diff --git a/notebooks/pka_prediction.ipynb b/notebooks/pka_prediction.ipynb
index 2548099..983c362 100644
--- a/notebooks/pka_prediction.ipynb
+++ b/notebooks/pka_prediction.ipynb
@@ -3,8 +3,8 @@
{
"cell_type": "markdown",
"metadata": {
- "id": "view-in-github",
- "colab_type": "text"
+ "colab_type": "text",
+ "id": "view-in-github"
},
"source": [
"![\"Open](\"https://colab.research.google.com/assets/colab-badge.svg\")
"
@@ -26,17 +26,17 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
+ "cellView": "form",
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "BrnGvVB1lZ6Y",
- "outputId": "8fcc5491-5389-4053-edcd-90a60aae86c0",
- "cellView": "form"
+ "outputId": "8fcc5491-5389-4053-edcd-90a60aae86c0"
},
"outputs": [
{
- "output_type": "stream",
"name": "stdout",
+ "output_type": "stream",
"text": [
"⏬ Downloading https://github.com/jaimergp/miniforge/releases/latest/download/Mambaforge-colab-Linux-x86_64.sh...\n",
"📦 Installing...\n",
@@ -58,17 +58,17 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
- "id": "cg5NTzCefRRX",
"cellView": "form",
"colab": {
"base_uri": "https://localhost:8080/"
},
+ "id": "cg5NTzCefRRX",
"outputId": "ba7174e7-28a7-444f-eb22-39459e3970fd"
},
"outputs": [
{
- "output_type": "stream",
"name": "stdout",
+ "output_type": "stream",
"text": [
"✨🍰✨ Everything looks OK!\n"
]
@@ -83,34 +83,19 @@
},
{
"cell_type": "code",
- "source": [
- "# @title Installing dependencies and pkasolver package (this might take up to 5 minutes)\n",
- "\n",
- "print('📦 Installing dependencies ...')\n",
- "!mamba install -c conda-forge rdkit > /dev/null\n",
- "print('🔥 Installing PyTorch and PyG ...')\n",
- "!pip install torch==1.9.1+cpu -f https://download.pytorch.org/whl/cpu/torch_stable.html > /dev/null\n",
- "!pip install torch-scatter -f https://data.pyg.org/whl/torch-1.9.1+cpu.html > /dev/null\n",
- "!pip install torch-sparse -f https://data.pyg.org/whl/torch-1.9.1+cpu.html > /dev/null\n",
- "!pip install torch-spline-conv torch-geometric==2.0.1 -f https://data.pyg.org/whl/torch-1.9.1+cpu.html > /dev/null\n",
- "!pip install cairosvg svgutils molvs > /dev/null\n",
- "print('✔️ Installing pkasolver package ...')\n",
- "!pip install -q git+https://github.com/mayrf/pkasolver.git > /dev/null\n",
- "print(\"🎉 Done!\")"
- ],
+ "execution_count": null,
"metadata": {
+ "cellView": "form",
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "4TZCXZ_IJXCz",
- "outputId": "bd23921a-e1d6-4fd7-faf5-ba85214e69cd",
- "cellView": "form"
+ "outputId": "bd23921a-e1d6-4fd7-faf5-ba85214e69cd"
},
- "execution_count": null,
"outputs": [
{
- "output_type": "stream",
"name": "stdout",
+ "output_type": "stream",
"text": [
"📦 Installing dependencies ...\n",
"🔥 Installing PyTorch and PyG ...\n",
@@ -118,52 +103,67 @@
"🎉 Done!\n"
]
}
+ ],
+ "source": [
+ "# @title Installing dependencies and pkasolver package (this might take up to 5 minutes)\n",
+ "\n",
+ "print('📦 Installing dependencies ...')\n",
+ "!mamba install -c conda-forge rdkit > /dev/null\n",
+ "print('🔥 Installing PyTorch and PyG ...')\n",
+ "!pip install torch==1.13.1+cpu -f https://download.pytorch.org/whl/cpu/torch_stable.html > /dev/null\n",
+ "!pip install torch-scatter -f https://data.pyg.org/whl/torch-1.13.1+cpu.html > /dev/null\n",
+ "!pip install torch-sparse -f https://data.pyg.org/whl/torch-1.13.1+cpu.html > /dev/null\n",
+ "!pip install torch-spline-conv torch-geometric==2.0.1 -f https://data.pyg.org/whl/torch-1.13.1+cpu.html > /dev/null\n",
+ "!pip install cairosvg svgutils molvs > /dev/null\n",
+ "print('✔️ Installing pkasolver package ...')\n",
+ "!pip install -q git+https://github.com/mayrf/pkasolver.git > /dev/null\n",
+ "print(\"🎉 Done!\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
- "id": "aw-6bqsym4hX",
"cellView": "form",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 1000
},
+ "id": "aw-6bqsym4hX",
"outputId": "0cf8e792-7e9c-4fbf-9e01-1665c9da94dc"
},
"outputs": [
{
- "output_type": "stream",
"name": "stdout",
+ "output_type": "stream",
"text": [
"🔮 Predicting...\n"
]
},
{
- "output_type": "stream",
"name": "stderr",
+ "output_type": "stream",
"text": [
"[query.py:297 - calculate_microstate_pka_values()] Using dimorphite-dl to identify protonation sites.\n"
]
},
{
- "output_type": "stream",
"name": "stdout",
+ "output_type": "stream",
"text": [
"Proposed mol at pH 7.4: CC(Cc1ccccc1)NC(=O)C([NH3+])CCCC[NH3+]\n",
"📸 Visualizing ...\n"
]
},
{
- "output_type": "display_data",
"data": {
+ "image/svg+xml": "