Merge branch 'switch-fp-generator' into dev/switch_to_fpgenerators

volkamerlab · May 15, 2023 · 8c788fa · 8c788fa
2 parents 520e4fd + 214d659
commit 8c788fa
Show file tree

Hide file tree

Showing 21 changed files with 6,968 additions and 9,028 deletions.
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -61,20 +61,17 @@ jobs:
         shell: bash -l {0}
         run: |
           cd docs/_build/html
-          python -m http.server > /dev/null &2>1&
-          npx broken-link-checker http://localhost:8000/ --ordered --recursive \
-            --exclude "*.txt" \
-            --exclude "https://onlinelibrary.wiley.com/doi/full/10.1002/cmdc.200700139" \
-            --exclude "https://onlinelibrary.wiley.com/doi/10.1002/9783527806539.*" \
-            --exclude "https://towardsdatascience.com" \
-            --exclude "https://medium.com" \
-            --exclude "https://*.medium.com" \
-            --exclude "http[s]://quora.com" \
-            --exclude "http[s]://doi.org" \
-            --exclude "ftp://*" \
-            --exclude "http://localhost:8000" \
-            --exclude "https://pubs.acs.org/doi/10.1021/acs.jcim.9b00662" \
-            --exclude "https://pubs.acs.org/doi/abs/10.1021/bk-2021-1387.ch010"
+          npx linkinator . --verbosity error --recurse --timeout 5000 \
+            -s "/*.txt" \
+            -s "https://onlinelibrary.wiley.com/doi/full/10.1002/cmdc.200700139" \
+            -s "https://onlinelibrary.wiley.com/doi/10.1002/9783527806539.*" \
+            -s "https://towardsdatascience.com" \
+            -s "https://medium.com" \
+            -s "https://*.medium.com" \
+            -s "http[s]://quora.com" \
+            -s "http[s]://doi.org/*" \
+            -s "http[s]://pubs.acs.org/*" \
+            -s "ftp://*" \
 
       - name: Check 404s (README)
         uses: gaurav-nelson/github-action-markdown-link-check@v1

diff --git a/teachopencadd/talktorials/T002_compound_adme/talktorial.ipynb b/teachopencadd/talktorials/T002_compound_adme/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T003_compound_unwanted_substructures/talktorial.ipynb b/teachopencadd/talktorials/T003_compound_unwanted_substructures/talktorial.ipynb
@@ -685,7 +685,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -699,7 +699,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.4"
+   "version": "3.9.16"
   },
   "toc-autonumbering": true,
   "widgets": {

diff --git a/teachopencadd/talktorials/T004_compound_similarity/talktorial.ipynb b/teachopencadd/talktorials/T004_compound_similarity/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T007_compound_activity_machine_learning/talktorial.ipynb b/teachopencadd/talktorials/T007_compound_activity_machine_learning/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T009_compound_ensemble_pharmacophores/talktorial.ipynb b/teachopencadd/talktorials/T009_compound_ensemble_pharmacophores/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T010_binding_site_comparison/talktorial.ipynb b/teachopencadd/talktorials/T010_binding_site_comparison/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T011_query_online_api_webservices/talktorial.ipynb b/teachopencadd/talktorials/T011_query_online_api_webservices/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T013_query_pubchem/talktorial.ipynb b/teachopencadd/talktorials/T013_query_pubchem/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T014_binding_site_detection/talktorial.ipynb b/teachopencadd/talktorials/T014_binding_site_detection/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb b/teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T018_automated_cadd_pipeline/utils/helpers/nglview.py b/teachopencadd/talktorials/T018_automated_cadd_pipeline/utils/helpers/nglview.py
@@ -47,7 +47,7 @@ def protein(input_type, input_value, output_image_filename=None):
     """
 
     if input_type == "pdb_code":
-        viewer = nv.show_pdbid(input_value, height="600px")
+        viewer = nv.show_pdbid(input_value)
     else:
         with open(input_value) as f:
             viewer = nv.show_file(f, ext=input_type, height="600px", default_representation=False)

diff --git a/teachopencadd/talktorials/T018_automated_cadd_pipeline/utils/helpers/pdb.py b/teachopencadd/talktorials/T018_automated_cadd_pipeline/utils/helpers/pdb.py
@@ -27,7 +27,7 @@ def read_pdb_file_content(input_type, input_value):
         Content of the PDB file as a single string.
     """
     if input_type == "pdb_code":
-        pdb_file_content = pypdb.get_pdb_file(input_value)
+        pdb_file_content = pypdb.clients.pdb.pdb_client.get_pdb_file(input_value)
     elif input_type == "pdb_filepath":
         with open(input_value) as f:
             pdb_file_content = f.read()
@@ -52,7 +52,7 @@ def fetch_and_save_pdb_file(pdb_code, output_filepath):
     pathlib.Path
         The full path of the saved PDB file.
     """
-    pdb_file_content = pypdb.get_pdb_file(pdb_code)
+    pdb_file_content = pypdb.clients.pdb.pdb_client.get_pdb_file(pdb_code)
     full_filepath = Path(output_filepath).with_suffix(".pdb")
     with open(full_filepath, "w") as f:
         f.write(pdb_file_content)

diff --git a/teachopencadd/talktorials/T018_automated_cadd_pipeline/utils/ligand.py b/teachopencadd/talktorials/T018_automated_cadd_pipeline/utils/ligand.py
@@ -7,6 +7,7 @@
 
 import pandas as pd  # for creating dataframes and handling data
 from rdkit.Chem import PandasTools # for displaying structures inside Pandas DataFrame
+PandasTools.RenderImagesInAllDataFrames(True)
 
 from .helpers import pubchem, rdkit
 

diff --git a/teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb b/teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T022_ligand_based_screening_neural_network/talktorial.ipynb b/teachopencadd/talktorials/T022_ligand_based_screening_neural_network/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T023_what_is_a_kinase/talktorial.ipynb b/teachopencadd/talktorials/T023_what_is_a_kinase/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T024_kinase_similarity_sequence/talktorial.ipynb b/teachopencadd/talktorials/T024_kinase_similarity_sequence/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T025_kinase_similarity_kissim/talktorial.ipynb b/teachopencadd/talktorials/T025_kinase_similarity_kissim/talktorial.ipynb
diff --git a/teachopencadd/talktorials/T026_kinase_similarity_ifp/talktorial.ipynb b/teachopencadd/talktorials/T026_kinase_similarity_ifp/talktorial.ipynb