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@dprada
dprada committed Nov 3, 2023
1 parent 7ac7b00 commit 7f6aec9
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Showing 2 changed files with 1 addition and 170 deletions.
50 changes: 1 addition & 49 deletions sandbox/Test2.ipynb → sandbox/Test.ipynb
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Expand Up @@ -10,12 +10,9 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"id": "08aee8bc-0efe-44a5-9aa6-24131ae8137e",
"metadata": {},
<<<<<<< HEAD
"outputs": [],
=======
"outputs": [
{
"data": {
Expand All @@ -30,31 +27,15 @@
"output_type": "display_data"
}
],
>>>>>>> 64e8c805958be78cd51fab8641486d745007536a
"source": [
"import molsysmt as msm\n",
"from molsysmt.systems import tests as tests_systems"
]
},
{
"cell_type": "code",
<<<<<<< HEAD
"execution_count": null,
"id": "2b932271-fce9-4e09-86b6-7198bb322224",
"metadata": {},
"outputs": [],
"source": [
"msm.get_form('traj.msmh5')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "af89aba5-62c5-4718-a355-2b8b591c1097",
=======
"execution_count": 2,
"id": "66ab3386-d6fa-4f56-b783-c407383cf8c9",
>>>>>>> 64e8c805958be78cd51fab8641486d745007536a
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -63,34 +44,6 @@
},
{
"cell_type": "code",
<<<<<<< HEAD
"execution_count": null,
"id": "677e2b3f-a1db-48c8-b56e-e13fca4efe7f",
"metadata": {},
"outputs": [],
"source": [
"output = aa.file['topology']['atoms']['name'][:].astype('int64')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "02853906-0d4d-485c-9f51-fd65f00b8d98",
"metadata": {},
"outputs": [],
"source": [
"output"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "93a36f08-4177-48d6-b4cc-ac5d71e98a0a",
"metadata": {},
"outputs": [],
"source": [
"msm.get('traj.msmh5', element='system', n_structures=True)"
=======
"execution_count": 3,
"id": "1ae40987-508b-4fb7-92e0-718d5c7a80da",
"metadata": {},
Expand Down Expand Up @@ -144,7 +97,6 @@
],
"source": [
"msm.info(molsys)"
>>>>>>> 64e8c805958be78cd51fab8641486d745007536a
]
},
{
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121 changes: 0 additions & 121 deletions sandbox/Test_4POC_2.ipynb → sandbox/Test_4POC.ipynb
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Expand Up @@ -5,94 +5,12 @@
"id": "85d75849-5640-43b7-8b93-87cdbf6b8792",
"metadata": {},
"source": [
<<<<<<< HEAD
"# Test"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "08aee8bc-0efe-44a5-9aa6-24131ae8137e",
"metadata": {},
"outputs": [],
"source": [
"import molsysmt as msm"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "2b932271-fce9-4e09-86b6-7198bb322224",
"metadata": {},
"outputs": [],
"source": [
"msm.get_form('traj.msmh5')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "af89aba5-62c5-4718-a355-2b8b591c1097",
"metadata": {},
"outputs": [],
"source": [
"aa = msm.convert('traj.msmh5', 'molsysmt.MSMH5FileHandler')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "677e2b3f-a1db-48c8-b56e-e13fca4efe7f",
"metadata": {},
"outputs": [],
"source": [
"output = aa.file['topology']['atoms']['name'][:].astype('int64')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "02853906-0d4d-485c-9f51-fd65f00b8d98",
"metadata": {},
"outputs": [],
"source": [
"output"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "93a36f08-4177-48d6-b4cc-ac5d71e98a0a",
"metadata": {},
"outputs": [],
"source": [
"msm.get('traj.msmh5', element='system', n_structures=True)"
=======
"# Test 4POC"
>>>>>>> 64e8c805958be78cd51fab8641486d745007536a
]
},
{
"cell_type": "code",
"execution_count": 1,
<<<<<<< HEAD
"id": "29eaa993-ce18-425e-b692-1a62dc1ccc6b",
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 'msm' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[1], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m molsys \u001b[38;5;241m=\u001b[39m \u001b[43mmsm\u001b[49m\u001b[38;5;241m.\u001b[39mconvert(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m4POC\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 2\u001b[0m molsys \u001b[38;5;241m=\u001b[39m msm\u001b[38;5;241m.\u001b[39mextract(molsys, selection\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmolecule_type==\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mprotein\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 3\u001b[0m molsys \u001b[38;5;241m=\u001b[39m msm\u001b[38;5;241m.\u001b[39mbuild\u001b[38;5;241m.\u001b[39madd_missing_hydrogens(molsys)\n",
"\u001b[0;31mNameError\u001b[0m: name 'msm' is not defined"
]
}
],
"source": [
=======
"id": "25e3878c-31e9-43e8-ae45-e364ca740f88",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -123,40 +41,10 @@
"metadata": {},
"outputs": [],
"source": [
>>>>>>> 64e8c805958be78cd51fab8641486d745007536a
"molsys = msm.convert('4POC')\n",
"molsys = msm.extract(molsys, selection='molecule_type==\"protein\"')\n",
"molsys = msm.build.add_missing_hydrogens(molsys)\n",
"molsys = msm.build.solvate(molsys)\n",
<<<<<<< HEAD
"forcefield = app.ForceField('amber14-all.xml', 'amber14/tip3p.xml')\n",
"topology = msm.convert(molsys, 'openmm.Topology')\n",
"system = forcefield.createSystem(topology, nonbondedMethod=app.PME,\n",
" nonbondedCutoff=1.2*unit.nanometer, constraints=app.HBonds)\n",
"integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picosecond, 2.0*unit.femtoseconds)\n",
"platform = mm.Platform.getPlatformByName(\"CPU\")\n",
"simulation = app.Simulation(topology, system, integrator, platform)\n",
"coordinates = msm.get(molsys, coordinates=True)\n",
"positions = msm.pyunitwizard.convert(coordinates[0], to_form='openmm.unit')\n",
"simulation.context.setPositions(positions)\n",
"simulation.minimizeEnergy()\n",
"from molsysmt.thirds.openmm.reporters import MolSysMTTrajectoryDictReporter\n",
"from molsysmt.thirds.openmm.reporters import MSMH5Reporter\n",
"dict_reporter = MolSysMTTrajectoryDictReporter(10)\n",
"simulation.reporters.append(dict_reporter)\n",
"msmh5_reporter = MSMH5Reporter('test.msmh5', 10, selection='all', steps=100,\n",
" topology=True, time=True, box=True, coordinates=True, velocities=False,\n",
" potentialEnergy=True, kineticEnergy=True, temperature=True,\n",
" includeInitialContext=True, constantReportInterval=True,\n",
" constantStepSize=True, constantBox=True,\n",
" compression='gzip', compression_opts=4,\n",
" int_precision='single', float_precision='single',\n",
" syntax='MolSysMT')\n",
"simulation.reporters.append(msmh5_reporter)\n",
"simulation.step(100)\n",
"traj = dict_reporter.finalize()\n",
"msmh5_reporter.close()"
=======
"\n",
"#molsys = msm.convert('initial.msmpk')"
]
Expand Down Expand Up @@ -323,17 +211,12 @@
],
"source": [
"simulation.step(100)"
>>>>>>> 64e8c805958be78cd51fab8641486d745007536a
]
},
{
"cell_type": "code",
"execution_count": null,
<<<<<<< HEAD
"id": "85b83722-f246-42bc-ae6b-77b579318514",
=======
"id": "7de00118-daec-4a61-a390-e60c8636c0f3",
>>>>>>> 64e8c805958be78cd51fab8641486d745007536a
"metadata": {},
"outputs": [],
"source": []
Expand All @@ -355,11 +238,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
<<<<<<< HEAD
"version": "3.10.13"
=======
"version": "3.10.12"
>>>>>>> 64e8c805958be78cd51fab8641486d745007536a
}
},
"nbformat": 4,
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