Merge branch 'main' of https://huggingface.co/spaces/simonduerr/metal3d

app.py

@@ -16,6 +16,10 @@ from utils.model import Model
 import numpy as np
 
 import os
+import moleculekit
+
+print(moleculekit.__version__)
+
 
 def update(inp, file, mode):
     try:

requirements.txt

@@ -1,8 +1,9 @@
-moleculekit 
+moleculekit==1.1.1
 torch
 py3Dmol
 pdb2pqr
 scipy
 ipywidgets
 numpy
-sklearn
+scikit-learn
+propka

utils/helpers.py

@@ -109,7 +109,7 @@ def get_all_metalbinding_resids(pdb_file):
     """
 
     try:
-        prot = Molecule(pdb_file)
+        prot = Molecule('files/2CBA.pdb')
     except:
         exit("could not read file")
     prot.filter("protein")

utils/voxelization.py

@@ -177,7 +177,7 @@ def processStructures(pdb_file, resids, clean=True):
 
     # load molecule using MoleculeKit
     try:
-        prot = Molecule(pdb_file)
+        prot = Molecule('files/2CBA.pdb')
     except:
         raise IOError("could not read pdbfile")