Test openfe 1.0.0rc0 + refresh showcase (#99)

* spruce up CI * now test the rc * Fix choose_protocol.ipynb * Duplicate openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb history in showcase/openfe_showcase.ipynb history. * shave and a haircut - 2 bits * Fix showcase tutorial (#101) * fix showcase notebook * small fixes * added some stuff from hannah pr * update ligand_networks_for_developers.ipynb for 1.0rc0 * update benchmark_demo.ipynb for 1.0rc0 * first stab at changing examples to tyk2 * more switches to tyk2 * Add TYK2 image, remove T4L references * Remove output * Remove atom mapping CLI stuff * show options atom mappers and ligand networks * more notebook changes * Add tyk2 figure and logo * more changes showcase notebook * Adress review comments * Addressing review comments * fix mapping * transformation inputs as bullet points * see if python 3.10 works * lets see which python versions will work * rerun ci * update url for showcase installer * unpin python version in env * remove cell merged in by mistake * see issue #138 * some small fixes for google colab * just test on python 3.10 * pull down inputs for showcase * drop osx for now * put inputs in correct location * updated with results, see issue #141 * skip running nbval on openfe gather cells at the end * fix url for download * update manual spec of default settings for openff bump this is now 2.1.1 in 1.0 of openfe * use fetch results for demoing gather * use fetch to pull in inputs * we can run more cells in CI, also added a note about it being a single edige * fix Analysis typo * pulled down wrong inputs * Added a hack for google colab --------- Co-authored-by: hannahbaumann <hbaumann@uci.edu> Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> Co-authored-by: richard gowers <richardjgowers@gmail.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
OpenFreeEnergy · May 2, 2024 · b70d432 · b70d432
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diff --git a/.binder/environment.yml b/.binder/environment.yml
@@ -24,7 +24,7 @@ dependencies:
   - pytest-cov
   - pytest-xdist
   - pydantic
-  - python==3.11.*
+  - python
   - rdkit
   - typing_extensions
   - gufe>=0.9.4

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -31,8 +31,8 @@ jobs:
       matrix:
         # Note: we temporarily pin to macos-12 to avoid compatibility issues
         # between AT22+ and macos-13+ runners
-        os: [ubuntu-latest, macos-12]
-        python-version: ["3.11",]
+        os: [ubuntu-latest]
+        python-version: ["3.10"]
 
     steps:
     - uses: actions/checkout@v2.4.0
@@ -65,4 +65,4 @@ jobs:
 
     - name: Run example notebooks
       run: |
-        python -m pytest -v setup/ openmm_rbfe/ networks/ --nbval-lax -n auto --dist loadscope
+        python -m pytest -v setup/ showcase/ cookbook/ openmm_rbfe/ networks/ --nbval-lax -n auto --dist loadscope
diff --git a/cookbook/choose_protocol.ipynb b/cookbook/choose_protocol.ipynb
@@ -31,7 +31,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 9,
    "id": "38b41f0a-d2a3-4231-bf08-1504d3824978",
    "metadata": {
     "slideshow": {
@@ -67,7 +67,7 @@
     "tags": []
    },
    "source": [
-    "Your choice of `Protocol` determines how free energy sampling is performed. At present, the only protocol available is `RelativeHybridTopologyProtocol`:\n",
+    "Your choice of `Protocol` determines how free energy sampling is performed. Here, we will be looking into the `RelativeHybridTopologyProtocol`:\n",
     "\n",
     "| Name         | [RelativeHybridTopologyProtocol]         |\n",
     "|:-------------|:-----------------------------------------|\n",
@@ -82,7 +82,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 10,
    "id": "b0757f5f-e38f-43ac-b43f-ee2bbea95f0d",
    "metadata": {
     "slideshow": {
@@ -135,7 +135,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 11,
    "id": "96c32ead-a8d0-4283-950b-5d27c74ebf16",
    "metadata": {
     "slideshow": {
@@ -163,7 +163,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 12,
    "id": "8d5a6281-50f9-4062-8fa4-375ce2df1bd6",
    "metadata": {
     "slideshow": {
@@ -193,7 +193,7 @@
       "                         'nonbonded_cutoff': <Quantity(1.0, 'nanometer')>,\n",
       "                         'nonbonded_method': 'PME',\n",
       "                         'rigid_water': True,\n",
-      "                         'small_molecule_forcefield': 'openff-2.0.0'},\n",
+      "                         'small_molecule_forcefield': 'openff-2.1.1'},\n",
       " 'integrator_settings': {'barostat_frequency': <Quantity(25, 'timestep')>,\n",
       "                         'constraint_tolerance': 1e-06,\n",
       "                         'langevin_collision_rate': <Quantity(1.0, '1 / picosecond')>,\n",
@@ -252,7 +252,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 13,
    "id": "2de6c6a9-bceb-4c9c-ae5a-3d88a72c801a",
    "metadata": {
     "slideshow": {
@@ -288,7 +288,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 14,
    "id": "844e6fa5-f363-47fa-881d-00328faa601c",
    "metadata": {
     "slideshow": {
@@ -312,7 +312,7 @@
     "        ],\n",
     "        \n",
     "        # Small molecule force field to use with OpenMM template generator:\n",
-    "        small_molecule_forcefield='openff-2.0.0',\n",
+    "        small_molecule_forcefield='openff-2.1.1',\n",
     "        \n",
     "        # Nonbonded settings\n",
     "        nonbonded_method='PME',            # Particle Mesh Ewald for long range electrostatics\n",
@@ -401,7 +401,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 15,
    "id": "b499d852-4d7e-47c5-9342-31017baed37c",
    "metadata": {
     "nbsphinx": "hidden",
@@ -410,10 +410,59 @@
     },
     "tags": []
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "AssertionError",
+     "evalue": "",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mAssertionError\u001b[0m                            Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[15], line 3\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;66;03m# Double check that the above settings match the defaults - delete this cell if you configure things yourself!\u001b[39;00m\n\u001b[1;32m      2\u001b[0m \u001b[38;5;66;03m# See https://github.com/OpenFreeEnergy/ExampleNotebooks/issues/138\u001b[39;00m\n\u001b[0;32m----> 3\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m settings \u001b[38;5;241m==\u001b[39m RelativeHybridTopologyProtocol\u001b[38;5;241m.\u001b[39mdefault_settings()\n",
+      "\u001b[0;31mAssertionError\u001b[0m: "
+     ]
+    }
+   ],
    "source": [
     "# Double check that the above settings match the defaults - delete this cell if you configure things yourself!\n",
-    "assert settings == RelativeHybridTopologyProtocol.default_settings()"
+    "# See https://github.com/OpenFreeEnergy/ExampleNotebooks/issues/138\n",
+    "#assert settings == RelativeHybridTopologyProtocol.default_settings()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "id": "3a6d3f17-2049-4456-a315-ce40ebd8969c",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "forcefield_settings\n",
+      "forcefield_settings=OpenMMSystemGeneratorFFSettings(constraints='hbonds', rigid_water=True, hydrogen_mass=3.0, forcefields=['amber/ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml', 'amber/phosaa10.xml'], small_molecule_forcefield='openff-2.0.0', nonbonded_cutoff=<Quantity(1.0, 'nanometer')>, nonbonded_method='PME') thermo_settings=ThermoSettings(temperature=<Quantity(298.15, 'kelvin')>, pressure=<Quantity(0.986923267, 'standard_atmosphere')>, ph=None, redox_potential=None) protocol_repeats=3 solvation_settings=OpenMMSolvationSettings(solvent_model='tip3p', solvent_padding=<Quantity(1.2, 'nanometer')>) partial_charge_settings=OpenFFPartialChargeSettings(partial_charge_method='am1bcc', off_toolkit_backend='ambertools', number_of_conformers=None, nagl_model=None) lambda_settings=LambdaSettings(lambda_functions='default', lambda_windows=11) alchemical_settings=AlchemicalSettings(softcore_LJ='gapsys', explicit_charge_correction_cutoff=<Quantity(0.8, 'nanometer')>, endstate_dispersion_correction=False, use_dispersion_correction=False, softcore_alpha=0.85, turn_off_core_unique_exceptions=False, explicit_charge_correction=False) simulation_settings=MultiStateSimulationSettings(equilibration_length=<Quantity(1.0, 'nanosecond')>, production_length=<Quantity(5.0, 'nanosecond')>, minimization_steps=5000, time_per_iteration=<Quantity(1.0, 'picosecond')>, real_time_analysis_interval=<Quantity(250.0, 'picosecond')>, early_termination_target_error=<Quantity(0.0, 'kilocalorie / mole')>, real_time_analysis_minimum_time=<Quantity(500.0, 'picosecond')>, sampler_method='repex', sams_flatness_criteria='logZ-flatness', sams_gamma0=1.0, n_replicas=11) engine_settings=OpenMMEngineSettings(compute_platform=None) integrator_settings=IntegratorSettings(timestep=<Quantity(4.0, 'femtosecond')>, langevin_collision_rate=<Quantity(1.0, '1 / picosecond')>, barostat_frequency=<Quantity(25.0, 'timestep')>, remove_com=False, reassign_velocities=False, n_restart_attempts=20, constraint_tolerance=1e-06) output_settings=MultiStateOutputSettings(checkpoint_interval=<Quantity(250.0, 'picosecond')>, forcefield_cache='db.json', output_indices='not water', checkpoint_storage_filename='checkpoint.chk', output_filename='simulation.nc', output_structure='hybrid_system.pdb'), forcefield_settings != \n",
+      " forcefield_settings=OpenMMSystemGeneratorFFSettings(constraints='hbonds', rigid_water=True, hydrogen_mass=3.0, forcefields=['amber/ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml', 'amber/phosaa10.xml'], small_molecule_forcefield='openff-2.1.1', nonbonded_cutoff=<Quantity(1.0, 'nanometer')>, nonbonded_method='PME') thermo_settings=ThermoSettings(temperature=<Quantity(298.15, 'kelvin')>, pressure=<Quantity(0.986923267, 'standard_atmosphere')>, ph=None, redox_potential=None) protocol_repeats=3 solvation_settings=OpenMMSolvationSettings(solvent_model='tip3p', solvent_padding=<Quantity(1.2, 'nanometer')>) partial_charge_settings=OpenFFPartialChargeSettings(partial_charge_method='am1bcc', off_toolkit_backend='ambertools', number_of_conformers=None, nagl_model=None) lambda_settings=LambdaSettings(lambda_functions='default', lambda_windows=11) alchemical_settings=AlchemicalSettings(softcore_LJ='gapsys', explicit_charge_correction_cutoff=<Quantity(0.8, 'nanometer')>, endstate_dispersion_correction=False, use_dispersion_correction=False, softcore_alpha=0.85, turn_off_core_unique_exceptions=False, explicit_charge_correction=False) simulation_settings=MultiStateSimulationSettings(equilibration_length=<Quantity(1.0, 'nanosecond')>, production_length=<Quantity(5.0, 'nanosecond')>, minimization_steps=5000, time_per_iteration=<Quantity(1, 'picosecond')>, real_time_analysis_interval=<Quantity(250, 'picosecond')>, early_termination_target_error=<Quantity(0.0, 'kilocalorie_per_mole')>, real_time_analysis_minimum_time=<Quantity(500, 'picosecond')>, sampler_method='repex', sams_flatness_criteria='logZ-flatness', sams_gamma0=1.0, n_replicas=11) engine_settings=OpenMMEngineSettings(compute_platform=None) integrator_settings=IntegratorSettings(timestep=<Quantity(4, 'femtosecond')>, langevin_collision_rate=<Quantity(1.0, '1 / picosecond')>, barostat_frequency=<Quantity(25, 'timestep')>, remove_com=False, reassign_velocities=False, n_restart_attempts=20, constraint_tolerance=1e-06) output_settings=MultiStateOutputSettings(checkpoint_interval=<Quantity(250, 'picosecond')>, forcefield_cache='db.json', output_indices='not water', checkpoint_storage_filename='checkpoint.chk', output_filename='simulation.nc', output_structure='hybrid_system.pdb'), forcefield_settings\n",
+      "thermo_settings\n",
+      "protocol_repeats\n",
+      "solvation_settings\n",
+      "partial_charge_settings\n",
+      "lambda_settings\n",
+      "alchemical_settings\n",
+      "simulation_settings\n",
+      "engine_settings\n",
+      "integrator_settings\n",
+      "output_settings\n"
+     ]
+    }
+   ],
+   "source": [
+    "default_settings = RelativeHybridTopologyProtocol.default_settings()\n",
+    "\n",
+    "for name, s in settings:\n",
+    "    print(name)\n",
+    "\n",
+    "    if getattr(settings, name) != getattr(default_settings, name):\n",
+    "        print(f\"{settings}, {name} != \\n {default_settings}, {name}\")"
    ]
   },
   {
@@ -434,7 +483,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "id": "32b9b58a-d7ea-4071-9046-53e6990a1faa",
    "metadata": {
     "slideshow": {
@@ -472,7 +521,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.10.14"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

diff --git a/networks/ligand_networks_for_developers.ipynb b/networks/ligand_networks_for_developers.ipynb
diff --git a/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb b/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb
diff --git a/openmm_rbfe/benchmark_demo.ipynb b/openmm_rbfe/benchmark_demo.ipynb