Add bond access and RWMol molecule editing

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() {

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/bond.rs

@@ -0,0 +1,81 @@
+#[cxx::bridge(namespace = "RDKit")]
+pub mod ffi {
+    #[repr(i32)]
+    #[derive(Debug, PartialEq)]
+    pub enum BondType {
+        UNSPECIFIED,
+        SINGLE,
+        DOUBLE,
+        TRIPLE,
+        QUADRUPLE,
+        QUINTUPLE,
+        HEXTUPLE,
+        ONEANDAHALF,
+        TWOANDAHALF,
+        THREEANDAHALF,
+        FOURANDAHALF,
+        FIVEANDAHALF,
+        AROMATIC,
+        IONIC,
+        HYDROGEN,
+        THREECENTER,
+        DATIVEONE,
+        DATIVE,
+        DATIVEL,
+        DATIVER,
+        OTHER,
+        ZERO,
+    }
+
+    #[repr(i32)]
+    #[derive(Debug, PartialEq)]
+    pub enum BondStereo {
+        STEREONONE,
+        STEREOANY,
+        STEREOZ,
+        STEREOE,
+        STEREOCIS,
+        STEREOTRANS,
+    }
+
+    #[repr(i32)]
+    #[derive(Debug, PartialEq)]
+    pub enum BondDir {
+        NONE,
+        BEGINWEDGE,
+        BEGINDASH,
+        ENDDOWNRIGHT,
+        ENDUPRIGHT,
+        EITHERDOUBLE,
+        UNKNOWN,
+    }
+
+    unsafe extern "C++" {
+        include!("wrapper/include/bond.h");
+
+        pub type ROMol = crate::ro_mol_ffi::ROMol;
+        pub type Bond;
+        pub type BondType;
+        pub type BondStereo;
+        pub type BondDir;
+
+        pub fn get_num_bonds(mol: &SharedPtr<ROMol>, only_heavy: bool) -> u32;
+        pub fn get_bond_with_idx(mol: &mut SharedPtr<ROMol>, idx: u32) -> Pin<&mut Bond>;
+        pub fn get_bond_idx_between_atoms(
+            mol: &SharedPtr<ROMol>,
+            begin_idx: u32,
+            end_idx: u32,
+        ) -> i32;
+
+        pub fn bond_get_bond_type(bond: Pin<&Bond>) -> BondType;
+        pub fn bond_get_bond_type_as_double(bond: Pin<&Bond>) -> f64;
+        pub fn bond_get_begin_atom_idx(bond: Pin<&Bond>) -> u32;
+        pub fn bond_get_end_atom_idx(bond: Pin<&Bond>) -> u32;
+        pub fn bond_get_other_atom_idx(bond: Pin<&Bond>, this_idx: u32) -> u32;
+        pub fn bond_get_is_aromatic(bond: Pin<&Bond>) -> bool;
+        pub fn bond_get_is_conjugated(bond: Pin<&Bond>) -> bool;
+        pub fn bond_get_stereo(bond: Pin<&Bond>) -> BondStereo;
+        pub fn bond_get_bond_dir(bond: Pin<&Bond>) -> BondDir;
+        pub fn bond_get_idx(bond: Pin<&Bond>) -> u32;
+    }
+}

rdkit-sys/src/bridge/mod.rs

@@ -1,3 +1,6 @@
+mod bond;
+pub use bond::ffi as bond_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 +83,8 @@ pub mod ffi {
         pub fn romol_set_hybridization(mol: &mut SharedPtr<ROMol>);
 
         pub fn clean_up(rw_mol: &mut SharedPtr<RWMol>);
+
+        pub fn sanitize_mol(mol: &mut SharedPtr<RWMol>) -> Result<()>;
+        pub fn kekulize_mol(mol: &mut SharedPtr<RWMol>) -> Result<()>;
     }
 }

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/src/bridge/rw_mol.rs

@@ -25,5 +25,18 @@ pub mod ffi {
         pub fn rw_mol_to_ro_mol(mol: SharedPtr<RWMol>) -> SharedPtr<ROMol>;
 
         pub fn smarts_to_mol(smarts: &CxxString) -> Result<SharedPtr<RWMol>>;
+
+        // Molecule editing
+        pub fn new_rw_mol() -> SharedPtr<RWMol>;
+        pub fn rw_mol_add_atom(mol: &mut SharedPtr<RWMol>, atomic_num: u32) -> u32;
+        pub fn rw_mol_add_bond(
+            mol: &mut SharedPtr<RWMol>,
+            begin_idx: u32,
+            end_idx: u32,
+            bond_order: i32,
+        ) -> u32;
+        pub fn rw_mol_remove_atom(mol: &mut SharedPtr<RWMol>, idx: u32);
+        pub fn rw_mol_remove_bond(mol: &mut SharedPtr<RWMol>, begin_idx: u32, end_idx: u32);
+        pub fn rw_mol_get_num_atoms(mol: &SharedPtr<RWMol>, only_explicit: bool) -> u32;
     }
 }

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/bond.h

@@ -0,0 +1,27 @@
+#pragma once
+
+#include "rust/cxx.h"
+#include <GraphMol/GraphMol.h>
+
+namespace RDKit {
+
+using BondType   = Bond::BondType;
+using BondStereo = Bond::BondStereo;
+using BondDir    = Bond::BondDir;
+
+unsigned int get_num_bonds(const std::shared_ptr<ROMol> &mol, bool only_heavy);
+Bond &get_bond_with_idx(std::shared_ptr<ROMol> &mol, unsigned int idx);
+int get_bond_idx_between_atoms(const std::shared_ptr<ROMol> &mol, unsigned int begin_idx, unsigned int end_idx);
+
+BondType bond_get_bond_type(const Bond &bond);
+double bond_get_bond_type_as_double(const Bond &bond);
+unsigned int bond_get_begin_atom_idx(const Bond &bond);
+unsigned int bond_get_end_atom_idx(const Bond &bond);
+unsigned int bond_get_other_atom_idx(const Bond &bond, unsigned int this_idx);
+bool bond_get_is_aromatic(const Bond &bond);
+bool bond_get_is_conjugated(const Bond &bond);
+BondStereo bond_get_stereo(const Bond &bond);
+BondDir bond_get_bond_dir(const Bond &bond);
+unsigned int bond_get_idx(const Bond &bond);
+
+} // namespace RDKit

rdkit-sys/wrapper/include/mol_ops.h

@@ -67,4 +67,6 @@ 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 sanitize_mol(std::shared_ptr<RWMol> &mol);
+void kekulize_mol(std::shared_ptr<RWMol> &mol);
 } // 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);