Add mol_to_rdkit_mol

CHANGELOG.md

@@ -7,6 +7,11 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [Unreleased]
 
+### Added
+
+- `mol_to_rdkit_mol` to convert the duckdb_rdkit molecule into a format compatible
+  with RDKit
+
 ## [0.3.0] - 2025-01-24
 
 ### Added

README.md

@@ -6,7 +6,8 @@ This repository is based on https://github.com/duckdb/extension-template, check
 
 ---
 
-This extension, duckdb_rdkit, allows you to use RDKit functionality within DuckDB.
+This extension, duckdb_rdkit, integrates RDKit into DuckDB to enable you to do
+cheminformatics work with DuckDB.
 
 ## Currently supported functionality:
 
@@ -16,7 +17,8 @@ This extension, duckdb_rdkit, allows you to use RDKit functionality within DuckD
 
 > [!IMPORTANT]  
 > The duckdb_rdkit molecule representation has additional metadata and cannot
-> be read directly by RDKit. You will get an error.
+> be read directly by RDKit. You will get an error. You can use `mol_to_rdkit_mol`
+> to convert the duckdb_rdkit molecule representation into one that is RDKit compatible.
 
 - Currently, can only be created from a SMILES in a variety of ways: inserting a valid SMILES
   string into a column that expects Mol, type conversion such as 'CC'::mol, or the mol_from_smiles function.
@@ -66,6 +68,11 @@ This extension, duckdb_rdkit, allows you to use RDKit functionality within DuckD
 
 - `mol_from_smiles(SMILES)`: returns a molecule for a SMILES string. Returns NULL if mol cannot be made from SMILES
 - `mol_to_smiles(mol)`: returns the SMILES string for a RDKit molecule
+- `mol_to_rdkit_mol(mol)`: returns the binary RDKit molecule in hexadecimal representation
+  - duckdb_rdkit has its own binary representation of molecules, which differs from RDKit’s format.
+    Use this function to extract a molecule from duckdb_rdkit and convert it
+    into a format compatible with RDKit. The returned value can be passed
+    to RDKit's `Chem.Mol` function for further processing in Python.
 
 ### Molecule descriptors
 
@@ -110,13 +117,15 @@ The easiest way to install RDKit is with conda, and I used [miniforge](https://g
 
 After installing conda, you can create a new
 conda environment and then install the packages needed.
-As of August 2024, I found installing these packages worked (librdkit-dev seems to have the relevant header files).
+`linux_conda_env.yml` or `osx_conda_env.yml` can be used to create a conda
+environment for building the extension.
 
 ```shell
 # activate your conda env and then in your conda env run:
 conda create -n rdkit_dev
 conda activate rdkit_dev
-conda install -c conda-forge -y boost-cpp boost cmake rdkit eigen librdkit-dev
+# or use the osx_conda_env.yml if you are on osx
+conda env update -f linux_conda_env.yml
 ```
 
 After installing the prerequisite software, you can run:

src/mol_formats.cpp

@@ -2,7 +2,9 @@
 #include "common.hpp"
 #include "duckdb/common/string_util.hpp"
 #include "duckdb/common/types.hpp"
+#include "duckdb/execution/expression_executor_state.hpp"
 #include "duckdb/function/function_set.hpp"
+#include "duckdb/main/extension_util.hpp"
 #include "types.hpp"
 #include "umbra_mol.hpp"
 #include <GraphMol/Descriptors/MolDescriptors.h>
@@ -100,6 +102,18 @@ void mol_from_smiles(DataChunk &args, ExpressionState &state, Vector &result) {
       });
 }
 
+void mol_to_rdkit_mol(DataChunk &args, ExpressionState &state, Vector &result) {
+  D_ASSERT(args.data.size() == 1);
+  auto &umbra_mol = args.data[0];
+  auto count = args.size();
+
+  UnaryExecutor::ExecuteWithNulls<string_t, string_t>(
+      umbra_mol, result, count,
+      [&](umbra_mol_t umbra_mol, ValidityMask &mask, idx_t idx) {
+        return StringVector::AddStringOrBlob(result, umbra_mol.GetBinaryMol());
+      });
+}
+
 void RegisterFormatFunctions(DatabaseInstance &instance) {
   // Register scalar functions
   ScalarFunctionSet mol_from_smiles_set("mol_from_smiles");
@@ -111,6 +125,11 @@ void RegisterFormatFunctions(DatabaseInstance &instance) {
   mol_to_smiles_set.AddFunction(
       ScalarFunction({Mol()}, LogicalType::VARCHAR, mol_to_smiles));
   ExtensionUtil::RegisterFunction(instance, mol_to_smiles_set);
+
+  ScalarFunctionSet mol_to_rdkit_mol_set("mol_to_rdkit_mol");
+  mol_to_rdkit_mol_set.AddFunction(
+      ScalarFunction({Mol()}, LogicalType::BLOB, mol_to_rdkit_mol));
+  ExtensionUtil::RegisterFunction(instance, mol_to_rdkit_mol_set);
 }
 
 } // namespace duckdb_rdkit

test/sql/mol_conversion.test

@@ -33,7 +33,7 @@ SELECT mol_from_smiles('NOTASMILES');
 NULL
 
 
-# mol_to_smiles can convert a proper RDKit pickled molecule back to the SMILES
+# mol_to_smiles can convert a binary molecule back to the SMILES
 query I
 SELECT mol_to_smiles(mol_from_smiles('C1=CC=CC=C1'))
 ----
@@ -45,4 +45,10 @@ SELECT 'C1=CC=CC=C1'::mol;
 ----
 c1ccccc1
 
+# mol_to_rdkit_mol can convert the internal representation of a molecule in 
+# duckdb (umbra_mol) to the RDKit molecule.  This will output hex representation
+query I
+SELECT mol_to_rdkit_mol('C'::mol);
+----
+\xEF\xBE\xAD\xDE\x00\x00\x00\x00\x10\x00\x00\x00\x01\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x00\x00\x00\x00\x80\x01\x06\x00@\x00\x00\x00\x04\x0BB\x00\x00\x00\x00\x17\x04\x00\x00\x00\x00\x00\x00\x00\x16