Add 3D conformer support and MolOps expansion

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "rdkit"
 version = "0.4.12"
-edition = "2021"
+edition = "2024"
 authors = ["Xavier Lange <xrlange@gmail.com>", "Javier Pineda <javierjpineda13@gmail.com"]
 license = "MIT"
 description = "High level RDKit functionality for rust"
@@ -17,7 +17,7 @@ cxx = "1"
 flate2 = "1"
 log = "0.4"
 rdkit-sys = { path = "rdkit-sys", version = "0.4.9" }
-thiserror = "1"
+thiserror = "2"
 
 [dev-dependencies]
-env_logger = "0.9.0"
+env_logger = "0.11"

README.md

@@ -2,7 +2,7 @@ RDKit
 ---
 
 A high-level library for performing common RDKit tasks such as SMILES parsing, molecule normalization, etc. Uses
-the C++ API via bindings from [rdkit-sys](https://crates.io/crate/rdkit-sys).
+the C++ API via bindings from [rdkit-sys](https://crates.io/crates/rdkit-sys).
 
 Notice: Requires rdkit 2023.09.1 or higher (like Ubuntu Noble 24.04)
 

benches/atom_iteration_benchmark.rs

@@ -0,0 +1,102 @@
+#![allow(soft_unstable)]
+#![feature(test)]
+extern crate test;
+
+use rdkit::ROMol;
+
+/// Drug-like molecules of varying size for realistic benchmarking.
+/// These cover common pharmaceutical scaffolds and natural products.
+const SMILES_SET: &[&str] = &[
+    // aspirin
+    "CC(=O)Oc1ccccc1C(=O)O",
+    // ibuprofen
+    "CC(C)Cc1ccc(cc1)C(C)C(=O)O",
+    // caffeine
+    "Cn1c(=O)c2c(ncn2C)n(C)c1=O",
+    // diazepam
+    "O=C1CN=C(c2ccccc2)c2cc(Cl)ccc2N1C",
+    // atorvastatin (lipitor)
+    "CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H](O)C[C@@H](O)CC(=O)O",
+    // taxol core
+    "CC1=C2C(OC(=O)c3ccccc3)C(O)C4(OC(=O)C(O)(CC(OC(=O)c5ccccc5)C1O)C24C)C(=O)c1ccc(OC)cc1",
+    // vancomycin fragment
+    "OC1C(O)C(OC2C(O)C(O)C(O)C(CO)O2)OC(CO)C1NC(=O)C1CC(O)CN1C(=O)C(NC(=O)C1CC(=O)NC(=O)C1O)C(O)c1ccc(O)cc1",
+];
+
+/// Baseline: SMILES parsing cost.
+#[bench]
+fn bench_parse_smiles(b: &mut test::bench::Bencher) {
+    b.iter(|| {
+        for smiles in SMILES_SET {
+            test::black_box(ROMol::from_smiles(smiles).unwrap());
+        }
+    });
+}
+
+/// Iterate all atoms via atom_ref (&self), read 7 properties per atom.
+/// This is the realistic featurization workload.
+#[bench]
+fn bench_atom_ref_all_properties(b: &mut test::bench::Bencher) {
+    let mols: Vec<ROMol> = SMILES_SET
+        .iter()
+        .map(|s| ROMol::from_smiles(s).unwrap())
+        .collect();
+
+    b.iter(|| {
+        for mol in &mols {
+            let n = mol.num_atoms(true);
+            for i in 0..n {
+                let atom = mol.atom_ref(i);
+                test::black_box(atom.symbol());
+                test::black_box(atom.get_atomic_num());
+                test::black_box(atom.get_formal_charge());
+                test::black_box(atom.get_is_aromatic());
+                test::black_box(atom.get_hybridization_type());
+                test::black_box(atom.get_degree());
+                test::black_box(atom.get_total_num_hs());
+            }
+        }
+    });
+}
+
+/// Same workload via atom_with_idx (&mut self).
+/// Regression guard: should be the same speed as atom_ref.
+#[bench]
+fn bench_atom_mut_all_properties(b: &mut test::bench::Bencher) {
+    let mut mols: Vec<ROMol> = SMILES_SET
+        .iter()
+        .map(|s| ROMol::from_smiles(s).unwrap())
+        .collect();
+
+    b.iter(|| {
+        for mol in &mut mols {
+            let n = mol.num_atoms(true);
+            for i in 0..n {
+                let atom = mol.atom_with_idx(i);
+                test::black_box(atom.symbol());
+                test::black_box(atom.get_atomic_num());
+                test::black_box(atom.get_formal_charge());
+                test::black_box(atom.get_is_aromatic());
+                test::black_box(atom.get_hybridization_type());
+                test::black_box(atom.get_degree());
+                test::black_box(atom.get_total_num_hs());
+            }
+        }
+    });
+}
+
+/// Clone cost alone. Useful for understanding the cost of cloning
+/// molecules when only &ROMol is available but mutation is needed.
+#[bench]
+fn bench_clone_molecules(b: &mut test::bench::Bencher) {
+    let mols: Vec<ROMol> = SMILES_SET
+        .iter()
+        .map(|s| ROMol::from_smiles(s).unwrap())
+        .collect();
+
+    b.iter(|| {
+        for mol in &mols {
+            test::black_box(mol.clone());
+        }
+    });
+}

rdkit-sys/Cargo.toml

@@ -2,7 +2,7 @@
 name = "rdkit-sys"
 authors = ["Xavier Lange (xrlange@gmail.com)", "chrissly31415"]
 version = "0.4.12"
-edition = "2021"
+edition = "2024"
 license = "MIT"
 description = "RDKit CFFI library builder and bindings"
 repository = "https://github.com/rdkit-rs/rdkit/tree/main/rdkit-sys"
@@ -14,9 +14,9 @@ exclude = ["rdkit-*", "*.tar.gz", "examples/"]
 cxx = "1.0.109"
 
 [build-dependencies]
-env_logger = "0.10.0"
+env_logger = "0.11"
 cxx-build = "1.0.109"
-which = "4.4.2"
+which = "8"
 
 [features]
 default = []

rdkit-sys/build.rs

@@ -1,4 +1,4 @@
-const CPP_VERSION_FLAG: &str = "-std=c++17";
+const CPP_VERSION_FLAG: &str = "-std=c++20";
 
 fn main() {
     if std::env::var("DOCS_RS").is_ok() {
@@ -122,17 +122,21 @@ fn main() {
         // "ChemReactions",
         // "ChemTransforms",
         "DataStructs",
-        // "Depictor",
+        "Depictor",
         "Descriptors",
+        "DistGeomHelpers",
+        "EigenSolvers",
         "FileParsers",
         "Fingerprints",
+        "ForceField",
+        "ForceFieldHelpers",
         // "GenericGroups",
         "GraphMol",
         "MolStandardize",
         // "MolTransforms",
-        // "PartialCharges",
+        "PartialCharges",
         "RDGeneral",
-        // "RDGeometryLib",
+        "RDGeometryLib",
         // "RingDecomposerLib",
         "ScaffoldNetwork",
         "SmilesParse",

rdkit-sys/rustfmt.toml

@@ -48,8 +48,8 @@ trailing_comma = "Vertical"
 match_block_trailing_comma = false
 blank_lines_upper_bound = 1
 blank_lines_lower_bound = 0
-edition = "2021"
-version = "One"
+edition = "2024"
+style_edition = "2024"
 inline_attribute_width = 0
 format_generated_files = true
 merge_derives = true

rdkit-sys/src/bridge/conformer.rs

@@ -0,0 +1,23 @@
+#[cxx::bridge(namespace = "RDKit")]
+pub mod ffi {
+    unsafe extern "C++" {
+        include!("wrapper/include/conformer.h");
+
+        pub type ROMol = crate::ro_mol_ffi::ROMol;
+
+        pub fn embed_molecule(mol: &mut SharedPtr<ROMol>) -> i32;
+        pub fn embed_multiple_confs(
+            mol: &mut SharedPtr<ROMol>,
+            num_confs: u32,
+        ) -> UniquePtr<CxxVector<i32>>;
+        pub fn compute_2d_coords(mol: &mut SharedPtr<ROMol>) -> u32;
+
+        pub fn mol_get_num_conformers(mol: &SharedPtr<ROMol>) -> u32;
+        pub fn conformer_is_3d(mol: &SharedPtr<ROMol>, conf_id: i32) -> bool;
+        pub fn get_atom_pos(
+            mol: &SharedPtr<ROMol>,
+            conf_id: i32,
+            atom_idx: u32,
+        ) -> UniquePtr<CxxVector<f64>>;
+    }
+}

rdkit-sys/src/bridge/mod.rs

@@ -1,3 +1,6 @@
+mod conformer;
+pub use conformer::ffi as conformer_ffi;
+
 mod descriptors;
 pub use descriptors::ffi as descriptors_ffi;
 
@@ -11,7 +14,7 @@ mod mol_standardize;
 pub use mol_standardize::ffi as mol_standardize_ffi;
 
 mod periodic_table;
-pub use periodic_table::{ffi as periodic_table_ffi, PeriodicTableOps};
+pub use periodic_table::{PeriodicTableOps, ffi as periodic_table_ffi};
 
 mod ro_mol;
 pub use ro_mol::ffi as ro_mol_ffi;

rdkit-sys/src/bridge/mol_ops.rs

@@ -83,5 +83,14 @@ pub mod ffi {
         pub fn romol_set_hybridization(mol: &mut SharedPtr<ROMol>);
 
         pub fn clean_up(rw_mol: &mut SharedPtr<RWMol>);
+
+        pub fn set_aromaticity(mol: &mut SharedPtr<RWMol>);
+        pub fn assign_stereochemistry(mol: &mut SharedPtr<ROMol>);
+        pub fn mol_get_formal_charge(mol: &SharedPtr<ROMol>) -> i32;
+
+        pub type ROMolVec;
+        pub fn get_mol_frags(mol: &SharedPtr<ROMol>) -> SharedPtr<ROMolVec>;
+        pub fn romol_vec_size(vec: &SharedPtr<ROMolVec>) -> u32;
+        pub fn romol_vec_get(vec: &SharedPtr<ROMolVec>, idx: u32) -> SharedPtr<ROMol>;
     }
 }

rdkit-sys/src/bridge/periodic_table.rs

@@ -43,7 +43,7 @@ pub trait PeriodicTableOps {
     fn getElementName(self, atomic_number: u32) -> String;
     fn getValenceList(self, atomic_number: u32) -> &'static CxxVector<i32>;
 }
-impl<'a> PeriodicTableOps for UniquePtr<PeriodicTable> {
+impl PeriodicTableOps for UniquePtr<PeriodicTable> {
     fn getElementSymbol(self, atomic_number: u32) -> String {
         ffi::getElementSymbol(atomic_number)
     }

rdkit-sys/src/bridge/ro_mol.rs

@@ -59,6 +59,7 @@ pub mod ffi {
 
         pub fn get_num_atoms(mol: &SharedPtr<ROMol>, onlyExplicit: bool) -> u32;
         pub fn get_atom_with_idx(mol: &mut SharedPtr<ROMol>, idx: u32) -> Pin<&mut Atom>;
+        pub fn get_atom_with_idx_const(mol: &SharedPtr<ROMol>, idx: u32) -> Pin<&Atom>;
         pub fn get_symbol(atom: Pin<&Atom>) -> String;
         pub fn get_is_aromatic(atom: Pin<&Atom>) -> bool;
         pub fn get_atomic_num(atom: Pin<&Atom>) -> i32;

rdkit-sys/tests/test_atoms.rs

@@ -17,7 +17,9 @@ fn test_atoms() {
 
     assert_eq!(
         &atoms,
-        &["C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C"]
+        &[
+            "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C"
+        ]
     );
 
     let mut atom = rdkit_sys::ro_mol_ffi::get_atom_with_idx(&mut romol, 2);

rdkit-sys/tests/test_ro_mol.rs

@@ -69,7 +69,10 @@ fn mol_to_molblock_test() {
     cxx::let_cxx_string!(smiles = "CC");
     let romol = rdkit_sys::ro_mol_ffi::smiles_to_mol(&smiles).unwrap();
     let molblock = rdkit_sys::ro_mol_ffi::mol_to_molblock(&romol);
-    assert_eq!(molblock, "\n     RDKit          2D\n\n  2  1  0  0  0  0  0  0  0  0999 V2000\n    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2990    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\nM  END\n");
+    assert_eq!(
+        molblock,
+        "\n     RDKit          2D\n\n  2  1  0  0  0  0  0  0  0  0999 V2000\n    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2990    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\nM  END\n"
+    );
 }
 
 #[test]

rdkit-sys/tests/test_rw_mol.rs

@@ -1,4 +1,4 @@
-use cxx::{let_cxx_string, SharedPtr};
+use cxx::{SharedPtr, let_cxx_string};
 use rdkit_sys::{ro_mol_ffi::ROMol, rw_mol_ffi::RWMol};
 
 #[test]
@@ -191,7 +191,10 @@ CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C
     let ro_mol = unsafe { std::mem::transmute::<SharedPtr<RWMol>, SharedPtr<ROMol>>(rw_mol) };
 
     let smiles = rdkit_sys::ro_mol_ffi::mol_to_smiles(&ro_mol);
-    assert_eq!("[H]C([H])([H])C(=O)OC([H])(C([H])([H])C(=O)[O-])C([H])([H])[N+](C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H]", &smiles);
+    assert_eq!(
+        "[H]C([H])([H])C(=O)OC([H])(C([H])([H])C(=O)[O-])C([H])([H])[N+](C([H])([H])[H])(C([H])([H])[H])C([H])([H])[H]",
+        &smiles
+    );
 }
 
 #[test]

rdkit-sys/wrapper/include/conformer.h

@@ -0,0 +1,17 @@
+#pragma once
+
+#include "rust/cxx.h"
+#include <GraphMol/GraphMol.h>
+
+namespace RDKit {
+
+int embed_molecule(std::shared_ptr<ROMol> &mol);
+std::unique_ptr<std::vector<int32_t>> embed_multiple_confs(std::shared_ptr<ROMol> &mol, unsigned int num_confs);
+unsigned int compute_2d_coords(std::shared_ptr<ROMol> &mol);
+
+unsigned int mol_get_num_conformers(const std::shared_ptr<ROMol> &mol);
+bool conformer_is_3d(const std::shared_ptr<ROMol> &mol, int conf_id);
+std::unique_ptr<std::vector<double>> get_atom_pos(const std::shared_ptr<ROMol> &mol, int conf_id,
+                                                  unsigned int atom_idx);
+
+} // namespace RDKit

rdkit-sys/wrapper/include/mol_ops.h

@@ -67,4 +67,13 @@ void romol_set_hybridization(std::shared_ptr<ROMol> &mol);
 
 // pub fn clean_up(rw_mol: &mut SharedPtr<RWMol>)
 void clean_up(std::shared_ptr<RWMol> &rw_mol);
+
+void set_aromaticity(std::shared_ptr<RWMol> &mol);
+void assign_stereochemistry(std::shared_ptr<ROMol> &mol);
+int mol_get_formal_charge(const std::shared_ptr<ROMol> &mol);
+
+struct ROMolVec;
+std::shared_ptr<ROMolVec> get_mol_frags(const std::shared_ptr<ROMol> &mol);
+unsigned int romol_vec_size(const std::shared_ptr<ROMolVec> &vec);
+std::shared_ptr<ROMol> romol_vec_get(const std::shared_ptr<ROMolVec> &vec, unsigned int idx);
 } // namespace RDKit

rdkit-sys/wrapper/include/ro_mol.h

@@ -29,6 +29,8 @@ unsigned int atom_sanitize_exception_get_atom_idx(const MolSanitizeExceptionUniq
 
 unsigned int get_num_atoms(const std::shared_ptr<ROMol> &mol, bool only_explicit);
 Atom &get_atom_with_idx(std::shared_ptr<ROMol> &mol, unsigned int idx);
+const Atom &get_atom_with_idx_const(const std::shared_ptr<ROMol> &mol,
+                                    unsigned int idx);
 rust::String get_symbol(const Atom &atom);
 bool get_is_aromatic(const Atom &atom);
 int get_atomic_num(const Atom &atom);

rdkit-sys/wrapper/src/conformer.cc

@@ -0,0 +1,27 @@
+#include "rust/cxx.h"
+#include <GraphMol/Depictor/RDDepictor.h>
+#include <GraphMol/DistGeomHelpers/Embedder.h>
+#include <GraphMol/GraphMol.h>
+
+namespace RDKit {
+
+int embed_molecule(std::shared_ptr<ROMol> &mol) { return DGeomHelpers::EmbedMolecule(*mol); }
+
+std::unique_ptr<std::vector<int32_t>> embed_multiple_confs(std::shared_ptr<ROMol> &mol, unsigned int num_confs) {
+	auto ids = DGeomHelpers::EmbedMultipleConfs(*mol, num_confs);
+	return std::make_unique<std::vector<int32_t>>(ids.begin(), ids.end());
+}
+
+unsigned int compute_2d_coords(std::shared_ptr<ROMol> &mol) { return RDDepict::compute2DCoords(*mol); }
+
+unsigned int mol_get_num_conformers(const std::shared_ptr<ROMol> &mol) { return mol->getNumConformers(); }
+
+bool conformer_is_3d(const std::shared_ptr<ROMol> &mol, int conf_id) { return mol->getConformer(conf_id).is3D(); }
+
+std::unique_ptr<std::vector<double>> get_atom_pos(const std::shared_ptr<ROMol> &mol, int conf_id,
+                                                  unsigned int atom_idx) {
+	const auto &pos = mol->getConformer(conf_id).getAtomPos(atom_idx);
+	return std::make_unique<std::vector<double>>(std::vector<double>{pos.x, pos.y, pos.z});
+}
+
+} // namespace RDKit