--- a +++ b/Prediction.ipynb @@ -0,0 +1,121 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "100%|██████████| 1/1 [00:00<00:00, 14.85it/s]\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Prediting SIF Stability...\n", + "Prediting SGF Stability...\n", + "Predicted SIF/SGF stability saved to the original file: Sample_Sequence.csv\n" + ] + }, + { + "data": { + "text/html": [ + "<div>\n", + "<style scoped>\n", + " .dataframe tbody tr th:only-of-type {\n", + " vertical-align: middle;\n", + " }\n", + "\n", + " .dataframe tbody tr th {\n", + " vertical-align: top;\n", + " }\n", + "\n", + " .dataframe thead th {\n", + " text-align: right;\n", + " }\n", + "</style>\n", + "<table border=\"1\" class=\"dataframe\">\n", + " <thead>\n", + " <tr style=\"text-align: right;\">\n", + " <th></th>\n", + " <th>Compound</th>\n", + " <th>SMILES</th>\n", + " <th>Stability_in_SIF</th>\n", + " <th>Stability_in_SGF</th>\n", + " </tr>\n", + " </thead>\n", + " <tbody>\n", + " <tr>\n", + " <th>0</th>\n", + " <td>Oxytocin</td>\n", + " <td>CC[C@H](C)[C@H]1C(=O)N[C@H](C(=O)N[C@H](C(=O)N...</td>\n", + " <td>Not Stable</td>\n", + " <td>Stable</td>\n", + " </tr>\n", + " </tbody>\n", + "</table>\n", + "</div>" + ], + "text/plain": [ + " Compound SMILES \\\n", + "0 Oxytocin CC[C@H](C)[C@H]1C(=O)N[C@H](C(=O)N[C@H](C(=O)N... \n", + "\n", + " Stability_in_SIF Stability_in_SGF \n", + "0 Not Stable Stable " + ] + }, + "execution_count": 1, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from lib.pred_util import model_predict, pep_feat, save_results\n", + "\n", + "#Define the path to the file that includes peptide sequence\n", + "Peptide_Path = 'Sample_Sequence.csv'\n", + "\n", + "#Featurising Peptides\n", + "peptide_features= pep_feat(Peptide_Path)\n", + "\n", + "#Make Predictions \n", + "SIF_Stability = model_predict(feat=peptide_features,Env='SIF')\n", + "SGF_Stability = model_predict(feat=peptide_features,Env='SGF')\n", + "\n", + "#Save Results\n", + "save_results(Peptide_Path,SIF_Stability,SGF_Stability)\n" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3.7.7 ('PolyML')", + "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": "3.7.7" + }, + "orig_nbformat": 4, + "vscode": { + "interpreter": { + "hash": "69caf7ba448ccac8f685f0c0ceaf2c2f7e62cc7bd75b28eb68285a65e0406c4e" + } + } + }, + "nbformat": 4, + "nbformat_minor": 2 +}