From aab59e87791618388a542c7a8118d9accaf9a1b8 Mon Sep 17 00:00:00 2001 From: Jessica Nash Date: Tue, 2 Jul 2024 19:04:59 -0400 Subject: [PATCH] update page title --- .../chapters/binding_site_investigation.ipynb | 61 ++++++++----------- 1 file changed, 24 insertions(+), 37 deletions(-) diff --git a/biochemist-python/chapters/binding_site_investigation.ipynb b/biochemist-python/chapters/binding_site_investigation.ipynb index 0e886df..c15b38b 100644 --- a/biochemist-python/chapters/binding_site_investigation.ipynb +++ b/biochemist-python/chapters/binding_site_investigation.ipynb @@ -5,7 +5,7 @@ "id": "224c908b-d8df-480f-8f50-351bb56df43b", "metadata": {}, "source": [ - "# Investigation the Binding Site\n", + "# Visualizing the Binding Site of a Protein-Ligand Complex\n", "\n", "\n", "Learning Objectives\n", @@ -30,7 +30,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 23, "id": "084d041c-6d26-4136-a3ff-2f5586c5ea26", "metadata": {}, "outputs": [ @@ -40,7 +40,7 @@ "200" ] }, - "execution_count": 1, + "execution_count": 23, "metadata": {}, "output_type": "execute_result" } @@ -68,7 +68,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 24, "id": "97d0596a-533f-4aa8-afb5-bb9d182788fd", "metadata": {}, "outputs": [], @@ -92,7 +92,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 25, "id": "1266c266-ab03-4aa9-b4b5-d097cbc9d5cf", "metadata": {}, "outputs": [], @@ -139,23 +139,10 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 26, "id": "30aa1905-a77c-4b67-aeef-bd22f6123af2", "metadata": {}, - "outputs": [ - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "b99491671e01419ea6e9dd4d41e4527f", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "import MDAnalysis as mda\n", "import nglview as nv\n", @@ -173,14 +160,14 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 27, "id": "22eab29a-8893-40e1-9b7c-8c82410c6998", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "2401aa6c72574b7daf42ea1fa5b8be4b", + "model_id": "4ab1c88c8dbe485bbc54fde11da772dc", "version_major": 2, "version_minor": 0 }, @@ -211,7 +198,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 28, "id": "59398872-79e2-4b19-a6a1-2a11305cb003", "metadata": {}, "outputs": [], @@ -232,14 +219,14 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 29, "id": "ec313913-e6a6-49de-99f5-88a8b2d5f029", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "e76e61ee77e54089b97cc13e88d4ba18", + "model_id": "1cb81a388c394b23aa00bd9b26735059", "version_major": 2, "version_minor": 0 }, @@ -284,7 +271,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 30, "id": "16e2bad0-0fab-437c-8e6b-f66c1a622b3a", "metadata": {}, "outputs": [], @@ -304,14 +291,14 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 31, "id": "43598dd2-503b-47f3-816d-e20039ced662", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "39f72e25876f4a59a5451baa0beb88fd", + "model_id": "5e36b064b16a443ba57fcb1ae58cb830", "version_major": 2, "version_minor": 0 }, @@ -329,14 +316,14 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 32, "id": "92c18c8c-a728-4d57-af48-b5551fab49f8", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "86508b08ae76439f89976b8e570328a8", + "model_id": "98b9ec951dd64e94a4b4d3a4e9b8a051", "version_major": 2, "version_minor": 0 }, @@ -582,7 +569,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "[17:18:26] WARNING: More than one matching pattern found - picking one\n", + "[17:30:37] WARNING: More than one matching pattern found - picking one\n", "\n" ] } @@ -688,7 +675,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "44c9a5ea8b784bb7bbb52e2d81408340", + "model_id": "dd2bb2945a984100ae6a949c99718578", "version_major": 2, "version_minor": 0 }, @@ -708,7 +695,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 22, "id": "9dc10fc4-2721-4a6a-98a4-350958a6b73e", "metadata": {}, "outputs": [ @@ -753,11 +740,11 @@ " });\n", " return network;\n", " }\n", - " nodes = [{"id": "ASN97.A", "label": "ASN97.A", "color": "#59bee3", "shape": "box", "borderWidth": 0, "physics": true, "mass": 2, "group": "protein", "residue_type": "Polar"}, {"id": "ASP189.A", "label": "ASP189.A", "color": "#e35959", "shape": "box", "borderWidth": 0, "physics": true, "mass": 2, "group": "protein", "residue_type": "Acidic"}, {"id": "GLN175.A", "label": "GLN175.A", "color": "#59bee3", "shape": "box", "borderWidth": 0, "physics": true, "mass": 2, "group": "protein", 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"dashes": [10], "group": "ligand", "width": 4}, {"from": 676064199768288179, "to": 7616605487933146360, "color": "black", "physics": false, "dashes": false, "group": "ligand", "width": 4}, {"from": 8205015407944528923, "to": -7596883567215709610, "color": "black", "physics": false, "dashes": false, "group": "ligand", "width": 4}, {"from": 25, "to": 27, "color": "black", "physics": false, "group": "ligand", "width": 4}, {"from": 27, "to": 61, "color": "black", "physics": false, "group": "ligand", "width": 4}, {"from": 27, "to": 62, "color": "black", "physics": false, "group": "ligand", "width": 4}, {"from": 9109355908060369854, "to": 3609141865272994084, "color": "black", "physics": false, "dashes": [10], "group": "ligand", "width": 4}, {"from": 8627230411913182353, "to": 8183001495646378461, "color": "black", "physics": false, "dashes": [10], "group": "ligand", "width": 4}];\n", " ifp = drawGraph('mynetwork', nodes, edges, {"width": "100%", "height": "500px", "nodes": {"font": {"size": 20}}, "physics": {"barnesHut": {"avoidOverlap": 0.8, "springConstant": 0.1}}});\n", " \n", - " legend_buttons = [{"index": 0, "label": "Acidic", "color": "#e35959", "group": "residues"}, {"index": 1, "label": "Aliphatic", "color": "#59e382", "group": "residues"}, {"index": 2, "label": "Aromatic", "color": "#b559e3", "group": "residues"}, {"index": 3, "label": "Basic", "color": "#5979e3", "group": "residues"}, {"index": 4, "label": "Polar", "color": "#59bee3", "group": "residues"}, {"index": 0, "label": "HBDonor/HBAcceptor", "color": "#59bee3", "group": "interactions"}, {"index": 1, "label": "Hydrophobic", "color": "#59e382", "group": "interactions"}, {"index": 2, "label": "VdWContact", "color": "#dfab43", "group": "interactions"}];\n", + " legend_buttons = [{"index": 0, "label": "Acidic", "color": "#e35959", "group": "residues"}, {"index": 1, "label": "Aliphatic", "color": "#59e382", "group": "residues"}, {"index": 2, "label": "Aromatic", "color": "#b559e3", "group": "residues"}, {"index": 3, "label": "Basic", "color": "#5979e3", "group": "residues"}, {"index": 4, "label": "Polar", "color": "#59bee3", "group": "residues"}, {"index": 0, "label": "HBAcceptor/HBDonor", "color": "#59bee3", "group": "interactions"}, {"index": 1, "label": "Hydrophobic", "color": "#59e382", "group": "interactions"}, {"index": 2, "label": "VdWContact", "color": "#dfab43", "group": "interactions"}];\n", " legend = document.getElementById('networklegend');\n", " var div_residues = document.createElement('div');\n", " var div_interactions = document.createElement('div');\n", @@ -866,7 +853,7 @@ "" ] }, - "execution_count": 23, + "execution_count": 22, "metadata": {}, "output_type": "execute_result" }