add example of id error

Author: Brandon Duane Walker

.github/workflows/docker_build.yml

@@ -26,7 +26,7 @@ jobs:
                      rename_residues_mol, combine_structure,
                      remove_terminal_residue_name_prefixes, molgan,
                      pdbbind_refined, onionnet-sfct, smina, pdbfixer,
-                     fix_pdb_atom_column, extract_protein, extract_ligand_protein, generate_conformers]  # No username for pdbind_refined
+                     fix_pdb_atom_column, extract_protein, generate_conformers]  # No username for pdbind_refined
         # skip data/ and cwl_adapters/file_format_conversions/biosimspace/
     runs-on: [ubuntu-latest]
 

cwl_adapters/extract_ligand_protein.cwl

@@ -50,6 +50,10 @@ outputs:
       loadContents: true
       outputEval: |
         ${
+          // check if self[0] exists
+          if (!self[0]) {
+            return null;
+          }
           // Read the contents of the file
           const lines = self[0].contents.split("\n");
           // Read boolean value from the first line

cwl_adapters/topology_check.cwl

@@ -34,7 +34,6 @@ sudo docker build --no-cache --pull -f Dockerfile_onionnet-sfct -t polusai/onion
 sudo docker build --no-cache --pull -f Dockerfile_smina -t cyangnyu/smina .
 sudo docker build --no-cache --pull -f Dockerfile_pdbfixer -t ndonyapour/pdbfixer .
 sudo docker build --no-cache --pull -f Dockerfile_extract_protein -t ndonyapour/extract_protein .
-sudo docker build --no-cache --pull -f Dockerfile_extract_ligand_protein -t mrbrandonwalker/extract_ligand_protein .
 sudo docker build --no-cache --pull -f Dockerfile_fix_pdb_atom_column -t ndonyapour/fix_pdb_atom_column .
 sudo docker build --no-cache --pull -f Dockerfile_generate_conformers -t ndonyapour/generate_conformers .
 

docker/dockerBuild.sh

@@ -28,6 +28,5 @@ docker pull mrbrandonwalker/diffdock_gpu
 docker pull mrbrandonwalker/diffdock_cpu
 docker pull ndonyapour/pdbfixer
 docker pull ndonyapour/extract_protein
-docker pull mrbrandonwalker/extract_ligand_protein
 docker pull ndonyapour/fix_pdb_atom_column
 docker pull ndonyapour/generate_conformers

dockerPull.sh

@@ -42,9 +42,7 @@ def get_net_charge(file_path: str, addhydrogens: bool = False) -> Optional[int]:
     if addhydrogens:
         mol = Chem.AddHs(mol)
     try:
-        AllChem.ComputeGasteigerCharges(mol,
-                                        nIter=50,
-                                        throwOnParamFailure=True)
+        AllChem.ComputeGasteigerCharges(mol, nIter=50, throwOnParamFailure=True)  # type: ignore
     except Exception:  # pylint: disable=broad-exception-caught
         return None
 

examples/scripts/Dockerfile_extract_ligand_protein

@@ -157,14 +157,14 @@ def load_data(input_excel_path: str, query: str, smiles_column: str, binding_dat
 
         # See https://www.rdkit.org/docs/GettingStartedInPython.html#working-with-3d-molecules
         mol_2D: rdkit.Chem.rdchem.Mol = Chem.MolFromSmiles(smiles)  # pylint: disable=c-extension-no-member,no-member
-        AllChem.Compute2DCoords(mol_2D)  # pylint: disable=no-member
+        AllChem.Compute2DCoords(mol_2D)  # type: ignore # pylint: disable=no-member
 
         # See https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.AddHs
         # NOTE: "Much of the code assumes that Hs are not included in the molecular topology,
         # so be very careful with the molecule that comes back from this function."
         mol_3D = Chem.AddHs(mol_2D)  # pylint: disable=no-member
-        AllChem.EmbedMolecule(mol_3D)  # pylint: disable=no-member
-        AllChem.MMFFOptimizeMolecule(mol_3D)  # pylint: disable=no-member
+        AllChem.EmbedMolecule(mol_3D)  # type: ignore # pylint: disable=no-member
+        AllChem.MMFFOptimizeMolecule(mol_3D)  # type: ignore # pylint: disable=no-member
 
         filename = f'ligand_{idx}.sdf'  # chemblid is NOT unique!
         writer = Chem.SDWriter(filename)  # pylint: disable=no-member

examples/scripts/calculate_net_charge.py

@@ -100,7 +100,7 @@ def get_properties(atom: Atom) -> dict:
     res_dict = {}
     res = atom.GetPDBResidueInfo()
     res_dict['GetResidueName'] = res.GetResidueName()
-    res_dict['GetResidueNumber'] = res.GetResidueNumber()
+    res_dict['GetResidueNumber'] = str(res.GetResidueNumber())
     res_dict['GetChainId'] = res.GetChainId()
     res_dict['GetName'] = res.GetName()
     prop_dict = {