Merge pull request #49 from NDoering99/main

make visualization easier to use

openmmdl/_version.py

@@ -1 +1 @@
-__version__ = "1.0.0+548.gc46c6f1.dirty"
+__version__ = "1.0.0+557.gc45a3eb.dirty"

openmmdl/openmmdl_analysis/visualization.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -11,22 +11,50 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
-    "filepath = '/your/file/path/Visualization' # add the filepath to the directory where openmmdl_analysis Visualization outputs are saved\n",
-    "ligname = 'UNK' # add the name of the ligand from the original PDB File"
+    "ligname = 'FMN' # add the name of the ligand from the original PDB File"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "09acfdb0e59f46d481905cef43c231c0",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "ThemeManager()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "4b33c5fd6d6541ed8b9766bdbfe27e42",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "NGLWidget(gui_style='ngl', layout=Layout(height='1000px', width='1000px'), max_frame=9999)"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
-    "# change receptor_type, width and height as needed (preset to protein and 1000x1000)\n",
-    "view = visualization(filepath, ligname)\n",
+    "# change receptor_type, width and height as needed (preset to receptor_type='protein or nucleic' and 1000x1000)\n",
+    "view = visualization(ligname)\n",
     "view.display(gui=True, style='ngl')"
    ]
   },
@@ -54,7 +82,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.10.10"
   },
   "vscode": {
    "interpreter": {

openmmdl/openmmdl_analysis/visualization_functions.py

@@ -6,6 +6,7 @@
 import nglview as nv
 import subprocess
 import os
+import shutil
 
 from openmmdl.openmmdl_analysis.barcode_generation import waterids_barcode_generator
 
@@ -136,22 +137,19 @@ def cloud_json_generation(df_all):
     return clouds
 
 
-def visualization(filepath, ligname, receptor_type='protein', height='1000px', width='1000px'):
+def visualization(ligname, receptor_type='protein or nucleic', height='1000px', width='1000px'):
     """Generates visualization of the trajectory with the interacting waters and interaction clouds.
     
     Args:
-        json_file_path (str): path to .json file containing the interaction clouds
-        pdb_file_path (str): path to pdb file (use interacting_waters.pdb for better visualization)
-        dcd_file_path (str): path to dcd file (use interacting_waters.dcd for better visualization)
-        interacting_waters_file_path (str): path to .pkl file containing the interacting water ids
-        receptor_type (str, optional): type of receptor. Defaults to 'protein'.
+        ligname (str): name of the ligand in the pdb file
+        receptor_type (str, optional): type of receptor. Defaults to 'protein or nucleic'.
         height (str, optional): height of the visualization. Defaults to '1000px'.
         width (str, optional): width of the visualization. Defaults to '1000px'.
     
     Returns:
         nglview widget: returns the nglview widget containing the visualization
     """
-    with open(f'{filepath}clouds.json') as f:
+    with open('clouds.json') as f:
         data = json.load(f)
 
     sphere_buffers = []
@@ -163,9 +161,9 @@ def visualization(filepath, ligname, receptor_type='protein', height='1000px', w
             sphere_buffer["radius"] += [cloud["radius"]]
         sphere_buffers.append(sphere_buffer)
 
-    pdb_structure = md.load(f'{filepath}interacting_waters.pdb')
-    dcd_trajectory = md.load(f'{filepath}interacting_waters.dcd', top=pdb_structure)
-    with open(f'{filepath}interacting_waters.pkl', 'rb') as f:
+    pdb_structure = md.load(f'interacting_waters.pdb')
+    dcd_trajectory = md.load(f'interacting_waters.dcd', top=pdb_structure)
+    with open(f'interacting_waters.pkl', 'rb') as f:
         interacting_watersids = pickle.load(f)
 
     view = nv.show_mdtraj(dcd_trajectory)
@@ -174,7 +172,7 @@ def visualization(filepath, ligname, receptor_type='protein', height='1000px', w
 
     for water in interacting_watersids:
         view.add_licorice(selection=f"water and {water}")
-    view.add_licorice(selection='ligand')
+    view.add_licorice(selection=ligname)
 
     for sphere_buffer, name in zip(sphere_buffers, ['hydrophobic', 'acceptor', 'donor', 'waterbridge', 'negative_ionizable', 'positive_ionizable', 'pistacking', 'pication', 'halogen', 'metal']):
         js = (
@@ -196,4 +194,6 @@ def visualization(filepath, ligname, receptor_type='protein', height='1000px', w
 def run_visualization():
     package_dir = os.path.dirname(__file__)
     notebook_path = os.path.join(package_dir, 'visualization.ipynb')
-    subprocess.run(['jupyter', 'notebook', notebook_path])
+    current_dir = os.getcwd()
+    shutil.copyfile(notebook_path, f'{current_dir}/visualization.ipynb')
+    subprocess.run(['jupyter', 'notebook', 'visualization.ipynb'])