OneScience-Group/ProteinMPNN
124
1{2 "cells": [3 {4 "cell_type": "markdown",5 "metadata": {6 "colab_type": "text",7 "id": "view-in-github"8 },9 "source": [10 "<a href=\"https://colab.research.google.com/github/dauparas/ProteinMPNN/blob/main/training/colab_training_example.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"11 ]12 },13 {14 "cell_type": "code",15 "execution_count": 2,16 "metadata": {17 "colab": {18 "base_uri": "https://localhost:8080/"19 },20 "id": "lPQopPm1WWrG",21 "outputId": "9546d08c-9248-445e-81b0-b3ba82f4a801"22 },23 "outputs": [24 {25 "name": "stdout",26 "output_type": "stream",27 "text": [28 "--2022-10-26 03:43:33-- https://files.ipd.uw.edu/pub/training_sets/pdb_2021aug02_sample.tar.gz\n",29 "Resolving files.ipd.uw.edu (files.ipd.uw.edu)... 198.48.92.75, 128.95.160.134, 128.95.160.135, ...\n",30 "Connecting to files.ipd.uw.edu (files.ipd.uw.edu)|198.48.92.75|:443... connected.\n",31 "HTTP request sent, awaiting response... 200 OK\n",32 "Length: 49690915 (47M) [application/octet-stream]\n",33 "Saving to: ‘pdb_2021aug02_sample.tar.gz’\n",34 "\n",35 "pdb_2021aug02_sampl 100%[===================>] 47.39M 13.5MB/s in 3.7s \n",36 "\n",37 "2022-10-26 03:43:38 (12.9 MB/s) - ‘pdb_2021aug02_sample.tar.gz’ saved [49690915/49690915]\n",38 "\n"39 ]40 }41 ],42 "source": [43 "!wget https://files.ipd.uw.edu/pub/training_sets/pdb_2021aug02_sample.tar.gz"44 ]45 },46 {47 "cell_type": "code",48 "execution_count": 3,49 "metadata": {50 "colab": {51 "base_uri": "https://localhost:8080/"52 },53 "id": "21to7lSNWemb",54 "outputId": "7a51e458-a4e4-4b79-d26b-81570e855d62"55 },56 "outputs": [57 {58 "name": "stdout",59 "output_type": "stream",60 "text": [61 "./pdb_2021aug02_sample/\n",62 "./pdb_2021aug02_sample/README\n",63 "./pdb_2021aug02_sample/list.csv\n",64 "./pdb_2021aug02_sample/pdb/\n",65 "./pdb_2021aug02_sample/pdb/l3/\n",66 "./pdb_2021aug02_sample/pdb/l3/5l3p.pt\n",67 "./pdb_2021aug02_sample/pdb/l3/5l3g_A.pt\n",68 "./pdb_2021aug02_sample/pdb/l3/5l3f.pt\n",69 "./pdb_2021aug02_sample/pdb/l3/5l3r_B.pt\n",70 "./pdb_2021aug02_sample/pdb/l3/4l3o_G.pt\n",71 "./pdb_2021aug02_sample/pdb/l3/1l3b_E.pt\n",72 "./pdb_2021aug02_sample/pdb/l3/3l3t_C.pt\n",73 "./pdb_2021aug02_sample/pdb/l3/6l3y_A.pt\n",74 "./pdb_2021aug02_sample/pdb/l3/5l3p_DB.pt\n",75 "./pdb_2021aug02_sample/pdb/l3/3l36_B.pt\n",76 "./pdb_2021aug02_sample/pdb/l3/2l3y_A.pt\n",77 "./pdb_2021aug02_sample/pdb/l3/2l36.pt\n",78 "./pdb_2021aug02_sample/pdb/l3/5l35_G.pt\n",79 "./pdb_2021aug02_sample/pdb/l3/3l33_F.pt\n",80 "./pdb_2021aug02_sample/pdb/l3/2l3n.pt\n",81 "./pdb_2021aug02_sample/pdb/l3/2l3x.pt\n",82 "./pdb_2021aug02_sample/pdb/l3/1l3r_B.pt\n",83 "./pdb_2021aug02_sample/pdb/l3/1l3g_A.pt\n",84 "./pdb_2021aug02_sample/pdb/l3/4l3e.pt\n",85 "./pdb_2021aug02_sample/pdb/l3/5l39_E.pt\n",86 "./pdb_2021aug02_sample/pdb/l3/4l3f_A.pt\n",87 "./pdb_2021aug02_sample/pdb/l3/4l31_C.pt\n",88 "./pdb_2021aug02_sample/pdb/l3/5l3k_C.pt\n",89 "./pdb_2021aug02_sample/pdb/l3/3l35.pt\n",90 "./pdb_2021aug02_sample/pdb/l3/6l37_B.pt\n",91 "./pdb_2021aug02_sample/pdb/l3/5l3p_CB.pt\n",92 "./pdb_2021aug02_sample/pdb/l3/4l3c_E.pt\n",93 "./pdb_2021aug02_sample/pdb/l3/3l3x_A.pt\n",94 "./pdb_2021aug02_sample/pdb/l3/6l3u_C.pt\n",95 "./pdb_2021aug02_sample/pdb/l3/4l3c_S.pt\n",96 "./pdb_2021aug02_sample/pdb/l3/3l3m.pt\n",97 "./pdb_2021aug02_sample/pdb/l3/7l38.pt\n",98 "./pdb_2021aug02_sample/pdb/l3/7l3v.pt\n",99 "./pdb_2021aug02_sample/pdb/l3/3l3s_L.pt\n",100 "./pdb_2021aug02_sample/pdb/l3/1l3v_C.pt\n",101 "./pdb_2021aug02_sample/pdb/l3/5l3p_I.pt\n",102 "./pdb_2021aug02_sample/pdb/l3/6l3x_D.pt\n",103 "./pdb_2021aug02_sample/pdb/l3/4l3n_B.pt\n",104 "./pdb_2021aug02_sample/pdb/l3/5l3s_G.pt\n",105 "./pdb_2021aug02_sample/pdb/l3/7l3e_A.pt\n",106 "./pdb_2021aug02_sample/pdb/l3/7l32_C.pt\n",107 "./pdb_2021aug02_sample/pdb/l3/6l3t_F.pt\n",108 "./pdb_2021aug02_sample/pdb/l3/6l35_I.pt\n",109 "./pdb_2021aug02_sample/pdb/l3/2l3d_A.pt\n",110 "./pdb_2021aug02_sample/pdb/l3/6l3u.pt\n",111 "./pdb_2021aug02_sample/pdb/l3/1l3k.pt\n",112 "./pdb_2021aug02_sample/pdb/l3/6l33_C.pt\n",113 "./pdb_2021aug02_sample/pdb/l3/4l3g_D.pt\n",114 "./pdb_2021aug02_sample/pdb/l3/3l3i_C.pt\n",115 "./pdb_2021aug02_sample/pdb/l3/6l3q_B.pt\n",116 "./pdb_2021aug02_sample/pdb/l3/1l33.pt\n",117 "./pdb_2021aug02_sample/pdb/l3/5l3o_B.pt\n",118 "./pdb_2021aug02_sample/pdb/l3/5l3z_A.pt\n",119 "./pdb_2021aug02_sample/pdb/l3/6l3t.pt\n",120 "./pdb_2021aug02_sample/pdb/l3/3l3o_H.pt\n",121 "./pdb_2021aug02_sample/pdb/l3/6l35_H.pt\n",122 "./pdb_2021aug02_sample/pdb/l3/1l38_A.pt\n",123 "./pdb_2021aug02_sample/pdb/l3/4l3b_A.pt\n",124 "./pdb_2021aug02_sample/pdb/l3/5l38_A.pt\n",125 "./pdb_2021aug02_sample/pdb/l3/1l32.pt\n",126 "./pdb_2021aug02_sample/pdb/l3/3l3i_B.pt\n",127 "./pdb_2021aug02_sample/pdb/l3/4l3g_E.pt\n",128 "./pdb_2021aug02_sample/pdb/l3/6l33_B.pt\n",129 "./pdb_2021aug02_sample/pdb/l3/1l3j.pt\n",130 "./pdb_2021aug02_sample/pdb/l3/5l3v_B.pt\n",131 "./pdb_2021aug02_sample/pdb/l3/5l3c_A.pt\n",132 "./pdb_2021aug02_sample/pdb/l3/7l3a.pt\n",133 "./pdb_2021aug02_sample/pdb/l3/3l32_B.pt\n",134 "./pdb_2021aug02_sample/pdb/l3/7l39.pt\n",135 "./pdb_2021aug02_sample/pdb/l3/6l3h_B.pt\n",136 "./pdb_2021aug02_sample/pdb/l3/3l34_H.pt\n",137 "./pdb_2021aug02_sample/pdb/l3/7l32_B.pt\n",138 "./pdb_2021aug02_sample/pdb/l3/3l3c_J.pt\n",139 "./pdb_2021aug02_sample/pdb/l3/5l3s_F.pt\n",140 "./pdb_2021aug02_sample/pdb/l3/1l3c_A.pt\n",141 "./pdb_2021aug02_sample/pdb/l3/6l3x_E.pt\n",142 "./pdb_2021aug02_sample/pdb/l3/5l3p_H.pt\n",143 "./pdb_2021aug02_sample/pdb/l3/4l39_A.pt\n",144 "./pdb_2021aug02_sample/pdb/l3/4l31_B.pt\n",145 "./pdb_2021aug02_sample/pdb/l3/4l3r.pt\n",146 "./pdb_2021aug02_sample/pdb/l3/5l39_D.pt\n",147 "./pdb_2021aug02_sample/pdb/l3/3l3l.pt\n",148 "./pdb_2021aug02_sample/pdb/l3/4l3c_R.pt\n",149 "./pdb_2021aug02_sample/pdb/l3/6l3u_B.pt\n",150 "./pdb_2021aug02_sample/pdb/l3/3l3z.pt\n",151 "./pdb_2021aug02_sample/pdb/l3/4l3c_D.pt\n",152 "./pdb_2021aug02_sample/pdb/l3/3l34.pt\n",153 "./pdb_2021aug02_sample/pdb/l3/5l3k_B.pt\n",154 "./pdb_2021aug02_sample/pdb/l3/3l3t_B.pt\n",155 "./pdb_2021aug02_sample/pdb/l3/1l3b_D.pt\n",156 "./pdb_2021aug02_sample/pdb/l3/3l3a_A.pt\n",157 "./pdb_2021aug02_sample/pdb/l3/4l3o_F.pt\n",158 "./pdb_2021aug02_sample/pdb/l3/5l3g.pt\n",159 "./pdb_2021aug02_sample/pdb/l3/5l3r_C.pt\n",160 "./pdb_2021aug02_sample/pdb/l3/5l3q.pt\n",161 "./pdb_2021aug02_sample/pdb/l3/5l30_B.pt\n",162 "./pdb_2021aug02_sample/pdb/l3/2l3y.pt\n",163 "./pdb_2021aug02_sample/pdb/l3/3l33_G.pt\n",164 "./pdb_2021aug02_sample/pdb/l3/2l3o.pt\n",165 "./pdb_2021aug02_sample/pdb/l3/5l35_F.pt\n",166 "./pdb_2021aug02_sample/pdb/l3/2l37.pt\n",167 "./pdb_2021aug02_sample/pdb/l3/7l3a_A.pt\n",168 "./pdb_2021aug02_sample/pdb/l3/3l36.pt\n",169 "./pdb_2021aug02_sample/pdb/l3/5l3p_CA.pt\n",170 "./pdb_2021aug02_sample/pdb/l3/6l37_A.pt\n",171 "./pdb_2021aug02_sample/pdb/l3/4l34_D.pt\n",172 "./pdb_2021aug02_sample/pdb/l3/3l3x.pt\n",173 "./pdb_2021aug02_sample/pdb/l3/3l3m_A.pt\n",174 "./pdb_2021aug02_sample/pdb/l3/4l3c_F.pt\n",175 "./pdb_2021aug02_sample/pdb/l3/3l3n.pt\n",176 "./pdb_2021aug02_sample/pdb/l3/3l3x_B.pt\n",177 "./pdb_2021aug02_sample/pdb/l3/4l3c_P.pt\n",178 "./pdb_2021aug02_sample/pdb/l3/5l39_F.pt\n",179 "./pdb_2021aug02_sample/pdb/l3/2l37_A.pt\n",180 "./pdb_2021aug02_sample/pdb/l3/4l3f.pt\n",181 "./pdb_2021aug02_sample/pdb/l3/4l3p.pt\n",182 "./pdb_2021aug02_sample/pdb/l3/7l3m_A.pt\n",183 "./pdb_2021aug02_sample/pdb/l3/4l3f_B.pt\n",184 "./pdb_2021aug02_sample/pdb/l3/2l35.pt\n",185 "./pdb_2021aug02_sample/pdb/l3/2l3l_A.pt\n",186 "./pdb_2021aug02_sample/pdb/l3/7l36_A.pt\n",187 "./pdb_2021aug02_sample/pdb/l3/5l35_D.pt\n",188 "./pdb_2021aug02_sample/pdb/l3/2l3m.pt\n",189 "./pdb_2021aug02_sample/pdb/l3/3l33_E.pt\n",190 "./pdb_2021aug02_sample/pdb/l3/1l3r_A.pt\n",191 "./pdb_2021aug02_sample/pdb/l3/5l3s.pt\n",192 "./pdb_2021aug02_sample/pdb/l3/5l3g_B.pt\n",193 "./pdb_2021aug02_sample/pdb/l3/5l3r_A.pt\n",194 "./pdb_2021aug02_sample/pdb/l3/5l3e.pt\n",195 "./pdb_2021aug02_sample/pdb/l3/1l3b_F.pt\n",196 "./pdb_2021aug02_sample/pdb/l3/4l3o_D.pt\n",197 "./pdb_2021aug02_sample/pdb/l3/5l3p_DA.pt\n",198 "./pdb_2021aug02_sample/pdb/l3/6l3y_B.pt\n",199 "./pdb_2021aug02_sample/pdb/l3/3l36_A.pt\n",200 "./pdb_2021aug02_sample/pdb/l3/1l3h.pt\n",201 "./pdb_2021aug02_sample/pdb/l3/6l3q_A.pt\n",202 "./pdb_2021aug02_sample/pdb/l3/7l3l_D.pt\n",203 "./pdb_2021aug02_sample/pdb/l3/5l3o_A.pt\n",204 "./pdb_2021aug02_sample/pdb/l3/1l30.pt\n",205 "./pdb_2021aug02_sample/pdb/l3/5l38_C.pt\n",206 "./pdb_2021aug02_sample/pdb/l3/6l3t_E.pt\n",207 "./pdb_2021aug02_sample/pdb/l3/1l3o_A.pt\n",208 "./pdb_2021aug02_sample/pdb/l3/4l3b_C.pt\n",209 "./pdb_2021aug02_sample/pdb/l3/4l35_A.pt\n",210 "./pdb_2021aug02_sample/pdb/l3/6l38.pt\n",211 "./pdb_2021aug02_sample/pdb/l3/6l35_J.pt\n",212 "./pdb_2021aug02_sample/pdb/l3/5l3p_JA.pt\n",213 "./pdb_2021aug02_sample/pdb/l3/2l3q_A.pt\n",214 "./pdb_2021aug02_sample/pdb/l3/6l3v.pt\n",215 "./pdb_2021aug02_sample/pdb/l3/1l34_A.pt\n",216 "./pdb_2021aug02_sample/pdb/l3/6l3x_G.pt\n",217 "./pdb_2021aug02_sample/pdb/l3/5l3p_J.pt\n",218 "./pdb_2021aug02_sample/pdb/l3/1l3c_C.pt\n",219 "./pdb_2021aug02_sample/pdb/l3/6l3m_D.pt\n",220 "./pdb_2021aug02_sample/pdb/l3/4l3n_A.pt\n",221 "./pdb_2021aug02_sample/pdb/l3/7l3p_A.pt\n",222 "./pdb_2021aug02_sample/pdb/l3/5l3s_D.pt\n",223 "./pdb_2021aug02_sample/pdb/l3/5l3p_MA.pt\n",224 "./pdb_2021aug02_sample/pdb/l3/3l3p_A.pt\n",225 "./pdb_2021aug02_sample/pdb/l3/7l3u.pt\n",226 "./pdb_2021aug02_sample/pdb/l3/7l3c.pt\n",227 "./pdb_2021aug02_sample/pdb/l3/5l34_A.pt\n",228 "./pdb_2021aug02_sample/pdb/l3/5l31_D.pt\n",229 "./pdb_2021aug02_sample/pdb/l3/7l32_A.pt\n",230 "./pdb_2021aug02_sample/pdb/l3/2l3h_A.pt\n",231 "./pdb_2021aug02_sample/pdb/l3/5l3s_E.pt\n",232 "./pdb_2021aug02_sample/pdb/l3/1l3c_B.pt\n",233 "./pdb_2021aug02_sample/pdb/l3/5l3p_K.pt\n",234 "./pdb_2021aug02_sample/pdb/l3/6l3x_F.pt\n",235 "./pdb_2021aug02_sample/pdb/l3/4l39_B.pt\n",236 "./pdb_2021aug02_sample/pdb/l3/5l3v_A.pt\n",237 "./pdb_2021aug02_sample/pdb/l3/4l3c_FA.pt\n",238 "./pdb_2021aug02_sample/pdb/l3/5l3c_B.pt\n",239 "./pdb_2021aug02_sample/pdb/l3/7l3b.pt\n",240 "./pdb_2021aug02_sample/pdb/l3/5l3p_VA.pt\n",241 "./pdb_2021aug02_sample/pdb/l3/3l32_A.pt\n",242 "./pdb_2021aug02_sample/pdb/l3/6l3h_A.pt\n",243 "./pdb_2021aug02_sample/pdb/l3/5l38_B.pt\n",244 "./pdb_2021aug02_sample/pdb/l3/4l3c_AA.pt\n",245 "./pdb_2021aug02_sample/pdb/l3/1l31.pt\n",246 "./pdb_2021aug02_sample/pdb/l3/5l3p_QA.pt\n",247 "./pdb_2021aug02_sample/pdb/l3/4l3g_F.pt\n",248 "./pdb_2021aug02_sample/pdb/l3/3l3i_A.pt\n",249 "./pdb_2021aug02_sample/pdb/l3/1l3i.pt\n",250 "./pdb_2021aug02_sample/pdb/l3/6l33_A.pt\n",251 "./pdb_2021aug02_sample/pdb/l3/7l3i_A.pt\n",252 "./pdb_2021aug02_sample/pdb/l3/6l3w.pt\n",253 "./pdb_2021aug02_sample/pdb/l3/6l3a.pt\n",254 "./pdb_2021aug02_sample/pdb/l3/2l33_A.pt\n",255 "./pdb_2021aug02_sample/pdb/l3/6l35_K.pt\n",256 "./pdb_2021aug02_sample/pdb/l3/6l39.pt\n",257 "./pdb_2021aug02_sample/pdb/l3/4l3b_B.pt\n",258 "./pdb_2021aug02_sample/pdb/l3/4l3w_A.pt\n",259 "./pdb_2021aug02_sample/pdb/l3/6l3t_D.pt\n",260 "./pdb_2021aug02_sample/pdb/l3/4l3j_A.pt\n",261 "./pdb_2021aug02_sample/pdb/l3/4l3c_OA.pt\n",262 "./pdb_2021aug02_sample/pdb/l3/2l3z.pt\n",263 "./pdb_2021aug02_sample/pdb/l3/2l3l.pt\n",264 "./pdb_2021aug02_sample/pdb/l3/3l33_D.pt\n",265 "./pdb_2021aug02_sample/pdb/l3/1l30_A.pt\n",266 "./pdb_2021aug02_sample/pdb/l3/5l35_E.pt\n",267 "./pdb_2021aug02_sample/pdb/l3/2l34.pt\n",268 "./pdb_2021aug02_sample/pdb/l3/3l3t_A.pt\n",269 "./pdb_2021aug02_sample/pdb/l3/4l3o_E.pt\n",270 "./pdb_2021aug02_sample/pdb/l3/1l3b_G.pt\n",271 "./pdb_2021aug02_sample/pdb/l3/5l3d.pt\n",272 "./pdb_2021aug02_sample/pdb/l3/5l3g_C.pt\n",273 "./pdb_2021aug02_sample/pdb/l3/5l3r.pt\n",274 "./pdb_2021aug02_sample/pdb/l3/5l30_A.pt\n",275 "./pdb_2021aug02_sample/pdb/l3/4l3c_Q.pt\n",276 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"./pdb_2021aug02_sample/pdb/l3/3l3p.pt\n",777 "./pdb_2021aug02_sample/pdb/l3/1l3x_A.pt\n",778 "./pdb_2021aug02_sample/pdb/l3/6l3v_F.pt\n",779 "./pdb_2021aug02_sample/pdb/l3/5l3p_IA.pt\n",780 "./pdb_2021aug02_sample/pdb/l3/5l3k_H.pt\n",781 "./pdb_2021aug02_sample/pdb/l3/4l37_B.pt\n",782 "./pdb_2021aug02_sample/pdb/l3/4l3c_BA.pt\n",783 "./pdb_2021aug02_sample/pdb/l3/3l3k_B.pt\n",784 "./pdb_2021aug02_sample/pdb/l3/4l3e_E.pt\n",785 "./pdb_2021aug02_sample/pdb/l3/6l31_B.pt\n",786 "./pdb_2021aug02_sample/pdb/l3/4l3o.pt\n",787 "./pdb_2021aug02_sample/pdb/l3/4l3y.pt\n",788 "./pdb_2021aug02_sample/pdb/l3/5l3p_RA.pt\n",789 "./pdb_2021aug02_sample/pdb/l3/4l37.pt\n",790 "./pdb_2021aug02_sample/pdb/l3/3l3q.pt\n",791 "./pdb_2021aug02_sample/pdb/l3/4l3c_O.pt\n",792 "./pdb_2021aug02_sample/pdb/l3/3l3g.pt\n",793 "./pdb_2021aug02_sample/pdb/l3/4l3c_Y.pt\n",794 "./pdb_2021aug02_sample/pdb/l3/5l3z.pt\n",795 "./pdb_2021aug02_sample/pdb/l3/1l3a_A.pt\n",796 "./pdb_2021aug02_sample/pdb/l3/5l3l.pt\n",797 "./pdb_2021aug02_sample/pdb/l3/3l35_F.pt\n",798 "./pdb_2021aug02_sample/pdb/l3/5l34.pt\n",799 "./pdb_2021aug02_sample/pdb/l3/7l30_B.pt\n",800 "./pdb_2021aug02_sample/pdb/l3/4l3c_EA.pt\n",801 "./pdb_2021aug02_sample/pdb/l3/5l3t_B.pt\n",802 "./pdb_2021aug02_sample/pdb/l3/5l3a_A.pt\n",803 "./pdb_2021aug02_sample/pdb/l3/5l3p_UA.pt\n",804 "./pdb_2021aug02_sample/pdb/l3/2l3d.pt\n",805 "./pdb_2021aug02_sample/pdb/l3/2l3r.pt\n",806 "./pdb_2021aug02_sample/pdb/l3/6l31.pt\n",807 "./pdb_2021aug02_sample/pdb/l3/3l3o_C.pt\n",808 "./pdb_2021aug02_sample/pdb/l3/1l3l_F.pt\n",809 "./pdb_2021aug02_sample/pdb/l3/6l35_C.pt\n",810 "./pdb_2021aug02_sample/pdb/l3/3l38_A.pt\n",811 "./pdb_2021aug02_sample/pdb/l3/4l3c_KA.pt\n",812 "./pdb_2021aug02_sample/pdb/l3/2l3b_A.pt\n",813 "./pdb_2021aug02_sample/pdb/l3/7l3o_C.pt\n",814 "./pdb_2021aug02_sample/pdb/l3/1l3w.pt\n",815 "./pdb_2021aug02_sample/pdb/l3/7l38_A.pt\n",816 "./pdb_2021aug02_sample/pdb/l3/1l3a.pt\n",817 "./pdb_2021aug02_sample/pdb/l3/4l33_B.pt\n",818 "./pdb_2021aug02_sample/pdb/l3/5l38_J.pt\n",819 "./pdb_2021aug02_sample/pdb/l3/1l3i_B.pt\n",820 "./pdb_2021aug02_sample/pdb/l3/1l39.pt\n",821 "./pdb_2021aug02_sample/pdb/l3/4l3c_LA.pt\n",822 "./pdb_2021aug02_sample/pdb/l3/2l39_A.pt\n",823 "./pdb_2021aug02_sample/pdb/l3/7l32.pt\n",824 "./pdb_2021aug02_sample/pdb/l3/7l3c_A.pt\n",825 "./pdb_2021aug02_sample/pdb/l3/4l3h_B.pt\n",826 "./pdb_2021aug02_sample/pdb/l3/3l3s_F.pt\n",827 "./pdb_2021aug02_sample/pdb/l3/7l3j.pt\n",828 "./pdb_2021aug02_sample/pdb/l3/5l3p_C.pt\n",829 "./pdb_2021aug02_sample/pdb/l3/6l3x_N.pt\n",830 "./pdb_2021aug02_sample/pdb/l3/5l3p_U.pt\n",831 "./pdb_2021aug02_sample/pdb/l3/5l32_B.pt\n",832 "./pdb_2021aug02_sample/pdb/l3/6l39_A.pt\n",833 "./pdb_2021aug02_sample/pdb/l3/3l34_C.pt\n",834 "./pdb_2021aug02_sample/pdb/l3/3l3v_B.pt\n",835 "./pdb_2021aug02_sample/pdb/l3/3l3c_A.pt\n",836 "./pdb_2021aug02_sample/pdb/l3/6l3n_C.pt\n",837 "./pdb_2021aug02_sample/pdb/l3/4l3q_A.pt\n",838 "./pdb_2021aug02_sample/pdb/l3/5l38_H.pt\n",839 "./pdb_2021aug02_sample/pdb/l3/2l35_A.pt\n",840 "./pdb_2021aug02_sample/pdb/l3/1l3c.pt\n",841 "./pdb_2021aug02_sample/pdb/l3/1l3u.pt\n",842 "./pdb_2021aug02_sample/pdb/l3/7l3o_A.pt\n",843 "./pdb_2021aug02_sample/pdb/l3/6l35_A.pt\n",844 "./pdb_2021aug02_sample/pdb/l3/3l3o_A.pt\n",845 "./pdb_2021aug02_sample/pdb/l3/3l3z_B.pt\n",846 "./pdb_2021aug02_sample/pdb/l3/6l33.pt\n",847 "./pdb_2021aug02_sample/pdb/l3/6l3n_A.pt\n",848 "./pdb_2021aug02_sample/pdb/l3/3l34_A.pt\n",849 "./pdb_2021aug02_sample/pdb/l3/7l31_E.pt\n",850 "./pdb_2021aug02_sample/pdb/l3/5l3p_W.pt\n",851 "./pdb_2021aug02_sample/pdb/l3/5l3e_B.pt\n",852 "./pdb_2021aug02_sample/pdb/l3/6l3x_L.pt\n",853 "./pdb_2021aug02_sample/pdb/l3/7l3h.pt\n",854 "./pdb_2021aug02_sample/pdb/l3/3l3s_D.pt\n",855 "./pdb_2021aug02_sample/pdb/l3/1l3p_A.pt\n",856 "./pdb_2021aug02_sample/pdb/l3/1l3e_B.pt\n",857 "./pdb_2021aug02_sample/pdb/l3/2l3n_A.pt\n",858 "./pdb_2021aug02_sample/pdb/l3/7l30.pt\n",859 "./pdb_2021aug02_sample/pdb/l3/5l37_D.pt\n",860 "./pdb_2021aug02_sample/pdb/l3/7l34_A.pt\n",861 "./pdb_2021aug02_sample/pdb/l3/2l3s_A.pt\n",862 "./pdb_2021aug02_sample/pdb/l3/3l3s.pt\n",863 "./pdb_2021aug02_sample/pdb/l3/4l3c_M.pt\n",864 "./pdb_2021aug02_sample/pdb/l3/6l3v_E.pt\n",865 "./pdb_2021aug02_sample/pdb/l3/4l37_A.pt\n",866 "./pdb_2021aug02_sample/pdb/l3/5l3m_A.pt\n",867 "./pdb_2021aug02_sample/pdb/l3/7l3n_D.pt\n",868 "./pdb_2021aug02_sample/pdb/l3/4l35.pt\n",869 "./pdb_2021aug02_sample/pdb/l3/5l3x_B.pt\n",870 "./pdb_2021aug02_sample/pdb/l3/6l3s_A.pt\n",871 "./pdb_2021aug02_sample/pdb/l3/2l3p.pt\n",872 "./pdb_2021aug02_sample/pdb/l3/2l3f.pt\n",873 "./pdb_2021aug02_sample/pdb/l3/5l36_A.pt\n",874 "./pdb_2021aug02_sample/pdb/l3/3l3g_B.pt\n",875 "./pdb_2021aug02_sample/pdb/l3/3l3r_A.pt\n",876 "./pdb_2021aug02_sample/pdb/l3/5l3q_D.pt\n",877 "./pdb_2021aug02_sample/pdb/l3/5l36.pt\n",878 "./pdb_2021aug02_sample/pdb/l3/3l35_D.pt\n",879 "./pdb_2021aug02_sample/pdb/l3/1l36_A.pt\n",880 "./pdb_2021aug02_sample/pdb/l3/4l3y_B.pt\n",881 "./pdb_2021aug02_sample/pdb/l3/5l3n.pt\n",882 "./pdb_2021aug02_sample/pdb/l3/1l3a_C.pt\n",883 "./pdb_2021aug02_sample/pdb/l3/4l3l_A.pt\n",884 "./pdb_2021aug02_sample/pdb/l3/5l3x.pt\n",885 "./pdb_2021aug02_sample/pdb/l3/3l30_A.pt\n",886 "./pdb_2021aug02_sample/pdb/l3/3l3g_C.pt\n",887 "./pdb_2021aug02_sample/pdb/l3/5l3t_A.pt\n",888 "./pdb_2021aug02_sample/pdb/l3/2l3g.pt\n",889 "./pdb_2021aug02_sample/pdb/l3/2l3q.pt\n",890 "./pdb_2021aug02_sample/pdb/l3/5l3y.pt\n",891 "./pdb_2021aug02_sample/pdb/l3/1l3a_B.pt\n",892 "./pdb_2021aug02_sample/pdb/l3/5l3o.pt\n",893 "./pdb_2021aug02_sample/pdb/l3/3l35_E.pt\n",894 "./pdb_2021aug02_sample/pdb/l3/5l37.pt\n",895 "./pdb_2021aug02_sample/pdb/l3/7l30_A.pt\n",896 "./pdb_2021aug02_sample/pdb/l3/2l3j_A.pt\n",897 "./pdb_2021aug02_sample/pdb/l3/6l3v_D.pt\n",898 "./pdb_2021aug02_sample/pdb/l3/4l3u_A.pt\n",899 "./pdb_2021aug02_sample/pdb/l3/7l3k_A.pt\n",900 "./pdb_2021aug02_sample/pdb/l3/4l3c_L.pt\n",901 "./pdb_2021aug02_sample/pdb/l3/3l3r.pt\n",902 "./pdb_2021aug02_sample/pdb/l3/4l3c_Z.pt\n",903 "./pdb_2021aug02_sample/pdb/l3/3l3d.pt\n",904 "./pdb_2021aug02_sample/pdb/l3/2l31_A.pt\n",905 "./pdb_2021aug02_sample/pdb/l3/3l3k_A.pt\n",906 "./pdb_2021aug02_sample/pdb/l3/4l3l.pt\n",907 "./pdb_2021aug02_sample/pdb/l3/6l31_A.pt\n",908 "./pdb_2021aug02_sample/pdb/l3/4l32_D.pt\n",909 "./pdb_2021aug02_sample/pdb/l3/4l3z.pt\n",910 "./pdb_2021aug02_sample/pdb/l3/4l34.pt\n",911 "./pdb_2021aug02_sample/pdb/l3/7l3n_E.pt\n",912 "./pdb_2021aug02_sample/pdb/l3/4l3f_H.pt\n",913 "./pdb_2021aug02_sample/pdb/l3/6l3x_M.pt\n",914 "./pdb_2021aug02_sample/pdb/l3/5l3p_V.pt\n",915 "./pdb_2021aug02_sample/pdb/l3/7l31_D.pt\n",916 "./pdb_2021aug02_sample/pdb/l3/5l32_A.pt\n",917 "./pdb_2021aug02_sample/pdb/l3/6l39_B.pt\n",918 "./pdb_2021aug02_sample/pdb/l3/3l3v_A.pt\n",919 "./pdb_2021aug02_sample/pdb/l3/5l37_E.pt\n",920 "./pdb_2021aug02_sample/pdb/l3/7l31.pt\n",921 "./pdb_2021aug02_sample/pdb/l3/7l3v_A.pt\n",922 "./pdb_2021aug02_sample/pdb/l3/4l3h_A.pt\n",923 "./pdb_2021aug02_sample/pdb/l3/3l3s_E.pt\n",924 "./pdb_2021aug02_sample/pdb/l3/7l3i.pt\n",925 "./pdb_2021aug02_sample/pdb/l3/1l32_A.pt\n",926 "./pdb_2021aug02_sample/pdb/l3/2l3w_A.pt\n",927 "./pdb_2021aug02_sample/pdb/l3/1l3t.pt\n",928 "./pdb_2021aug02_sample/pdb/l3/1l3b.pt\n",929 "./pdb_2021aug02_sample/pdb/l3/5l38_I.pt\n",930 "./pdb_2021aug02_sample/pdb/l3/4l33_A.pt\n",931 "./pdb_2021aug02_sample/pdb/l3/1l3i_A.pt\n",932 "./pdb_2021aug02_sample/pdb/l3/6l32.pt\n",933 "./pdb_2021aug02_sample/pdb/l3/5l3i_A.pt\n",934 "./pdb_2021aug02_sample/pdb/l3/6l3w_A.pt\n",935 "./pdb_2021aug02_sample/pdb/l3/1l3l_E.pt\n",936 "./pdb_2021aug02_sample/test_clusters.txt\n",937 "./pdb_2021aug02_sample/valid_clusters.txt\n"938 ]939 }940 ],941 "source": [942 "!tar xvf \"pdb_2021aug02_sample.tar.gz\""943 ]944 },945 {946 "cell_type": "code",947 "execution_count": 4,948 "metadata": {949 "id": "Ul9pmaQzXAg3"950 },951 "outputs": [],952 "source": [953 "import sys"954 ]955 },956 {957 "cell_type": "code",958 "execution_count": 5,959 "metadata": {960 "id": "o-03W_vgWguT"961 },962 "outputs": [],963 "source": [964 "sys.path.append(\"/content/ProteinMPNN/training\")"965 ]966 },967 {968 "cell_type": "code",969 "execution_count": 6,970 "metadata": {971 "id": "6-xXsyM-W_7k"972 },973 "outputs": [],974 "source": [975 "from training import main as run_training"976 ]977 },978 {979 "cell_type": "code",980 "execution_count": 13,981 "metadata": {982 "id": "mks1E1FTXGXL"983 },984 "outputs": [],985 "source": [986 "# argparser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)\n",987 "\n",988 "# argparser.add_argument(\"--path_for_training_data\", type=str, default=\"my_path/pdb_2021aug02\", help=\"path for loading training data\") \n",989 "# argparser.add_argument(\"--path_for_outputs\", type=str, default=\"./test\", help=\"path for logs and model weights\")\n",990 "# argparser.add_argument(\"--previous_checkpoint\", type=str, default=\"\", help=\"path for previous model weights, e.g. file.pt\")\n",991 "# argparser.add_argument(\"--num_epochs\", type=int, default=200, help=\"number of epochs to train for\")\n",992 "# argparser.add_argument(\"--save_model_every_n_epochs\", type=int, default=10, help=\"save model weights every n epochs\")\n",993 "# argparser.add_argument(\"--reload_data_every_n_epochs\", type=int, default=2, help=\"reload training data every n epochs\")\n",994 "# argparser.add_argument(\"--num_examples_per_epoch\", type=int, default=1000000, help=\"number of training example to load for one epoch\")\n",995 "# argparser.add_argument(\"--batch_size\", type=int, default=10000, help=\"number of tokens for one batch\")\n",996 "# argparser.add_argument(\"--max_protein_length\", type=int, default=10000, help=\"maximum length of the protein complext\")\n",997 "# argparser.add_argument(\"--hidden_dim\", type=int, default=128, help=\"hidden model dimension\")\n",998 "# argparser.add_argument(\"--num_encoder_layers\", type=int, default=3, help=\"number of encoder layers\") \n",999 "# argparser.add_argument(\"--num_decoder_layers\", type=int, default=3, help=\"number of decoder layers\")\n",1000 "# argparser.add_argument(\"--num_neighbors\", type=int, default=48, help=\"number of neighbors for the sparse graph\") \n",1001 "# argparser.add_argument(\"--dropout\", type=float, default=0.1, help=\"dropout level; 0.0 means no dropout\")\n",1002 "# argparser.add_argument(\"--backbone_noise\", type=float, default=0.2, help=\"amount of noise added to backbone during training\") \n",1003 "# argparser.add_argument(\"--rescut\", type=float, default=3.5, help=\"PDB resolution cutoff\")\n",1004 "# argparser.add_argument(\"--debug\", type=bool, default=False, help=\"minimal data loading for debugging\")\n",1005 "# argparser.add_argument(\"--gradient_norm\", type=float, default=-1.0, help=\"clip gradient norm, set to negative to omit clipping\")\n",1006 "# argparser.add_argument(\"--mixed_precision\", type=bool, default=True, help=\"train with mixed precision\")\n",1007 "\n",1008 "# args = argparser.parse_args() \n",1009 "# main(args)\n",1010 "\n",1011 "class MyArgs(object):\n",1012 " def __init__(self):\n",1013 " self.path_for_training_data = \"/content/pdb_2021aug02_sample\"\n",1014 " self.path_for_outputs = \"/content/test\"\n",1015 " self.previous_checkpoint = \"\"\n",1016 " self.num_epochs = 50\n",1017 " self.save_model_every_n_epochs = 5\n",1018 " self.reload_data_every_n_epochs = 4\n",1019 " self.num_examples_per_epoch = 200\n",1020 " self.batch_size = 2000\n",1021 " self.max_protein_length = 2000\n",1022 " self.hidden_dim = 128\n",1023 " self.num_encoder_layers = 3\n",1024 " self.num_decoder_layers = 3\n",1025 " self.num_neighbors = 32\n",1026 " self.dropout = 0.1\n",1027 " self.backbone_noise = 0.1\n",1028 " self.rescut = 3.5\n",1029 " self.debug = False\n",1030 " self.gradient_norm = -1.0 #no norm\n",1031 " self.mixed_precision= True \n",1032 "\n",1033 "args = MyArgs()"1034 ]1035 },1036 {1037 "cell_type": "code",1038 "execution_count": 15,1039 "metadata": {1040 "id": "6csB6zUrbcAH"1041 },1042 "outputs": [],1043 "source": [1044 "#epoch - number of times data is trained on\n",1045 "#step - number of optimizer steps\n",1046 "#time - time in seconds for one epoch to finish\n",1047 "#train - training perplexity = exp(average categorical cross entropy)\n",1048 "#valid - validation perplexity\n",1049 "#train_acc - training accuracy\n",1050 "#valid_acc - validation accuracy"1051 ]1052 },1053 {1054 "cell_type": "code",1055 "execution_count": 14,1056 "metadata": {1057 "colab": {1058 "base_uri": "https://localhost:8080/"1059 },1060 "id": "68wFaZ0IXHzj",1061 "outputId": "52c84f9e-599b-4ca4-b46f-25170828a310"1062 },1063 "outputs": [1064 {1065 "name": "stderr",1066 "output_type": "stream",1067 "text": [1068 "/usr/local/lib/python3.7/dist-packages/torch/utils/data/dataloader.py:566: UserWarning: This DataLoader will create 4 worker processes in total. Our suggested max number of worker in current system is 2, which is smaller than what this DataLoader is going to create. Please be aware that excessive worker creation might get DataLoader running slow or even freeze, lower the worker number to avoid potential slowness/freeze if necessary.\n",1069 " cpuset_checked))\n",1070 "/usr/local/lib/python3.7/dist-packages/torch/utils/checkpoint.py:25: UserWarning: None of the inputs have requires_grad=True. Gradients will be None\n",1071 " warnings.warn(\"None of the inputs have requires_grad=True. Gradients will be None\")\n"1072 ]1073 },1074 {1075 "name": "stdout",1076 "output_type": "stream",1077 "text": [1078 "epoch: 1, step: 4, time: 1.3, train: 32.478, valid: 26.652, train_acc: 0.057, valid_acc: 0.060\n",1079 "epoch: 2, step: 8, time: 1.4, train: 31.076, valid: 24.790, train_acc: 0.056, valid_acc: 0.067\n",1080 "epoch: 3, step: 12, time: 0.9, train: 28.561, valid: 22.354, train_acc: 0.058, valid_acc: 0.075\n",1081 "epoch: 4, step: 16, time: 0.9, train: 25.958, valid: 20.493, train_acc: 0.063, valid_acc: 0.090\n",1082 "epoch: 5, step: 22, time: 1.6, train: 23.583, valid: 19.557, train_acc: 0.065, valid_acc: 0.114\n",1083 "epoch: 6, step: 28, time: 1.5, train: 21.809, valid: 19.653, train_acc: 0.069, valid_acc: 0.104\n",1084 "epoch: 7, step: 34, time: 1.5, train: 20.483, valid: 19.440, train_acc: 0.074, valid_acc: 0.105\n",1085 "epoch: 8, step: 40, time: 1.2, train: 19.474, valid: 19.000, train_acc: 0.097, valid_acc: 0.122\n",1086 "epoch: 9, step: 46, time: 2.0, train: 19.268, valid: 17.082, train_acc: 0.093, valid_acc: 0.116\n",1087 "epoch: 10, step: 52, time: 2.3, train: 18.658, valid: 16.812, train_acc: 0.097, valid_acc: 0.109\n",1088 "epoch: 11, step: 58, time: 2.3, train: 18.158, valid: 16.962, train_acc: 0.105, valid_acc: 0.120\n",1089 "epoch: 12, step: 64, time: 1.7, train: 17.705, valid: 16.780, train_acc: 0.109, valid_acc: 0.120\n",1090 "epoch: 13, step: 69, time: 32.2, train: 18.135, valid: 16.984, train_acc: 0.105, valid_acc: 0.116\n",1091 "epoch: 14, step: 74, time: 1.9, train: 18.008, valid: 17.287, train_acc: 0.106, valid_acc: 0.120\n",1092 "epoch: 15, step: 79, time: 2.0, train: 17.833, valid: 17.172, train_acc: 0.118, valid_acc: 0.111\n",1093 "epoch: 16, step: 84, time: 1.7, train: 17.451, valid: 16.884, train_acc: 0.119, valid_acc: 0.115\n",1094 "epoch: 17, step: 90, time: 3.0, train: 18.145, valid: 17.919, train_acc: 0.111, valid_acc: 0.129\n",1095 "epoch: 18, step: 96, time: 2.8, train: 17.651, valid: 17.883, train_acc: 0.103, valid_acc: 0.103\n",1096 "epoch: 19, step: 102, time: 2.0, train: 17.608, valid: 17.774, train_acc: 0.104, valid_acc: 0.126\n",1097 "epoch: 20, step: 108, time: 2.3, train: 17.374, valid: 18.082, train_acc: 0.114, valid_acc: 0.132\n",1098 "epoch: 21, step: 114, time: 31.8, train: 17.079, valid: 18.081, train_acc: 0.123, valid_acc: 0.117\n",1099 "epoch: 22, step: 120, time: 2.5, train: 16.938, valid: 18.005, train_acc: 0.130, valid_acc: 0.133\n",1100 "epoch: 23, step: 126, time: 1.6, train: 16.719, valid: 18.174, train_acc: 0.123, valid_acc: 0.116\n",1101 "epoch: 24, step: 132, time: 1.2, train: 16.580, valid: 17.844, train_acc: 0.129, valid_acc: 0.136\n",1102 "epoch: 25, step: 139, time: 2.6, train: 16.797, valid: 15.777, train_acc: 0.118, valid_acc: 0.125\n",1103 "epoch: 26, step: 146, time: 2.7, train: 16.433, valid: 15.730, train_acc: 0.125, valid_acc: 0.134\n",1104 "epoch: 27, step: 153, time: 1.8, train: 16.127, valid: 15.673, train_acc: 0.127, valid_acc: 0.135\n",1105 "epoch: 28, step: 160, time: 1.8, train: 15.798, valid: 15.235, train_acc: 0.124, valid_acc: 0.148\n",1106 "epoch: 29, step: 166, time: 31.4, train: 16.003, valid: 15.344, train_acc: 0.139, valid_acc: 0.146\n",1107 "epoch: 30, step: 172, time: 2.7, train: 15.639, valid: 15.524, train_acc: 0.146, valid_acc: 0.133\n",1108 "epoch: 31, step: 178, time: 1.9, train: 15.546, valid: 14.927, train_acc: 0.142, valid_acc: 0.153\n",1109 "epoch: 32, step: 184, time: 1.7, train: 15.215, valid: 15.001, train_acc: 0.155, valid_acc: 0.155\n",1110 "epoch: 33, step: 190, time: 4.9, train: 15.418, valid: 15.358, train_acc: 0.144, valid_acc: 0.137\n",1111 "epoch: 34, step: 196, time: 3.2, train: 15.255, valid: 14.912, train_acc: 0.144, valid_acc: 0.152\n",1112 "epoch: 35, step: 202, time: 1.9, train: 14.925, valid: 14.894, train_acc: 0.153, valid_acc: 0.156\n",1113 "epoch: 36, step: 208, time: 2.0, train: 14.736, valid: 14.729, train_acc: 0.154, valid_acc: 0.168\n",1114 "epoch: 37, step: 214, time: 32.7, train: 14.467, valid: 17.068, train_acc: 0.152, valid_acc: 0.140\n",1115 "epoch: 38, step: 220, time: 2.8, train: 14.410, valid: 16.987, train_acc: 0.158, valid_acc: 0.122\n",1116 "epoch: 39, step: 226, time: 2.0, train: 14.101, valid: 16.935, train_acc: 0.162, valid_acc: 0.123\n",1117 "epoch: 40, step: 232, time: 2.4, train: 14.034, valid: 17.452, train_acc: 0.168, valid_acc: 0.131\n",1118 "epoch: 41, step: 237, time: 4.0, train: 15.268, valid: 16.151, train_acc: 0.158, valid_acc: 0.147\n",1119 "epoch: 42, step: 242, time: 2.2, train: 15.403, valid: 16.473, train_acc: 0.147, valid_acc: 0.148\n",1120 "epoch: 43, step: 247, time: 1.6, train: 15.008, valid: 17.016, train_acc: 0.161, valid_acc: 0.129\n",1121 "epoch: 44, step: 252, time: 2.0, train: 14.492, valid: 16.040, train_acc: 0.168, valid_acc: 0.152\n",1122 "epoch: 45, step: 258, time: 32.4, train: 14.046, valid: 14.339, train_acc: 0.172, valid_acc: 0.161\n",1123 "epoch: 46, step: 264, time: 2.4, train: 13.564, valid: 13.959, train_acc: 0.179, valid_acc: 0.156\n",1124 "epoch: 47, step: 270, time: 1.8, train: 13.514, valid: 14.189, train_acc: 0.181, valid_acc: 0.151\n",1125 "epoch: 48, step: 276, time: 1.5, train: 13.257, valid: 13.961, train_acc: 0.180, valid_acc: 0.160\n",1126 "epoch: 49, step: 281, time: 4.1, train: 13.741, valid: 16.552, train_acc: 0.176, valid_acc: 0.154\n",1127 "epoch: 50, step: 286, time: 2.2, train: 13.157, valid: 17.389, train_acc: 0.180, valid_acc: 0.130\n"1128 ]1129 }1130 ],1131 "source": [1132 "run_training(args)"1133 ]1134 }1135 ],1136 "metadata": {1137 "accelerator": "GPU",1138 "colab": {1139 "authorship_tag": "ABX9TyNOXLieRc+7DSEUOVtmG9NS",1140 "collapsed_sections": [],1141 "include_colab_link": true,1142 "provenance": []1143 },1144 "kernelspec": {1145 "display_name": "Python 3",1146 "name": "python3"1147 },1148 "language_info": {1149 "name": "python"1150 }1151 },1152 "nbformat": 4,1153 "nbformat_minor": 01154}1155