fix cyclic hallucination weights

Author: sokrypton

af/examples/af_cyc_design.ipynb

@@ -16,8 +16,13 @@
         "id": "OA2k3sAYuiXe"
       },
       "source": [
-        "#AfCysDesign (WIP)\n",
-        "Backprop through AlphaFold for protein design with cyclic support\n"
+        "#af_cys_design\n",
+        "\n",
+        "**Cyclic peptide structure prediction and design using AlphaFold**\n",
+        "\n",
+        "Stephen Rettie, Katelyn Campbell, Asim Bera, Alex Kang, Simon Kozlov, Joshmyn De La Cruz, Victor Adebomi, Guangfeng Zhou, Frank DiMaio, Sergey Ovchinnikov, Gaurav Bhardwaj\n",
+        "\n",
+        "doi: https://doi.org/10.1101/2023.02.25.529956\n"
       ]
     },
     {
@@ -197,6 +202,7 @@
         "# pre-design with gumbel initialization and softmax activation\n",
         "af_model.restart(mode=\"gumbel\")\n",
         "af_model.set_opt(\"con\", binary=True, cutoff=21.6875, num=af_model._len, seqsep=0)\n",
+        "af_model.set_weights(pae=1, plddt=1, con=0.5)\n",
         "af_model.design_soft(50)\n",
         "\n",
         "# three stage design  \n",