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miguelgondumiguelgondu
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Updates the build to the changes in the interface
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17 files changed

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‎docs/poli-docs/_build/.doctrees/environment.pickle

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‎docs/poli-docs/_build/.doctrees/understanding_foldx/01-single-mutation-using-foldx/index.doctree

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‎docs/poli-docs/_build/.doctrees/using_poli/optimization_examples/protein-stability-foldx/optimizing_protein_stability.doctree

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‎docs/poli-docs/_build/.doctrees/using_poli/the_basics/intro_to_poli.doctree

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‎docs/poli-docs/_build/.doctrees/using_poli/the_basics/isolation.doctree

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‎docs/poli-docs/_build/.jupyter_cache/executed/93cca8082af33d502625c354077d38c3/base.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"['aloha',\n",
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" 'dockstring',\n",
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" 'drd3_docking',\n",
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" 'foldx_rfp_lambo',\n",
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" 'foldx_sasa',\n",
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" 'foldx_stability',\n",
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" 'foldx_stability_and_sasa',\n",
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" 'gfp_cbas',\n",
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" 'gfp_select',\n",
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" 'penalized_logp_lambo',\n",
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" 'rasp',\n",
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" 'rdkit_logp',\n",
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" 'rdkit_qed',\n",
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" 'rfp_foldx_stability_and_sasa',\n",
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" 'sa_tdc',\n",
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" 'super_mario_bros',\n",
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" 'toy_continuous_problem',\n",
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" 'white_noise']"
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]
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},
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"execution_count": 1,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"from poli.core.registry import get_problems\n",
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"get_problems(only_available=False)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [],
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"source": [
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"problem_name = \"foldx_stability\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"3ned_Repair.pdb optimizing_protein_stability.ipynb\r\n"
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]
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}
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],
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"source": [
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"!ls"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"True"
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]
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},
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"execution_count": 4,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"from pathlib import Path\n",
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"\n",
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"wildtype_pdb_path = Path(\"./3ned_Repair.pdb\").resolve()\n",
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"wildtype_pdb_path.exists() # Should say True"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {
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"tags": [
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"hide-output"
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]
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"poli 🧪: creating an isolated black box function.\n",
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"poli 🧪: starting the isolated objective process.\n"
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]
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}
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],
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"source": [
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"from poli import objective_factory\n",
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"\n",
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"f, x0, y0 = objective_factory.create(\n",
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" name=\"foldx_stability\",\n",
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" wildtype_pdb_path=wildtype_pdb_path\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/Users/sjt972/anaconda3/envs/poli-docs2/lib/python3.9/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
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" from .autonotebook import tqdm as notebook_tqdm\n"
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]
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}
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],
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"source": [
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"from poli_baselines.solvers.simple.random_mutation import RandomMutation\n",
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"solver = RandomMutation(\n",
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" black_box=f,\n",
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" x0=x0,\n",
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" y0=y0,\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {
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"tags": [
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"hide-output"
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]
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},
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"outputs": [],
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"source": [
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"solver.solve(max_iter=3)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"All y values: [array([[9.41639]]), array([[5.56267]]), array([[0.846902]]), array([[9.39441]])]\n",
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"best stability: [9.41639]\n",
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"Associated sequence: EEDNMAIIKEFMRFKTHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEACSERMYPEDGALKGEMKMRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNTNTKLDITSHNEDYTIVEQYERNEGRHSTGGMDELYK\n"
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]
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}
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],
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"source": [
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"print(f\"All y values: {solver.history['y']}\")\n",
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"print(f\"best stability: {solver.get_best_performance()}\")\n",
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"print(f\"Associated sequence: {''.join(solver.get_best_solution().flatten())}\")"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "poli-dev",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.18"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

‎docs/poli-docs/_build/.jupyter_cache/global.db

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‎docs/poli-docs/_build/html/_sources/using_poli/optimization_examples/protein-stability-foldx/optimizing_protein_stability.ipynb

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" 'rasp',\n",
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" 'rdkit_logp',\n",
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" 'rdkit_qed',\n",
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" 'rfp_foldx_stability_and_sasa',\n",
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" 'sa_tdc',\n",
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" 'super_mario_bros',\n",
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" 'toy_continuous_problem',\n",
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"f, x0, y0 = objective_factory.create(\n",
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" name=\"foldx_stability\",\n",
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" caller_info=None,\n",
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" observer=None,\n",
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")"
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]
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.17"
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"version": "3.9.18"
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},
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"orig_nbformat": 4
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},

‎docs/poli-docs/_build/html/reports/using_poli/the_basics/isolation.err.log

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File "<string>", line 1, in <module>
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ModuleNotFoundError: No module named 'register'
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----- stderr -----
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CRITICAL:root:Path: /opt/homebrew/bin:/Users/sjt972/anaconda3/envs/poli__dockstring/bin:/Users/sjt972/anaconda3/condabin:/Users/sjt972/autodock_vina_1_1_2_mac_catalina_64bit/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Library/TeX/texbin:/usr/local/go/bin:/Users/sjt972/.cargo/bin:/opt/homebrew/bin:/Users/sjt972/autodock_vina_1_1_2_mac_catalina_64bit/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Library/TeX/texbin:/usr/local/go/bin:/opt/homebrew/bin:/Users/sjt972/anaconda3/bin:/Users/sjt972/anaconda3/condabin:/Users/sjt972/autodock_vina_1_1_2_mac_catalina_64bit/bin:/Users/sjt972/.cargo/bin:/Users/sjt972/anaconda3/bin
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CRITICAL:root:Path: /opt/homebrew/opt/openjdk/bin:/opt/homebrew/bin:/Users/sjt972/anaconda3/envs/poli__dockstring/bin:/Users/sjt972/anaconda3/condabin:/Users/sjt972/autodock_vina_1_1_2_mac_catalina_64bit/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Library/TeX/texbin:/usr/local/go/bin:/Users/sjt972/.cargo/bin
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CRITICAL:root:Python path: ['/Users/sjt972/Projects/poli/src/poli', '/Users/sjt972/Projects/poli-docs/docs/poli-docs/using_poli/the_basics', '/Users/sjt972/anaconda3/envs/poli-docs2/lib/python3.9/site-packages/poli/objective_repository/dockstring', '/Users/sjt972/anaconda3/envs/poli__dockstring/lib/python39.zip', '/Users/sjt972/anaconda3/envs/poli__dockstring/lib/python3.9', '/Users/sjt972/anaconda3/envs/poli__dockstring/lib/python3.9/lib-dynload', '/Users/sjt972/anaconda3/envs/poli__dockstring/lib/python3.9/site-packages', '/Users/sjt972/Projects/poli/src', '', '/Users/sjt972/anaconda3/envs/poli-docs2/lib/python3.9/site-packages/poli/objective_repository/dockstring']
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CRITICAL:root:Path: :/Users/sjt972/anaconda3/envs/poli-docs2/lib/python3.9/site-packages/poli/objective_repository/dockstring
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CRITICAL:root:Path: :/Users/sjt972/anaconda3/envs/poli-docs2/lib/python3.9/site-packages/poli/objective_repository/dockstring

‎docs/poli-docs/_build/html/searchindex.js

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