Make templates aligned with the new version of the Databank

scripts/FormFactor_to_TotalDensity_model_training_walkthrough.ipynb

@@ -60,26 +60,38 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Initialize the NMR lipids databank\n",
-    "\n",
     "import sys\n",
     "import os\n",
+    "import re\n",
+    "\n",
+    "# This installs FAIRMD Lipids in your python environment,\n",
+    "# you can use the same commands on your local machine if you run it locally.\n",
+    "\n",
+    "!pip install fairmd-lipids\n",
+    "\n",
+    "if not os.environ.get(\"FMDL_DATA_PATH\", False):    \n",
+    "    if os.path.isdir('BilayerData'):\n",
+    "        print(\"Folder BilayerData already exist. Skip clonning..\")\n",
+    "    else:\n",
+    "        !fmdl_initialize_data stable\n",
+    "    with open(\"databank_env.rc\") as f:\n",
+    "        for s in f.readlines():\n",
+    "            m = re.match(r\"^export\\s+([A-Z_][A-Z0-9_]*)=(.+)$\", s)\n",
+    "            if m:\n",
+    "                key, value = m.groups()\n",
+    "                print(f\"Setting {key}={value}\")\n",
+    "                os.environ[key] = value\n",
     "\n",
+    "# On local machine, you can set NMLDB_DATA_PATH to the path where you cloned the BilayerData repository.\n",
+    "\n",
+    "# ML libraries\n",
+    "!pip3 install scikeras\n",
+    "!pip3 install scikit-learn==1.5.2\n",
+    "\n",
+    "# -- additional functions --\n",
     "if 'google.colab' in sys.modules:\n",
-    "    !git clone https://github.com/NMRlipids/Databank\n",
-    "    %cd Databank\n",
-    "    !git submodule update --init --remote\n",
-    "    !sed -i '/numpy/s/^/# /' Scripts/DatabankLib/requirements.txt\n",
-    "    !pip3 install .\n",
-    "    os.environ[\"NMLDB_ROOT_PATH\"] = \"/content/Databank\"\n",
-    "    databankPath = \"/content/Databank\"\n",
-    "    !pip3 install scikeras\n",
-    "    !pip3 install scikit-learn==1.5.2\n",
-    "    # -- additional functions --\n",
-    "    %cd /content\n",
     "    !git clone https://github.com/NMRLipids/databank-template.git\n",
-    "    %cd /content/Databank\n",
-    "    sys.path.append('/content/databank-template/scripts')\n",
+    "    sys.path.append('./databank-template/scripts')\n",
     "\n",
     "# On local machine, you should set NMLDB_ROOT_PATH to the path where you cloned the repository.\n",
     "# You can do it either from command line or here by uncommenting the next line:\n",
@@ -145,12 +157,12 @@
    ],
    "source": [
     "# -- databank imports --\n",
-    "from DatabankLib.core import initialize_databank\n",
-    "from DatabankLib.databankLibrary import GetEquilibrationTimes, getHydrationLevel\n",
-    "from DatabankLib.plottings import *\n",
+    "from fairmd.lipids.core import initialize_databank\n",
+    "from fairmd.lipids.databankLibrary import GetEquilibrationTimes, getHydrationLevel\n",
+    "from fairmd.lipids.plottings import *\n",
     "\n",
     "# -- additional functions --\n",
-    "from new_functions import *\n"
+    "from new_functions import *"
    ]
   },
   {
@@ -11583,5 +11595,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

scripts/new_functions/databank_functions.py

@@ -3,7 +3,7 @@
 from typing import Any, Literal
 import os
 
-import DatabankLib as dlb
+import fairmd.lipids as dlb
 
 logger = logging.getLogger(__name__)
 
@@ -55,7 +55,7 @@ def get_form_factor_and_total_density_pair(
 
     :return: Form factor and total density of the simulation.
     """
-    system_endpath = os.path.join(dlb.NMLDB_SIMU_PATH, system["path"])
+    system_endpath = os.path.join(dlb.FMDL_SIMU_PATH, system["path"])
     form_factor_path = os.path.join(system_endpath, "FormFactor.json")
     total_density_path = os.path.join(system_endpath, "TotalDensity.json")