ligand_allosteric.name | \n",
" structure.dfg | \n",
@@ -5031,6 +5058,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -5050,6 +5078,7 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
" \n",
" \n",
" \n",
@@ -5062,11 +5091,14 @@
" Human | \n",
" 509 | \n",
" BRAF | \n",
+ " ['BRAF'] | \n",
" RAF | \n",
" TKL | \n",
" QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... | \n",
" QH1 | \n",
" - | \n",
+ " <NA> | \n",
+ " <NA> | \n",
" 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... | \n",
" - | \n",
" in | \n",
@@ -5077,6 +5109,7 @@
" 61 | \n",
" 0.806 | \n",
" 2.028 | \n",
+ " 0000000000000000000000000000000000000000000000... | \n",
" <NA> | \n",
" <NA> | \n",
" <NA> | \n",
@@ -5096,6 +5129,7 @@
" NaN | \n",
" NaN | \n",
" HUMAN/BRAF/6uuo_chainA | \n",
+ " <NA> | \n",
" \n",
" \n",
"\n",
@@ -5108,14 +5142,14 @@
" structure.chain species.klifs kinase.klifs_id kinase.klifs_name \\\n",
"0 A Human 509 BRAF \n",
"\n",
- " kinase.family kinase.group \\\n",
- "0 RAF TKL \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 ['BRAF'] RAF TKL \n",
"\n",
" structure.pocket ligand.expo_id \\\n",
"0 QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ... QH1 \n",
"\n",
- " ligand_allosteric.expo_id \\\n",
- "0 - \n",
+ " ligand_allosteric.expo_id ligand.klifs_id ligand_allosteric.klifs_id \\\n",
+ "0 - \n",
"\n",
" ligand.name ligand_allosteric.name \\\n",
"0 1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf... - \n",
@@ -5126,8 +5160,11 @@
" structure.qualityscore structure.missing_residues \\\n",
"0 5.2 7 \n",
"\n",
- " structure.missing_atoms structure.rmsd1 structure.rmsd2 structure.front \\\n",
- "0 61 0.806 2.028 \n",
+ " structure.missing_atoms structure.rmsd1 structure.rmsd2 \\\n",
+ "0 61 0.806 2.028 \n",
+ "\n",
+ " interaction.fingerprint structure.front \\\n",
+ "0 0000000000000000000000000000000000000000000000... \n",
"\n",
" structure.gate structure.back structure.fp_i structure.fp_ii \\\n",
"0 False False \n",
@@ -5144,8 +5181,8 @@
" structure.grich_distance structure.grich_angle structure.grich_rotation \\\n",
"0 NaN NaN NaN \n",
"\n",
- " structure.filepath \n",
- "0 HUMAN/BRAF/6uuo_chainA "
+ " structure.filepath structure.curation_flag \n",
+ "0 HUMAN/BRAF/6uuo_chainA "
]
},
"execution_count": 58,
@@ -5165,7 +5202,7 @@
{
"data": {
"text/plain": [
- "(1, 41)"
+ "(1, 46)"
]
},
"execution_count": 59,
@@ -5216,13 +5253,6 @@
"execution_count": 61,
"metadata": {},
"outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "WARNING:opencadd.databases.klifs.remote:This method uses this lookup: ligand KLIFS ID > Ligand Expo ID > structures.The KLIFS Swagger API offers no direct structure search by ligand KLIFS ID.However, one Ligand Expo ID can be represented by multiple ligand KLIFS IDs. Thus, in rare cases, this method will return also structure that are not connected to the input ligand KLIFS ID but to a mutual Ligand Expo ID.\n"
- ]
- },
{
"data": {
"text/html": [
@@ -5251,11 +5281,14 @@
" species.klifs | \n",
" kinase.klifs_id | \n",
" kinase.klifs_name | \n",
+ " kinase.names | \n",
" kinase.family | \n",
" kinase.group | \n",
" structure.pocket | \n",
" ligand.expo_id | \n",
" ligand_allosteric.expo_id | \n",
+ " ligand.klifs_id | \n",
+ " ligand_allosteric.klifs_id | \n",
" ligand.name | \n",
" ligand_allosteric.name | \n",
" structure.dfg | \n",
@@ -5266,6 +5299,7 @@
" structure.missing_atoms | \n",
" structure.rmsd1 | \n",
" structure.rmsd2 | \n",
+ " interaction.fingerprint | \n",
" structure.front | \n",
" structure.gate | \n",
" structure.back | \n",
@@ -5285,23 +5319,27 @@
" structure.grich_angle | \n",
" structure.grich_rotation | \n",
" structure.filepath | \n",
+ " structure.curation_flag | \n",
" \n",
" \n",
" \n",
" \n",
" 0 | \n",
- " 8733 | \n",
+ " 8735 | \n",
" 5m5a | \n",
- " B | \n",
+ " A | \n",
" A | \n",
" Human | \n",
" 128 | \n",
" MELK | \n",
" <NA> | \n",
" <NA> | \n",
+ " <NA> | \n",
" ETIGTGGFAKVKLVAIKIMRIKTEIEALKNLRQHICQLYHVFMVLE... | \n",
" KSA | \n",
" - | \n",
+ " 100 | \n",
+ " 0 | \n",
" <NA> | \n",
" <NA> | \n",
" in | \n",
@@ -5312,6 +5350,7 @@
" 0 | \n",
" 0.775 | \n",
" 2.083 | \n",
+ " <NA> | \n",
" True | \n",
" False | \n",
" False | \n",
@@ -5331,21 +5370,25 @@
" 51.023800 | \n",
" 60.378601 | \n",
" <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" 1 | \n",
- " 8735 | \n",
+ " 8733 | \n",
" 5m5a | \n",
- " A | \n",
+ " B | \n",
" A | \n",
" Human | \n",
" 128 | \n",
" MELK | \n",
" <NA> | \n",
" <NA> | \n",
+ " <NA> | \n",
" ETIGTGGFAKVKLVAIKIMRIKTEIEALKNLRQHICQLYHVFMVLE... | \n",
" KSA | \n",
" - | \n",
+ " 100 | \n",
+ " 0 | \n",
" <NA> | \n",
" <NA> | \n",
" in | \n",
@@ -5356,6 +5399,7 @@
" 0 | \n",
" 0.775 | \n",
" 2.083 | \n",
+ " <NA> | \n",
" True | \n",
" False | \n",
" False | \n",
@@ -5375,6 +5419,7 @@
" 51.023800 | \n",
" 60.378601 | \n",
" <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" ... | \n",
@@ -5419,6 +5464,11 @@
" ... | \n",
" ... | \n",
" ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
+ " ... | \n",
"
\n",
" \n",
" 12 | \n",
@@ -5431,9 +5481,12 @@
" MAP2K1 | \n",
" <NA> | \n",
" <NA> | \n",
+ " <NA> | \n",
" SELGAGNGGVVFKMARKLIQIIRELQVLHECNPYIVGFYGASICME... | \n",
" KSA | \n",
" - | \n",
+ " 100 | \n",
+ " 0 | \n",
" <NA> | \n",
" <NA> | \n",
" in | \n",
@@ -5444,6 +5497,7 @@
" 0 | \n",
" 0.816 | \n",
" 2.199 | \n",
+ " <NA> | \n",
" True | \n",
" False | \n",
" False | \n",
@@ -5463,6 +5517,7 @@
" 51.288502 | \n",
" 69.366898 | \n",
" <NA> | \n",
+ " False | \n",
"
\n",
" \n",
" 13 | \n",
@@ -5475,9 +5530,12 @@
" MET | \n",
" <NA> | \n",
" <NA> | \n",
+ " <NA> | \n",
" EVIGRGHFGCVYHCAVKSLQFLTEGIIMKDFSPNVLSLLGILVVLP... | \n",
" KSA | \n",
" - | \n",
+ " 100 | \n",
+ " 0 | \n",
" <NA> | \n",
" <NA> | \n",
" in | \n",
@@ -5488,6 +5546,7 @@
" 0 | \n",
" 0.848 | \n",
" 2.189 | \n",
+ " <NA> | \n",
" True | \n",
" False | \n",
" False | \n",
@@ -5507,16 +5566,17 @@
" 66.349403 | \n",
" 48.160198 | \n",
" <NA> | \n",
+ " False | \n",
"
\n",
" \n",
"\n",
- "14 rows × 41 columns
\n",
+ "14 rows × 46 columns
\n",
""
],
"text/plain": [
" structure.klifs_id structure.pdb_id structure.alternate_model \\\n",
- "0 8733 5m5a B \n",
- "1 8735 5m5a A \n",
+ "0 8735 5m5a A \n",
+ "1 8733 5m5a B \n",
".. ... ... ... \n",
"12 3317 3eqf - \n",
"13 2991 1r0p - \n",
@@ -5528,12 +5588,12 @@
"12 A Human 383 MAP2K1 \n",
"13 A Human 446 MET \n",
"\n",
- " kinase.family kinase.group \\\n",
- "0 \n",
- "1 \n",
- ".. ... ... \n",
- "12 \n",
- "13 \n",
+ " kinase.names kinase.family kinase.group \\\n",
+ "0 \n",
+ "1 \n",
+ ".. ... ... ... \n",
+ "12 \n",
+ "13 \n",
"\n",
" structure.pocket ligand.expo_id \\\n",
"0 ETIGTGGFAKVKLVAIKIMRIKTEIEALKNLRQHICQLYHVFMVLE... KSA \n",
@@ -5542,33 +5602,40 @@
"12 SELGAGNGGVVFKMARKLIQIIRELQVLHECNPYIVGFYGASICME... KSA \n",
"13 EVIGRGHFGCVYHCAVKSLQFLTEGIIMKDFSPNVLSLLGILVVLP... KSA \n",
"\n",
- " ligand_allosteric.expo_id ligand.name ligand_allosteric.name structure.dfg \\\n",
- "0 - in \n",
- "1 - in \n",
- ".. ... ... ... ... \n",
- "12 - in \n",
- "13 - in \n",
- "\n",
- " structure.ac_helix structure.resolution structure.qualityscore \\\n",
- "0 in 1.9 8.0 \n",
- "1 in 1.9 8.0 \n",
- ".. ... ... ... \n",
- "12 out 2.7 8.0 \n",
- "13 out 1.8 8.0 \n",
- "\n",
- " structure.missing_residues structure.missing_atoms structure.rmsd1 \\\n",
- "0 0 0 0.775 \n",
- "1 0 0 0.775 \n",
- ".. ... ... ... \n",
- "12 0 0 0.816 \n",
- "13 0 0 0.848 \n",
- "\n",
- " structure.rmsd2 structure.front structure.gate structure.back \\\n",
- "0 2.083 True False False \n",
- "1 2.083 True False False \n",
- ".. ... ... ... ... \n",
- "12 2.199 True False False \n",
- "13 2.189 True False False \n",
+ " ligand_allosteric.expo_id ligand.klifs_id ligand_allosteric.klifs_id \\\n",
+ "0 - 100 0 \n",
+ "1 - 100 0 \n",
+ ".. ... ... ... \n",
+ "12 - 100 0 \n",
+ "13 - 100 0 \n",
+ "\n",
+ " ligand.name ligand_allosteric.name structure.dfg structure.ac_helix \\\n",
+ "0 in in \n",
+ "1 in in \n",
+ ".. ... ... ... ... \n",
+ "12 in out \n",
+ "13