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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# API"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from chroma import api\n",
"api.register_key(\"2cdade6d058b4fd1b85fa5badb501312\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# unconditional sample"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from chroma import Chroma\n",
"\n",
"chroma = Chroma()\n",
"protein = chroma.sample(chain_lengths=[300])\n",
"\n",
"protein.to(\"sample.cif\")\n",
"\n",
"display(protein)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# conditional sample"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"from chroma import Chroma, conditioners\n",
"\n",
"chroma = Chroma()\n",
"conditioner = conditioners.SymmetryConditioner(G=\"C_3\", num_chain_neighbors=2)\n",
"protein = chroma.sample(\n",
" chain_lengths=[100],\n",
" conditioner=conditioner,\n",
" langevin_factor=8,\n",
" inverse_temperature=8,\n",
" sde_func=\"langevin\",\n",
" potts_symmetry_order=conditioner.potts_symmetry_order)\n",
"\n",
"protein.to(\"sample-C3.cif\")\n",
"display(protein)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# design"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Redesign a Protein\n",
"from chroma import Protein, Chroma\n",
"chroma = Chroma()\n",
"\n",
"protein = Protein('1GFP',device='cuda')\n",
"protein = chroma.design(protein)\n",
"\n",
"\n",
"protein.to(\"1GFP-redesign.cif\")\n",
"display(protein)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Redesign"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Redesign a Protein\n",
"from chroma import Protein, Chroma\n",
"chroma = Chroma()\n",
"\n",
"protein = Protein('sample.cif',device='cuda') # PDB is fine too\n",
"protein = chroma.design(protein, design_selection=\"resid 20-50 around 5.0\") # 5 angstrom bubble around indices 20-50\n",
"\n",
"protein.to(\"my_favorite_protein_redesign.cif\")\n",
"display(protein)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.0"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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