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Update changelog with current commits #95

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Mar 21, 2024
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11 changes: 11 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,17 @@ The rules for this file:
* accompany each entry with github issue/PR number (Issue #xyz)
-->

## v0.3.5 -- 2024-03-21

### Authors
<!-- GitHub usernames of contributors to this release -->
- @Yoshanuikabundi
- @lilyminium

### Fixed
- Fixes to docs and examples (Issue #92, PR #73)


## v0.3.4 -- 2024-02-15

### Authors
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314 changes: 314 additions & 0 deletions examples/x-distances.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "8a760402-7d7f-4fc9-a54b-e033bf035101",
"metadata": {},
"outputs": [
{
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"version_major": 2,
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"metadata": {},
"output_type": "display_data"
}
],
"source": [
"import mdtraj\n",
"import nglview\n",
"import openmm\n",
"import openmm.unit\n",
"from openff.toolkit import Molecule, ForceField\n",
"from openff.units import unit\n",
"\n",
"def viz(\n",
" smiles: str,\n",
" force_field: ForceField,\n",
") -> nglview.NGLWidget:\n",
" molecule = Molecule.from_smiles(smiles, allow_undefined_stereo=True)\n",
" molecule.generate_conformers(n_conformers=1)\n",
"\n",
" interchange = force_field.create_interchange(molecule.to_topology())\n",
" print(len(interchange.collections[\"VirtualSites\"].key_map))\n",
"\n",
" return interchange._visualize_nglview(include_virtual_sites=True)\n"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "f920795f-0d48-4b2b-a83b-dedbfe011e01",
"metadata": {},
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{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/lily/micromamba/envs/openff-toolkit-test/lib/python3.11/site-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X\n",
" warnings.warn(\"Failed to guess the mass for the following atom types: {}\".format(atom_type))\n"
]
}
],
"source": [
"import MDAnalysis as mda\n",
"\n",
"u = mda.Universe(\"xyz_with_extra_point_charges.xyz\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "9d60218e-d206-47ac-8935-181786528221",
"metadata": {},
"outputs": [],
"source": [
"ff = ForceField(\"openff-2.1.0.offxml\")\n",
"handler = ff.get_parameter_handler(\"VirtualSites\")\n",
"handler.add_parameter({\n",
" \"type\": \"BondCharge\",\n",
" \"smirks\": \"[#6A:2]-[#35:1]\",\n",
" \"name\": \"EP1\",\n",
" \"distance\": 0.41 * unit.angstrom,\n",
" \"charge_increment\": [\n",
" -0.082 * unit.elementary_charge,\n",
" 0.0 * unit.elementary_charge\n",
" ],\n",
" \"sigma\": 0.0 * unit.angstrom,\n",
" \"epsilon\": 0.0 * unit.kilojoules_per_mole,\n",
" \"match\": \"all_permutations\"\n",
" })\n",
"handler.add_parameter({\n",
" \"type\": \"BondCharge\",\n",
" \"smirks\": \"[#6A:1]-[#35:2]\",\n",
" \"name\": \"EP2\",\n",
" \"distance\": -1.53 * unit.angstrom,\n",
" \"charge_increment\": [\n",
" -0.082 * unit.elementary_charge,\n",
" 0.0 * unit.elementary_charge\n",
" ],\n",
" \"sigma\": 0.0 * unit.angstrom,\n",
" \"epsilon\": 0.0 * unit.kilojoules_per_mole,\n",
" \"match\": \"all_permutations\"\n",
" })"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "608e8c74-b467-477f-bc84-f863a5f51bd5",
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2\n"
]
},
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},
"text/plain": [
"NGLWidget()"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"viz(\"CBr\", ff)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "af278af1-7493-40e9-8680-55ca50e83111",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array(['Br', 'X', 'X', 'C', 'H', 'H', 'H'], dtype=object)"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"u.atoms.names"
]
},
{
"cell_type": "code",
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"id": "3236b28d-cb6c-4ae5-b86c-0b0bef076461",
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{
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"1.5275864220791338"
]
},
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"metadata": {},
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],
"source": [
"u.atoms[[3, 1]].bond.value()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "06b1f884-3d60-4408-8322-632307fd18ed",
"metadata": {},
"outputs": [
{
"ename": "SyntaxError",
"evalue": "invalid syntax (567753897.py, line 1)",
"output_type": "error",
"traceback": [
"\u001b[0;36m Cell \u001b[0;32mIn[7], line 1\u001b[0;36m\u001b[0m\n\u001b[0;31m u.atoms[[, 2]].bond.value()\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
]
}
],
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"u.atoms[[, 2]].bond.value()"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "d07d5fb6",
"metadata": {},
"outputs": [
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"model_id": "76e7ee5c169a45a2a5a011041aa56f35",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"NGLWidget()"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"nglview.show_mdanalysis(u)"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "ab368fa9-a265-4fb1-84bb-8fdb60e526e9",
"metadata": {},
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{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "79764fbc727a4c648f40f7d5cd8d9ff2",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"NGLWidget()"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"nglview.show_mdanalysis(u.atoms[[0, 1, 3, 4, 5, 6]])"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "f750c5fe",
"metadata": {},
"outputs": [
{
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"text/plain": [
"NGLWidget()"
]
},
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"output_type": "display_data"
}
],
"source": [
"nglview.show_mdanalysis(u.atoms[[0, 2, 3, 4, 5, 6]])"
]
},
{
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"execution_count": null,
"id": "6d8dee0e",
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}
],
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"language": "python",
"name": "openff-toolkit-test"
},
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"name": "ipython",
"version": 3
},
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"mimetype": "text/x-python",
"name": "python",
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},
"toc": {
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"number_sections": true,
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"toc_position": {},
"toc_section_display": true,
"toc_window_display": false
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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