include .bed file in classical Michrom tutorial

README.rst

@@ -49,13 +49,13 @@ The following code snippet shows how to generate a single chromosome polymer mod
 ::
 
       from OpenMiChroM.ChromDynamics import MiChroM
-      sim = MiChroM(name='GM12878_chr10', temperature=1.0, timeStep=0.01)
-      sim.setup(platform="Cuda")
-      sim.saveFolder('GM12878_chr10_simulation')
-      sim.buildClassicMichrom(ChromSeq='inputs/chr10_beads.txt')
+      sim = MiChroM(name='stomach_GRCh38', temperature=1.0, timeStep=0.01)
+      sim.setup(platform="cuda")
+      sim.saveFolder('stomach_GRCh38_chr10_simulation')
+      sim.buildClassicMichrom(ChromSeq='inputs/stomach_GRCh38.bed', chromosome='chr10')
 
-      sim.createReporters(statistics=True, traj=True, trajFormat="swb", energyComponents=True, interval=1000)
-      sim.run(nsteps=10**6, report=True, interval=10**4)
+      sim.createReporters(statistics=True, traj=True, trajFormat="cndb", energyComponents=True, interval=10**3)
+      sim.run(nsteps=10**5, report=True, interval=10**4)
 
 
 Resources

Tutorials/Chromosomes_simulations/Tutorial_MiChroM_Simulation.ipynb

@@ -11,18 +11,55 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "    ***************************************************************************************     \n",
+      "     **** **** *** *** *** *** *** *** OpenMiChroM-1.1.01 *** *** *** *** *** *** **** ****     \n",
+      "\n",
+      "         OpenMiChroM is a Python library for performing chromatin dynamics simulations.         \n",
+      "                            OpenMiChroM uses the OpenMM Python API,                             \n",
+      "                employing the MiChroM (Minimal Chromatin Model) energy function.                \n",
+      "      The chromatin dynamics simulations generate an ensemble of 3D chromosomal structures      \n",
+      "      that are consistent with experimental Hi-C maps, also allows simulations of a single      \n",
+      "                 or multiple chromosome chain using High-Performance Computing                  \n",
+      "                            in different platforms (GPUs and CPUs).                             \n",
+      "\n",
+      "         OpenMiChroM documentation is available at https://open-michrom.readthedocs.io          \n",
+      "\n",
+      "         OpenMiChroM is described in: Oliveira Junior, A. B & Contessoto, V, G et. al.          \n",
+      "      A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes.       \n",
+      "                  Journal of Molecular Biology. doi:10.1016/j.jmb.2020.10.034.                  \n",
+      "               We also thank the polychrom <https://github.com/open2c/polychrom>                \n",
+      "                 where part of this code was inspired - 10.5281/zenodo.3579472.                 \n",
+      "\n",
+      "                    Copyright (c) 2024, The OpenMiChroM development team at                     \n",
+      "                                        Rice University                                         \n",
+      "    ***************************************************************************************     \n"
+     ]
+    }
+   ],
    "source": [
-    "sim = MiChroM(name='GM12878_chr10', temperature=1.0, timeStep=0.01)"
+    "sim = MiChroM(name='stomach_GRCh38', temperature=1.0, timeStep=0.01)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Using platform: CUDA\n"
+     ]
+    }
+   ],
    "source": [
     "sim.setup(platform=\"Cuda\")"
    ]
@@ -38,9 +75,39 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "FENEBond was added\n",
+      "AngleForce was added\n",
+      "RepulsiveSoftCore was added\n",
+      "TypetoType was added\n",
+      "IdealChromosome was added\n",
+      "FlatBottomHarmonic was added\n",
+      "Setting positions... loaded!\n",
+      "Setting velocities... loaded!\n",
+      "Context created!\n",
+      "\n",
+      "Simulation name: stomach_GRCh38\n",
+      "Number of beads: 2702, Number of chains: 1\n",
+      "Potential energy: 63.93571, Kinetic Energy: 1.51567 at temperature: 1.0\n",
+      "\n",
+      "Potential energy per forceGroup:\n",
+      "                                  Values\n",
+      "FENEBond                   55114.613361\n",
+      "AngleForce                     0.993050\n",
+      "RepulsiveSoftCore              0.000000\n",
+      "TypetoType                  -216.843586\n",
+      "IdealChromosome               -1.082162\n",
+      "FlatBottomHarmonic        117856.612623\n",
+      "Potential Energy (total)  172754.293286\n"
+     ]
+    }
+   ],
    "source": [
     "sim.buildClassicMichrom(ChromSeq='inputs/stomach_GRCh38.bed', chromosome='chr11')\n"
    ]
@@ -56,9 +123,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "#\"Progress (%)\"\t\"Step\"\t\"Speed (ns/day)\"\t\"Time Remaining\"\n",
+      "10.0%\t10000\t0\t--\n",
+      "20.0%\t20000\t1.46e+04\t0:04\n",
+      "30.0%\t30000\t1.44e+04\t0:04\n",
+      "40.0%\t40000\t1.38e+04\t0:03\n",
+      "50.0%\t50000\t1.34e+04\t0:03\n",
+      "60.0%\t60000\t1.3e+04\t0:02\n",
+      "70.0%\t70000\t1.28e+04\t0:02\n",
+      "80.0%\t80000\t1.26e+04\t0:01\n",
+      "90.0%\t90000\t1.25e+04\t0:00\n",
+      "100.0%\t100000\t1.24e+04\t0:00\n"
+     ]
+    }
+   ],
    "source": [
     "sim.run(nsteps=10**5, report=True, interval=10**4) #inbetween"
    ]