Fixes error in 2D depiction due to RDKIt update (#35)

* Add adjustDegree = False to adjust query params

This fixes an issue that changed between RDKit 2024.9.6 and 2025.3.1.
Details in rdkit/rdkit#8592

* Update tests for NumPy 2.0+ compatibility

* Update pyproject.toml and poetry.lock for 2025-07

* 🐛 Add depitions to results only if they are successful

* 🎨 make templates to be None for failed DepictionResult

* 🎨 make the rdkit 2d depiction using coordgen library explicit

* ✨ Add rdkit depictions

* 📝 update changelog

* 🔖 bump version number

---------

Co-authored-by: David W.H. Swenson <dwhs@hyperblazer.net>
Co-authored-by: roshan <roshan@ebi.ac.uk>

Author: 3 people

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## RELEASE 1.0.0 - Sep 4, 2025
+
+### Features
+* Support for RDKit 2025 and NumPy 2.0
+* Uses both coordgen library and the default RDKit functionality to generate 2D depictions
+
 ## RELEASE 0.8.6 - Oct 28, 2024
 
 ### Features

pdbeccdutils/core/depictions.py

@@ -33,7 +33,7 @@
 from pdbeccdutils.helpers.mol_tools import fix_conformer
 from pdbeccdutils.utils import config
 from rdkit import Chem, Geometry
-from rdkit.Chem import AllChem, rdCoordGen
+from rdkit.Chem import AllChem, rdCoordGen, rdDepictor
 from scipy.spatial import KDTree
 
 
@@ -101,6 +101,7 @@ def depict_molecule(
 
         templateMol = Chem.RWMol(temp_mol).GetMol()
         pubchemMol = Chem.RWMol(temp_mol).GetMol()
+        rdkitMolCd = Chem.RWMol(temp_mol).GetMol()
         rdkitMol = Chem.RWMol(temp_mol).GetMol()
         results = []
 
@@ -110,11 +111,14 @@ def depict_molecule(
             else None
         )
         template_res = self._get_2D_by_template(templateMol) if self.templates else []
+        rdkit_res_cd = self._get_2D_by_rdkit_coordgen(rdkitMolCd)
         rdkit_res = self._get_2D_by_rdkit(rdkitMol)
 
-        if pubchem_res is not None:
+        if (pubchem_res is not None) and (pubchem_res.source.name == 'PubChem'):
             results.append(pubchem_res)
-        if rdkit_res is not None:
+        if rdkit_res_cd.source.name == 'RDKit':
+            results.append(rdkit_res_cd)
+        if rdkit_res.source.name == 'RDKit':
             results.append(rdkit_res)
 
         results = results + template_res
@@ -129,7 +133,7 @@ def depict_molecule(
 
         return DepictionResult(
             source=DepictionSource.Failed,
-            template_name="",
+            template_name=None,
             mol=None,
             score=float("inf"),
         )
@@ -180,6 +184,30 @@ def _load_template(self, path):
 
         return mol
 
+    def _get_2D_by_rdkit_coordgen(self, mol):
+        """
+        Get depiction done using solely the default RDKit coordgen functionality.
+
+        Args:
+            mol (rdkit.Chem.rdchem.Mol): Mol to be depicted
+
+        Returns:
+            DepictionResult: Depiction with some usefull metadata
+        """
+        try:
+            rdCoordGen.AddCoords(mol, self.coordgen_params)
+            flaws = DepictionValidator(mol).depiction_score()
+            return DepictionResult(
+                source=DepictionSource.RDKit, template_name=None, mol=mol, score=flaws
+            )
+        except Exception:
+            return DepictionResult(
+                source=DepictionSource.Failed,
+                template_name=None,
+                mol=None,
+                score=float("inf"),
+            )
+
     def _get_2D_by_rdkit(self, mol):
         """
         Get depiction done using solely the default RDKit functionality.
@@ -191,7 +219,8 @@ def _get_2D_by_rdkit(self, mol):
             DepictionResult: Depiction with some usefull metadata
         """
         try:
-            rdCoordGen.AddCoords(mol, self.coordgen_params)
+            rdDepictor.SetPreferCoordGen(False)
+            rdDepictor.Compute2DCoords(mol, useRingTemplates=True)
             flaws = DepictionValidator(mol).depiction_score()
             return DepictionResult(
                 source=DepictionSource.RDKit, template_name=None, mol=mol, score=flaws

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pdbeccdutils"
-version = "0.8.6"
+version = "1.0.0"
 description = "Toolkit to parse and process small molecules in wwPDB"
 authors = ["Protein Data Bank in Europe <pdbehelp@ebi.ac.uk>"]
 license = "Apache License 2.0."