added raw data analysis

examples/illustrations/lysozyme-in-water.ipynb

@@ -0,0 +1,61 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/simon/.local/lib/python3.11/site-packages/MDAnalysis/topology/TPRParser.py:161: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13\n",
+      "  import xdrlib\n"
+     ]
+    }
+   ],
+   "source": [
+    "import numpy as np\n",
+    "import MDAnalysis as mda\n",
+    "import nmrformd as nmrmd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys, os, git\n",
+    "current_path = os.getcwd()\n",
+    "git_repo = git.Repo(current_path, search_parent_directories=True)\n",
+    "git_path = git_repo.git.rev_parse(\"--show-toplevel\")\n",
+    "sys.path.append(git_path+\"/examples/pyplot-perso/\")\n",
+    "from color_series1 import colors\n",
+    "from functions import complete_panel, save_figure, set_boundaries, add_subplotlabels, set_boundaries\n",
+    "path_figures = \"/docs/source/figures/illustrations/lysozyme-in-water/\""
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.11.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

examples/illustrations/lysozyme-in-water/analysis.ipynb

@@ -0,0 +1,146 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import MDAnalysis as mda\n",
+    "import nmrformd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys, os, git\n",
+    "current_path = os.getcwd()\n",
+    "git_repo = git.Repo(current_path, search_parent_directories=True)\n",
+    "git_path = git_repo.git.rev_parse(\"--show-toplevel\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def save_result(data, name = \"intra_H2O\"):\n",
+    "    \"\"\"Save the correlation functions in dictionary\"\"\"\n",
+    "    if not os.path.exists(\"raw_data/\"):\n",
+    "        os.makedirs(\"raw_data/\")\n",
+    "    saving_file = \"raw_data/\" + name + \".npy\"\n",
+    "    t = data.t\n",
+    "    f = data.f\n",
+    "    C = data.gij[0]\n",
+    "    R1 = data.R1\n",
+    "    R2 = data.R2\n",
+    "    N = data.group_j.atoms.n_atoms\n",
+    "    try:\n",
+    "        previous_dictionary = np.load(saving_file, allow_pickle=True)\n",
+    "        t_prev = np.real(previous_dictionary.item()[\"t\"])\n",
+    "        assert len(t_prev) == len(t)\n",
+    "        C_prev = np.real(previous_dictionary.item()[\"C\"])\n",
+    "        R1_prev = np.real(previous_dictionary.item()[\"R1\"])\n",
+    "        R2_prev = np.real(previous_dictionary.item()[\"R2\"])\n",
+    "        N_prev = np.real(previous_dictionary.item()[\"N\"])\n",
+    "        C = (C*N + C_prev*N_prev) / (N_prev + N)\n",
+    "        R1 = (R1*N + R1_prev*N_prev) / (N_prev + N)\n",
+    "        R2 = (R2*N + R2_prev*N_prev) / (N_prev + N)\n",
+    "        N += N_prev\n",
+    "    except:\n",
+    "        pass\n",
+    "    dictionary = {\n",
+    "    \"t\": t,\n",
+    "    \"f\": f,\n",
+    "    \"C\": C,\n",
+    "    \"N\": N,\n",
+    "    \"R1\": R1,\n",
+    "    \"R2\": R2,\n",
+    "    }\n",
+    "    np.save(saving_file, dictionary)\n",
+    "    return N"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "folder = git_path + \"/nmrformd-data/HEWL-in-water/raw-data/water-to-protein-0.73/\"\n",
+    "tpr = folder+\"prod.tpr\"\n",
+    "all_xtc = [folder+\"prod1.xtc\",\n",
+    "           folder+\"prod2.xtc\",\n",
+    "           folder+\"prod3.xtc\",\n",
+    "           folder+\"prod4.xtc\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "u = mda.Universe(tpr, all_xtc)\n",
+    "# isolate the hydrogen from water and from the protein\n",
+    "H2O = u.select_atoms(\"name HW1 HW2\")\n",
+    "HEWL = u.select_atoms(\"\")\n",
+    "for name in np.unique(u.atoms.names):\n",
+    "    if (name[0] == \"H\") & (name != \"HW1\") & (name != \"HW2\"):\n",
+    "        HEWL += u.select_atoms(\"name \"+name)\n",
+    "ALL = H2O + HEWL\n",
+    "while 1 < 2:\n",
+    "    # H2O-H2O\n",
+    "    intra_H2O = nmrformd.NMR(u, atom_group=H2O, neighbor_group=H2O, type_analysis=\"intra_molecular\", number_i=1)\n",
+    "    inter_H2O = nmrformd.NMR(u, atom_group=H2O, neighbor_group=H2O, type_analysis=\"inter_molecular\", number_i=1)\n",
+    "    full_H2O = nmrformd.NMR(u, atom_group=H2O, neighbor_group=H2O, number_i=1)\n",
+    "    # HEWL-HEWL\n",
+    "    intra_HEWL = nmrformd.NMR(u, atom_group=HEWL, neighbor_group=HEWL, type_analysis=\"intra_molecular\", number_i=1)\n",
+    "    inter_HEWL = nmrformd.NMR(u, atom_group=HEWL, neighbor_group=HEWL, type_analysis=\"inter_molecular\", number_i=1)\n",
+    "    full_HEWL = nmrformd.NMR(u, atom_group=HEWL, neighbor_group=HEWL, number_i=1)\n",
+    "    # H2O-HEWL\n",
+    "    inter_H2O_HEWL = nmrformd.NMR(u, atom_group=H2O, neighbor_group=HEWL, number_i=1)\n",
+    "    inter_HEWL_H2O = nmrformd.NMR(u, atom_group=HEWL, neighbor_group=H2O, number_i=1)\n",
+    "    # FULL\n",
+    "    FULL = nmrformd.NMR(u, atom_group=ALL, neighbor_group=ALL, number_i=1)\n",
+    "    # save_results\n",
+    "    N = save_result(intra_H2O, name = \"intra_H2O\")\n",
+    "    print(\"Number of cycle:\", N)\n",
+    "    N = save_result(inter_H2O, name = \"inter_H2O\")\n",
+    "    N = save_result(full_H2O, name = \"full_H2O\")\n",
+    "    N = save_result(intra_HEWL, name = \"intra_HEWL\")\n",
+    "    N = save_result(inter_HEWL, name = \"inter_HEWL\")\n",
+    "    N = save_result(full_HEWL, name = \"full_HEWL\")\n",
+    "    N = save_result(inter_H2O_HEWL, name = \"inter_H2O_HEWL\")\n",
+    "    N = save_result(inter_HEWL_H2O, name = \"inter_HEWL_H2O\")\n",
+    "    N = save_result(FULL, name = \"FULL\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.11.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}