Merge pull request #94 from JohnsonBiophysicsLab/pip-test

Pip test

Author: yingyue2030699

demo/Hete-3mer-8ERQ.ipynb

@@ -33,7 +33,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Successfully downloaded assembly file: /Users/sikao/Documents/8erq_dir/8erq-assembly1.cif.gz\n",
+      "Successfully downloaded assembly file: /Users/yueying/Documents/8erq_dir/8erq-assembly1.cif.gz\n",
       "Binding interfaces detected:\n",
       "Chain A:\n",
       "  Center of Mass (COM): (269.01806640625, 242.17724609375, 295.64739990234375)\n",
@@ -89,9 +89,9 @@
       "{'H': 'A', 'L': 'B', 'A': 'C'}\n",
       "Homologous chain groups identified:\n",
       "[['A'], ['H'], ['L']]\n",
-      "Regularized coarse-grained structure saved to /Users/sikao/Documents/8erq_dir/regularized_coarse_grained_structure.cif.\n",
-      "PyMOL script saved to /Users/sikao/Documents/8erq_dir/visualize_regularized_coarse_grained.pml.\n",
-      "Model saved successfully to /Users/sikao/Documents/8erq_dir/8erq_model.json\n"
+      "Regularized coarse-grained structure saved to /Users/yueying/Documents/8erq_dir/regularized_coarse_grained_structure.cif.\n",
+      "PyMOL script saved to /Users/yueying/Documents/8erq_dir/visualize_regularized_coarse_grained.pml.\n",
+      "Model saved successfully to /Users/yueying/Documents/8erq_dir/8erq_model.json\n"
      ]
     }
    ],
@@ -218,6 +218,105 @@
     "subprocess.run([\"pymol\", \"-cq\", f\"{abs_save_folder}/visualize_regularized_coarse_grained.pml\"], check=True)\n",
     "display(Image(filename=f\"{abs_save_folder}/comparison_regularized.png\"))"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Working directory set to: /Users/yueying/Documents/8erq_dir\n",
+      "start parameters\n",
+      "\tnItr = 20000000\n",
+      "\ttimeStep = 0.5\n",
+      "\ttimeWrite = 20000\n",
+      "\ttrajWrite = 2000000\n",
+      "\tpdbWrite = 2000000\n",
+      "\trestartWrite = 100000\n",
+      "\tcheckPoint = 100000\n",
+      "\ttransitionWrite = 100000\n",
+      "\tclusterOverlapCheck = false\n",
+      "\tscaleMaxDisplace = 100.0\n",
+      "\toverlapSepLimit = 0.1\n",
+      "end parameters\n",
+      "\n",
+      "start boundaries\n",
+      "\tWaterBox = [600.0, 600.0, 600.0]\n",
+      "\thasCompartment = false\n",
+      "\tcompartmentR = 0\n",
+      "\tcompartmentSiteD = 0\n",
+      "\tcompartmentSiteRho = 0\n",
+      "\tWaterBox = [600.0, 600.0, 600.0]\n",
+      "end boundaries\n",
+      "\n",
+      "start molecules\n",
+      "\tA : 100\n",
+      "\tB : 100\n",
+      "\tC : 100\n",
+      "end molecules\n",
+      "\n",
+      "start reactions\n",
+      "\tC(A1) + A(C1) <-> C(A1!1).A(C1!1)\n",
+      "\t\tonRate3Dka = 10.0\n",
+      "\t\toffRatekb = 1591598.2278125454\n",
+      "\t\tsigma = 0.9322358965873718\n",
+      "\t\tnorm1 = [0, 0, 1]\n",
+      "\t\tnorm2 = [0, 0, 1]\n",
+      "\t\tassocAngles = [1.714723, 1.771477, -2.872323, 1.016331, -2.661668]\n",
+      "\t\tlength3Dto2D = 2.0\n",
+      "\t\tbindRadSameCom = 1.5\n",
+      "\t\tloopCoopFactor = 1.0\n",
+      "\t\texcludeVolumeBound = False\n",
+      "\n",
+      "\tC(B1) + B(C1) <-> C(B1!1).B(C1!1)\n",
+      "\t\tonRate3Dka = 10.0\n",
+      "\t\toffRatekb = 4198547.726575994\n",
+      "\t\tsigma = 0.7177354693412781\n",
+      "\t\tnorm1 = [0, 0, 1]\n",
+      "\t\tnorm2 = [0, 0, 1]\n",
+      "\t\tassocAngles = [2.744988, 2.569596, 0.642691, -1.523236, 1.645259]\n",
+      "\t\tlength3Dto2D = 2.0\n",
+      "\t\tbindRadSameCom = 1.5\n",
+      "\t\tloopCoopFactor = 1.0\n",
+      "\t\texcludeVolumeBound = False\n",
+      "\n",
+      "\tA(B1) + B(A1) <-> A(B1!1).B(A1!1)\n",
+      "\t\tonRate3Dka = 10.0\n",
+      "\t\toffRatekb = 0.060219999999999996\n",
+      "\t\tsigma = 0.6551324129104614\n",
+      "\t\tnorm1 = [0, 0, 1]\n",
+      "\t\tnorm2 = [0, 0, 1]\n",
+      "\t\tassocAngles = [2.525500, 2.750069, -2.409915, -1.480280, -2.301118]\n",
+      "\t\tlength3Dto2D = 2.0\n",
+      "\t\tbindRadSameCom = 1.5\n",
+      "\t\tloopCoopFactor = 1.0\n",
+      "\t\texcludeVolumeBound = False\n",
+      "\n",
+      "end reactions\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "# create the Simulation object using the Simulation class\n",
+    "# the simulation is connected to the PDBModel object created above\n",
+    "simulation = ion.Simulation(pdb_model, save_folder)\n",
+    "\n",
+    "# generate the NERDSS input files for the simulation\n",
+    "simulation.generate_nerdss_input()\n",
+    "\n",
+    "simulation.modify_inp_file(\n",
+    "    {'nItr': 20000000, 'timeStep': 0.5,\n",
+    "    'timeWrite': 20000, 'trajWrite': 2000000,\n",
+    "    'pdbWrite': 2000000,\n",
+    "    'WaterBox': [600.0, 600.0, 600.0]}\n",
+    "    )\n",
+    "\n",
+    "simulation.print_inp_file()"
+   ]
   }
  ],
  "metadata": {
@@ -236,7 +335,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.21"
+   "version": "3.9.23"
   }
  },
  "nbformat": 4,

demo/Homo-180mer-8LQP.ipynb

@@ -7820,6 +7820,29 @@
     "subprocess.run([\"pymol\", \"-cq\", f\"{abs_save_folder}/visualize_regularized_coarse_grained.pml\"], check=True)\n",
     "display(Image(filename=f\"{abs_save_folder}/comparison_regularized.png\"))"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# create the Simulation object using the Simulation class\n",
+    "# the simulation is connected to the PDBModel object created above\n",
+    "simulation = ion.Simulation(pdb_model, save_folder)\n",
+    "\n",
+    "# generate the NERDSS input files for the simulation\n",
+    "simulation.generate_nerdss_input()\n",
+    "\n",
+    "simulation.modify_inp_file(\n",
+    "    {'nItr': 20000000, 'timeStep': 0.5,\n",
+    "    'timeWrite': 20000, 'trajWrite': 2000000,\n",
+    "    'pdbWrite': 2000000, 'A': 1000,\n",
+    "    'WaterBox': [600.0, 600.0, 600.0]}\n",
+    "    )\n",
+    "\n",
+    "simulation.print_inp_file()"
+   ]
   }
  ],
  "metadata": {

demo/Homo-18mer-5L93.ipynb

@@ -968,6 +968,29 @@
     "subprocess.run([\"pymol\", \"-cq\", f\"{abs_save_folder}/visualize_regularized_coarse_grained.pml\"], check=True)\n",
     "display(Image(filename=f\"{abs_save_folder}/comparison_regularized.png\"))"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# create the Simulation object using the Simulation class\n",
+    "# the simulation is connected to the PDBModel object created above\n",
+    "simulation = ion.Simulation(pdb_model, save_folder)\n",
+    "\n",
+    "# generate the NERDSS input files for the simulation\n",
+    "simulation.generate_nerdss_input()\n",
+    "\n",
+    "simulation.modify_inp_file(\n",
+    "    {'nItr': 20000000, 'timeStep': 0.5,\n",
+    "    'timeWrite': 20000, 'trajWrite': 2000000,\n",
+    "    'pdbWrite': 2000000,\n",
+    "    'WaterBox': [600.0, 600.0, 600.0]}\n",
+    "    )\n",
+    "\n",
+    "simulation.print_inp_file()"
+   ]
   }
  ],
  "metadata": {