remove PIL py3dmol

app.py

@@ -1,7 +1,7 @@
 import gradio as gr
-from PIL import Image
-import base64
-import io
+# from PIL import Image
+# import base64
+# import io
 import glob
 import numpy as np
 from gradio_molecule3d import Molecule3D

core/utils/visualize.py

@@ -1,93 +1,93 @@
-import os
-import py3Dmol
-from rdkit import Chem
-
-
-def visualize_complex(pdb_block, sdf_block, show_protein_surface=True, show_ligand=True, show_ligand_surface=True):
-    view = py3Dmol.view()
-
-    # Add protein to the canvas
-    view.addModel(pdb_block, 'pdb')
-    if show_protein_surface:
-        view.addSurface(py3Dmol.VDW, {'opacity': 0.7, 'color': 'white'}, {'model': -1})
-    else:
-        view.setStyle({'model': -1}, {'cartoon': {'color': 'spectrum'}, 'line': {}})
-    view.setStyle({'model': -1}, {"cartoon": {"style": "edged", 'opacity': 0}})
-
-    # Add ligand to the canvas
-    if show_ligand:
-        view.addModel(sdf_block, 'sdf')
-        view.setStyle({'model': -1}, {'stick': {}})
-        # view.setStyle({'model': -1}, {'cartoon': {'color': 'spectrum'}, 'line': {}})
-        if show_ligand_surface:
-            view.addSurface(py3Dmol.VDW, {'opacity': 0.8}, {'model': -1})
-
-    view.zoomTo()
-    return view
-
-
-def visualize_data(data, root, show_ligand=True, show_surface=True):
-    protein_path = os.path.join(root, data.protein_filename)
-    ligand_path = os.path.join(root, data.ligand_filename)
-    with open(protein_path, 'r') as f:
-        pdb_block = f.read()
-    with open(ligand_path, 'r') as f:
-        sdf_block = f.read()
-    return visualize_complex(pdb_block, sdf_block, show_ligand=show_ligand, show_surface=show_surface)
-
-
-def visualize_generated_mol(protein_filename, mol, root, show_surface=False, opacity=0.5):
-    protein_path = os.path.join(root, protein_filename)
-    with open(protein_path, 'r') as f:
-        pdb_block = f.read()
-
-    view = py3Dmol.view()
-
-    # Add protein to the canvas
-    view.addModel(pdb_block, 'pdb')
-    view.setStyle({'model': -1}, {'cartoon': {'color': 'spectrum'}, 'line': {}})
-
-    mblock = Chem.MolToMolBlock(mol)
-    view.addModel(mblock, 'mol')
-    view.setStyle({'model': -1}, {'stick': {}, 'sphere': {'radius': 0.35}})
-    if show_surface:
-        view.addSurface(py3Dmol.SAS, {'opacity': opacity}, {'model': -1})
-
-    view.zoomTo()
-    return view
-
-
-def MolTo3DView(mol, size=(300, 300), style="stick", surface=False, opacity=0.5):
-    """Draw molecule in 3D
-
-    Args:
-    ----
-        mol: rdMol, molecule to show
-        size: tuple(int, int), canvas size
-        style: str, type of drawing molecule
-               style can be 'line', 'stick', 'sphere', 'carton'
-        surface, bool, display SAS
-        opacity, float, opacity of surface, range 0.0-1.0
-    Return:
-    ----
-        viewer: py3Dmol.view, a class for constructing embedded 3Dmol.js views in ipython notebooks.
-    """
-    assert style in ('line', 'stick', 'sphere', 'carton')
-
-    viewer = py3Dmol.view(width=size[0], height=size[1])
-    if isinstance(mol, list):
-        for i, m in enumerate(mol):
-            mblock = Chem.MolToMolBlock(m)
-            viewer.addModel(mblock, 'mol' + str(i))
-    elif len(mol.GetConformers()) > 1:
-        for i in range(len(mol.GetConformers())):
-            mblock = Chem.MolToMolBlock(mol, confId=i)
-            viewer.addModel(mblock, 'mol' + str(i))
-    else:
-        mblock = Chem.MolToMolBlock(mol)
-        viewer.addModel(mblock, 'mol')
-    viewer.setStyle({style: {}})
-    if surface:
-        viewer.addSurface(py3Dmol.SAS, {'opacity': opacity})
-    viewer.zoomTo()
-    return viewer
+# import os
+# import py3Dmol
+# from rdkit import Chem
+
+
+# def visualize_complex(pdb_block, sdf_block, show_protein_surface=True, show_ligand=True, show_ligand_surface=True):
+#     view = py3Dmol.view()
+
+#     # Add protein to the canvas
+#     view.addModel(pdb_block, 'pdb')
+#     if show_protein_surface:
+#         view.addSurface(py3Dmol.VDW, {'opacity': 0.7, 'color': 'white'}, {'model': -1})
+#     else:
+#         view.setStyle({'model': -1}, {'cartoon': {'color': 'spectrum'}, 'line': {}})
+#     view.setStyle({'model': -1}, {"cartoon": {"style": "edged", 'opacity': 0}})
+
+#     # Add ligand to the canvas
+#     if show_ligand:
+#         view.addModel(sdf_block, 'sdf')
+#         view.setStyle({'model': -1}, {'stick': {}})
+#         # view.setStyle({'model': -1}, {'cartoon': {'color': 'spectrum'}, 'line': {}})
+#         if show_ligand_surface:
+#             view.addSurface(py3Dmol.VDW, {'opacity': 0.8}, {'model': -1})
+
+#     view.zoomTo()
+#     return view
+
+
+# def visualize_data(data, root, show_ligand=True, show_surface=True):
+#     protein_path = os.path.join(root, data.protein_filename)
+#     ligand_path = os.path.join(root, data.ligand_filename)
+#     with open(protein_path, 'r') as f:
+#         pdb_block = f.read()
+#     with open(ligand_path, 'r') as f:
+#         sdf_block = f.read()
+#     return visualize_complex(pdb_block, sdf_block, show_ligand=show_ligand, show_surface=show_surface)
+
+
+# def visualize_generated_mol(protein_filename, mol, root, show_surface=False, opacity=0.5):
+#     protein_path = os.path.join(root, protein_filename)
+#     with open(protein_path, 'r') as f:
+#         pdb_block = f.read()
+
+#     view = py3Dmol.view()
+
+#     # Add protein to the canvas
+#     view.addModel(pdb_block, 'pdb')
+#     view.setStyle({'model': -1}, {'cartoon': {'color': 'spectrum'}, 'line': {}})
+
+#     mblock = Chem.MolToMolBlock(mol)
+#     view.addModel(mblock, 'mol')
+#     view.setStyle({'model': -1}, {'stick': {}, 'sphere': {'radius': 0.35}})
+#     if show_surface:
+#         view.addSurface(py3Dmol.SAS, {'opacity': opacity}, {'model': -1})
+
+#     view.zoomTo()
+#     return view
+
+
+# def MolTo3DView(mol, size=(300, 300), style="stick", surface=False, opacity=0.5):
+#     """Draw molecule in 3D
+
+#     Args:
+#     ----
+#         mol: rdMol, molecule to show
+#         size: tuple(int, int), canvas size
+#         style: str, type of drawing molecule
+#                style can be 'line', 'stick', 'sphere', 'carton'
+#         surface, bool, display SAS
+#         opacity, float, opacity of surface, range 0.0-1.0
+#     Return:
+#     ----
+#         viewer: py3Dmol.view, a class for constructing embedded 3Dmol.js views in ipython notebooks.
+#     """
+#     assert style in ('line', 'stick', 'sphere', 'carton')
+
+#     viewer = py3Dmol.view(width=size[0], height=size[1])
+#     if isinstance(mol, list):
+#         for i, m in enumerate(mol):
+#             mblock = Chem.MolToMolBlock(m)
+#             viewer.addModel(mblock, 'mol' + str(i))
+#     elif len(mol.GetConformers()) > 1:
+#         for i in range(len(mol.GetConformers())):
+#             mblock = Chem.MolToMolBlock(mol, confId=i)
+#             viewer.addModel(mblock, 'mol' + str(i))
+#     else:
+#         mblock = Chem.MolToMolBlock(mol)
+#         viewer.addModel(mblock, 'mol')
+#     viewer.setStyle({style: {}})
+#     if surface:
+#         viewer.addSurface(py3Dmol.SAS, {'opacity': opacity})
+#     viewer.zoomTo()
+#     return viewer

requirements.txt

@@ -9,9 +9,6 @@ matplotlib==3.4.3
 numpy==1.23.1
 openbabel==3.1.1.1
 overrides==7.7.0
-Pillow==9.2.0
-Pillow==10.3.0
-py3Dmol==2.1.0
 pytorch_lightning==2.0.8
 PyYAML==6.0.1
 PyYAML==6.0.1

visualize.py

@@ -1,93 +0,0 @@
-import os
-import py3Dmol
-from rdkit import Chem
-
-
-def visualize_complex(pdb_block, sdf_block, show_protein_surface=True, show_ligand=True, show_ligand_surface=True):
-    view = py3Dmol.view()
-
-    # Add protein to the canvas
-    view.addModel(pdb_block, 'pdb')
-    if show_protein_surface:
-        view.addSurface(py3Dmol.VDW, {'opacity': 0.7, 'color': 'white'}, {'model': -1})
-    else:
-        view.setStyle({'model': -1}, {'cartoon': {'color': 'spectrum'}, 'line': {}})
-    view.setStyle({'model': -1}, {"cartoon": {"style": "edged", 'opacity': 0}})
-
-    # Add ligand to the canvas
-    if show_ligand:
-        view.addModel(sdf_block, 'sdf')
-        view.setStyle({'model': -1}, {'stick': {}})
-        # view.setStyle({'model': -1}, {'cartoon': {'color': 'spectrum'}, 'line': {}})
-        if show_ligand_surface:
-            view.addSurface(py3Dmol.VDW, {'opacity': 0.8}, {'model': -1})
-
-    view.zoomTo()
-    return view
-
-
-def visualize_data(data, root, show_ligand=True, show_surface=True):
-    protein_path = os.path.join(root, data.protein_filename)
-    ligand_path = os.path.join(root, data.ligand_filename)
-    with open(protein_path, 'r') as f:
-        pdb_block = f.read()
-    with open(ligand_path, 'r') as f:
-        sdf_block = f.read()
-    return visualize_complex(pdb_block, sdf_block, show_ligand=show_ligand, show_surface=show_surface)
-
-
-def visualize_generated_mol(protein_filename, mol, root, show_surface=False, opacity=0.5):
-    protein_path = os.path.join(root, protein_filename)
-    with open(protein_path, 'r') as f:
-        pdb_block = f.read()
-
-    view = py3Dmol.view()
-
-    # Add protein to the canvas
-    view.addModel(pdb_block, 'pdb')
-    view.setStyle({'model': -1}, {'cartoon': {'color': 'spectrum'}, 'line': {}})
-
-    mblock = Chem.MolToMolBlock(mol)
-    view.addModel(mblock, 'mol')
-    view.setStyle({'model': -1}, {'stick': {}, 'sphere': {'radius': 0.35}})
-    if show_surface:
-        view.addSurface(py3Dmol.SAS, {'opacity': opacity}, {'model': -1})
-
-    view.zoomTo()
-    return view
-
-
-def MolTo3DView(mol, size=(300, 300), style="stick", surface=False, opacity=0.5):
-    """Draw molecule in 3D
-
-    Args:
-    ----
-        mol: rdMol, molecule to show
-        size: tuple(int, int), canvas size
-        style: str, type of drawing molecule
-               style can be 'line', 'stick', 'sphere', 'carton'
-        surface, bool, display SAS
-        opacity, float, opacity of surface, range 0.0-1.0
-    Return:
-    ----
-        viewer: py3Dmol.view, a class for constructing embedded 3Dmol.js views in ipython notebooks.
-    """
-    assert style in ('line', 'stick', 'sphere', 'carton')
-
-    viewer = py3Dmol.view(width=size[0], height=size[1])
-    if isinstance(mol, list):
-        for i, m in enumerate(mol):
-            mblock = Chem.MolToMolBlock(m)
-            viewer.addModel(mblock, 'mol' + str(i))
-    elif len(mol.GetConformers()) > 1:
-        for i in range(len(mol.GetConformers())):
-            mblock = Chem.MolToMolBlock(mol, confId=i)
-            viewer.addModel(mblock, 'mol' + str(i))
-    else:
-        mblock = Chem.MolToMolBlock(mol)
-        viewer.addModel(mblock, 'mol')
-    viewer.setStyle({style: {}})
-    if surface:
-        viewer.addSurface(py3Dmol.SAS, {'opacity': opacity})
-    viewer.zoomTo()
-    return viewer