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Fixes for steered MD tutorial and update to RBFE tutorial #33

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Fixes for steered MD tutorial and update to RBFE tutorial #33

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d5fd254
Updates RBFE notebook to support cinnabar 0.4.1
mb2055 Feb 21, 2025
fdc42f5
Update README to new cinnabar version
mb2055 Feb 21, 2025
b142b50
Updates CollectiveVariable.RMSD to new API
mb2055 Feb 21, 2025
9b59d85
Updates to be consistent with older versions.
mb2055 Feb 24, 2025
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39 changes: 13 additions & 26 deletions 03_steered_md/01_setup_sMD.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -128,6 +128,7 @@
"outputs": [],
"source": [
"from get_tutorial import download\n",
"\n",
"download(\"01\")"
]
},
Expand Down Expand Up @@ -200,22 +201,7 @@
"metadata": {},
"outputs": [],
"source": [
"reference = BSS.IO.readMolecules(\"data/reference.pdb\").getMolecule(0)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9f45911c",
"metadata": {},
"outputs": [],
"source": [
"rmsd_indices = []\n",
"for residue in reference.getResidues():\n",
" if 178 <= residue.index() <= 184:\n",
" for atom in residue.getAtoms():\n",
" if atom.element() != \"Hydrogen (H, 1)\":\n",
" rmsd_indices.append(atom.index())"
"reference = BSS.IO.readMolecules(\"data/reference.pdb\")"
]
},
{
Expand All @@ -225,7 +211,13 @@
"metadata": {},
"outputs": [],
"source": [
"rmsd_cv = BSS.Metadynamics.CollectiveVariable.RMSD(system, reference, rmsd_indices)"
"rmsd_cv = BSS.Metadynamics.CollectiveVariable.RMSD(\n",
" system,\n",
" reference,\n",
" \"molidx 0 and (not residx 178:185) and (not element H)\",\n",
" \"residx 178:185 and not element H\",\n",
" reference_mapping={0: 0},\n",
")"
]
},
{
Expand Down Expand Up @@ -336,9 +328,7 @@
"metadata": {},
"outputs": [],
"source": [
"process = BSS.Process.Gromacs(\n",
" system,\n",
" protocol)"
"process = BSS.Process.Gromacs(system, protocol)"
]
},
{
Expand Down Expand Up @@ -390,8 +380,7 @@
"metadata": {},
"outputs": [],
"source": [
"process = BSS.Process.Amber(\n",
" system, protocol)"
"process = BSS.Process.Amber(system, protocol)"
]
},
{
Expand Down Expand Up @@ -617,8 +606,7 @@
"outputs": [],
"source": [
"# pass exe=f'{os.environ[\"AMBERHOME\"]}/bin/pmemd.cuda to use the faster MD engine pmemd\n",
"process = BSS.Process.Amber(\n",
" system, protocol)"
"process = BSS.Process.Amber(system, protocol)"
]
},
{
Expand Down Expand Up @@ -696,8 +684,7 @@
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.13"
"pygments_lexer": "ipython3"
},
"vscode": {
"interpreter": {
Expand Down
92 changes: 70 additions & 22 deletions 04_fep/02_RBFE/02_analysis_rbfe.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,7 @@
"outputs": [],
"source": [
"from get_tutorial import download\n",
"\n",
"download(\"02\")"
]
},
Expand Down Expand Up @@ -221,7 +222,9 @@
" new_file_name = f\"analysis/outputs/results_{results_all_files.index(file)}.csv\"\n",
" with open(new_file_name, \"w\") as result_file:\n",
" writer = csv.writer(result_file, delimiter=\",\")\n",
" writer.writerow([\"lig_1\", \"lig_2\", \"freenrg(kcal/mol)\", \"error(kcal/mol)\", \"engine\"])\n",
" writer.writerow(\n",
" [\"lig_1\", \"lig_2\", \"freenrg(kcal/mol)\", \"error(kcal/mol)\", \"engine\"]\n",
" )\n",
"\n",
" for row, index in pd.read_csv(file).iterrows():\n",
" pert = f\"{index['lig_1']}~{index['lig_2']}\"\n",
Expand Down Expand Up @@ -290,7 +293,9 @@
"# write these to a csv file\n",
"with open(\"analysis/outputs/computed_perturbations_average.csv\", \"w\") as comp_pert_file:\n",
" writer = csv.writer(comp_pert_file, delimiter=\",\")\n",
" writer.writerow([\"lig_1\", \"lig_2\", \"freenrg(kcal/mol)\", \"error(kcal/mol)\", \"engine\"])\n",
" writer.writerow(\n",
" [\"lig_1\", \"lig_2\", \"freenrg(kcal/mol)\", \"error(kcal/mol)\", \"engine\"]\n",
" )\n",
" for pert in perturbations:\n",
" ddGs = comp_dict_list[pert]\n",
" lig_0 = pert.split(\"~\")[0]\n",
Expand Down Expand Up @@ -360,7 +365,9 @@
"# write these to a csv file\n",
"with open(\"analysis/outputs/experimental_perturbations.csv\", \"w\") as exp_pert_file:\n",
" writer = csv.writer(exp_pert_file, delimiter=\",\")\n",
" writer.writerow([\"lig_1\", \"lig_2\", \"freenrg(kcal/mol)\", \"error(kcal/mol)\", \"engine\"])\n",
" writer.writerow(\n",
" [\"lig_1\", \"lig_2\", \"freenrg(kcal/mol)\", \"error(kcal/mol)\", \"engine\"]\n",
" )\n",
"\n",
" for pert in perturbations:\n",
" lig_0 = pert.split(\"~\")[0]\n",
Expand Down Expand Up @@ -527,7 +534,15 @@
"metadata": {},
"outputs": [],
"source": [
"from cinnabar import wrangle, plotting"
"# Import cinnbar, API changes depending on version\n",
"try:\n",
" from cinnabar import wrangle, plotting\n",
"\n",
" cinnabar_is_old = True\n",
"except:\n",
" from cinnabar import FEMap, plotting\n",
"\n",
" cinnabar_is_old = False"
]
},
{
Expand Down Expand Up @@ -644,11 +659,32 @@
"metadata": {},
"outputs": [],
"source": [
"network = wrangle.FEMap(f\"analysis/outputs/cinnabar_data.csv\")\n",
"# plot the perturbations\n",
"plotting.plot_DDGs(network.graph, title=\"DDGs\", filename=f\"analysis/outputs/DDGs.png\", figsize=6)\n",
"# plot the ligands\n",
"plotting.plot_DGs(network.graph, title=\"DGs\", filename=f\"analysis/outputs/DGs.png\", figsize=6)"
"if cinnabar_is_old:\n",
" network = wrangle.FEMap(f\"analysis/outputs/cinnabar_data.csv\")\n",
" # plot the perturbations\n",
" plotting.plot_DDGs(\n",
" network.graph, title=\"DDGs\", filename=f\"analysis/outputs/DDGs.png\", figsize=6\n",
" )\n",
" # plot the ligands\n",
" plotting.plot_DGs(\n",
" network.graph, title=\"DGs\", filename=f\"analysis/outputs/DGs.png\", figsize=6\n",
" )\n",
"else:\n",
" network = FEMap.from_csv(f\"analysis/outputs/cinnabar_data.csv\")\n",
" # plot the perturbations\n",
" plotting.plot_DDGs(\n",
" network.to_legacy_graph(),\n",
" title=\"DDGs\",\n",
" filename=f\"analysis/outputs/DDGs.png\",\n",
" figsize=6,\n",
" )\n",
" # plot the ligands\n",
" plotting.plot_DGs(\n",
" network.to_legacy_graph(),\n",
" title=\"DGs\",\n",
" filename=f\"analysis/outputs/DGs.png\",\n",
" figsize=6,\n",
" )"
]
},
{
Expand Down Expand Up @@ -737,7 +773,7 @@
"<b>Exercise 2.1.1: Excluding intermediates from the Network analysis</b>\n",
"</div>\n",
"\n",
"Try exculding this perturbation and rerunning the above Network analysis. First, we need to remove the perturbation. Then, we need to make sure that our new output image is being saved using a different file path. Adjust these in the cells below where the #FIXME is. \n"
"Try excluding this perturbation and rerunning the above Network analysis. First, we need to remove the perturbation. Then, we need to make sure that our new output image is being saved using a different file path. Adjust these in the cells below where the #FIXME is. \n"
]
},
{
Expand Down Expand Up @@ -876,11 +912,19 @@
" if pert in perturbations:\n",
" writer.writerow([lig_0, lig_1, comp_ddG, comp_err, \"0.0\"])\n",
"\n",
"network = wrangle.FEMap(f\"analysis/outputs/cinnabar_data_outliers_removed.csv\")\n",
"# plot the perturbations\n",
"plotting.plot_DDGs(network.graph, title=\"DDGs\", filename=f\"analysis/outputs/DDGs_outliers_removed.png\", figsize=6)\n",
"# plot the ligands\n",
"plotting.plot_DGs(network.graph, title=\"DGs\", filename=f\"analysis/outputs/DGs_outliers_removed.png\", figsize=6)\n",
"if cinnabar_is_old:\n",
" network = wrangle.FEMap(f\"analysis/outputs/cinnabar_data_outliers_removed.csv\")\n",
" # plot the perturbations\n",
" plotting.plot_DDGs(network.graph, title=\"DDGs\", filename=f\"analysis/outputs/DDGs_outliers_removed.png\", figsize=6)\n",
" # plot the ligands\n",
" plotting.plot_DGs(network.graph, title=\"DGs\", filename=f\"analysis/outputs/DGs_outliers_removed.png\", figsize=6)\n",
"else:\n",
" network = FEMap.from_csv(f\"analysis/outputs/cinnabar_data_outliers_removed.csv\")\n",
" # plot the perturbations\n",
" plotting.plot_DDGs(network.to_legacy_graph(), title=\"DDGs\", filename=f\"analysis/outputs/DDGs_outliers_removed.png\", figsize=6)\n",
" # plot the ligands\n",
" plotting.plot_DGs(network.to_legacy_graph(), title=\"DGs\", filename=f\"analysis/outputs/DGs_outliers_removed.png\", figsize=6)\n",
"\n",
"```\n",
"\n",
"</details>"
Expand Down Expand Up @@ -924,11 +968,16 @@
"<details><summary {style='color:green;font-weight:bold'}> Click here to see solution to Exercise. </summary>\n",
"\n",
"```python\n",
"\n",
"lig_dict = {entry[1]['name']:entry[1]['calc_DG'] for entry in network.graph.nodes.data()}\n",
"lig_df = pd.DataFrame.from_dict(lig_dict, orient=\"index\", columns=[\"calc_DG\"])\n",
"lig_df.to_csv(\"analysis/outputs/ligand_calc_DG.csv\")\n",
"lig_df.sort_values(\"calc_DG\")\n",
"if cinnabar_is_old:\n",
" lig_dict = {entry[1]['name']:entry[1]['calc_DG'] for entry in network.graph.nodes.data()}\n",
" lig_df = pd.DataFrame.from_dict(lig_dict, orient=\"index\", columns=[\"calc_DG\"])\n",
" lig_df.to_csv(\"analysis/outputs/ligand_calc_DG.csv\")\n",
" lig_df.sort_values(\"calc_DG\")\n",
"else:\n",
" lig_dict = {entry[0]:entry[1]['calc_DG'] for entry in network.to_legacy_graph().nodes.data()}\n",
" lig_df = pd.DataFrame.from_dict(lig_dict, orient=\"index\", columns=[\"calc_DG\"])\n",
" lig_df.to_csv(\"analysis/outputs/ligand_calc_DG.csv\")\n",
" lig_df.sort_values(\"calc_DG\")\n",
"\n",
"```\n",
"\n",
Expand Down Expand Up @@ -978,8 +1027,7 @@
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.11"
"pygments_lexer": "ipython3"
},
"varInspector": {
"cols": {
Expand Down
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -7,7 +7,7 @@ These tutorials have been tested with BioSimSpace 2023.5.0 on a linux-64 platfor
* Gromacs (tested with 2023.1)
* AmberTools (tested with 23.3)
* PLUMED (tested with 2.9.0)
* cinnabar (tested with 0.3.0)
* cinnabar (tested with 0.4.1)
* alchemlyb (tested with 1.0.1)

# Installation instructions
Expand Down