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Add bond access and RWMol molecule editing#51

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sharifhsn wants to merge 15 commits intordkit-rs:mainfrom
sharifhsn:pr/bond-editing
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Add bond access and RWMol molecule editing#51
sharifhsn wants to merge 15 commits intordkit-rs:mainfrom
sharifhsn:pr/bond-editing

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@sharifhsn sharifhsn commented Mar 15, 2026

Note: This PR is stacked on #50. The diff below includes #50's changes. The unique files for this PR are: bond.{h,cc,rs}, rw_mol.{h,cc,rs}, mol_ops.{h,cc,rs} modifications, test_bond.rs, test_rw_mol_editing.rs.

Bond access

Bond<'a> follows the same Pin<&'a mut> lifetime pattern as Atom<'a>:

let mut mol = ROMol::from_smiles("c1ccccc1").unwrap();
let bond = mol.bond_with_idx(0);

assert_eq!(bond.bond_type(), BondType::AROMATIC);
assert!(bond.is_aromatic());
assert_eq!(bond.begin_atom_idx(), 0);
assert_eq!(bond.end_atom_idx(), 1);

Also exposes BondType, BondStereo, BondDir as CXX shared enums, and adds num_bonds(), bond_between_atoms() on ROMol.

RWMol editing

Build molecules programmatically:

let mut mol = RWMol::new();
mol.add_atom(6); // carbon
mol.add_atom(6);
mol.add_atom(8); // oxygen
mol.add_bond(0, 1, BondType::SINGLE);
mol.add_bond(1, 2, BondType::SINGLE);
sanitize_mol(&mut mol).unwrap();

assert_eq!(mol.as_smiles(), "CCO"); // ethanol

Also adds remove_atom(), remove_bond(), num_atoms(), Default impl, and sanitize_mol()/kekulize_mol() which are needed to validate constructed molecules.

🤖 Generated with Claude Code

sharifhsn and others added 15 commits March 13, 2026 22:37
RDKit 2025.09.x uses constexpr virtual destructors and override
functions in its headers (e.g. Geometry/point.h), which require
C++20. Building with -std=c++17 causes compilation failures.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Fixes mismatched_lifetime_syntaxes warning by making the elided
lifetime on Atom<'_> explicit, matching the &mut self borrow.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Remove unused lifetime parameter 'a from PeriodicTableOps impl,
and replace names.len() != 0 with !names.is_empty().

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
The 'version' key is deprecated in current rustfmt. Replace with
'style_edition = "2021"' in both workspace and rdkit-sys configs.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Bind get_periodic_table() to a local variable instead of using it
as a temporary in tail expressions. In Rust 2024, temporaries in
tail expressions are dropped before locals, which would drop the
PeriodicTable UniquePtr before the CxxString it borrows.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Update edition to 2024 in both Cargo.toml files and rustfmt configs.
Apply 2024 style formatting: types before functions/macros in imports,
and long assert_eq! macro calls wrapped across multiple lines.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Add get_atom_with_idx_const that takes const shared_ptr<ROMol>& and
returns const Atom&, using RDKit's const overload of getAtomWithIdx.
This maps to Pin<&Atom> in CXX, enabling &self access on the Rust side.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
AtomRef<'a> holds Pin<&'a Atom> (const) and exposes all read-only
atom methods. ROMol::atom_ref(&self) returns AtomRef, eliminating
the need to clone molecules just to read atom properties.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Verify AtomRef returns identical values for all read-only methods,
property getters work, multiple AtomRefs coexist (no &mut needed),
and iteration over all atoms works via &self.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Benchmarks for the featurization hot path with 7 drug-like molecules:
- atom_ref (const, &self): ~7μs for 7 properties across all atoms
- atom_with_idx (&mut self): ~7μs same, but requires &mut
- clone + featurize (&ROMol callers): ~46μs — 6.5x slower due to clone
Shows AtomRef eliminates the clone tax for read-only workflows.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- thiserror 1 -> 2 (derive macro API unchanged for our usage)
- env_logger 0.9/0.10 -> 0.11 (init() API unchanged)
- which 4 -> 8 (which::which() API unchanged)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Remove inflated clone+featurize and redundant one-property benchmarks.
Keep: atom_ref vs atom_mut (regression guard), clone cost, parse baseline.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
crates.io/crate/ → crates.io/crates/ (missing plural)

Closes rdkit-rs#49

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Bond<'a> follows the same Pin<&'a mut> pattern as Atom<'a>.
Provides 10 getters: bond_type, bond_type_as_double, begin/end_atom_idx,
other_atom_idx, is_aromatic, is_conjugated, stereo, bond_dir, idx.

ROMol gains num_bonds(), bond_with_idx(), and bond_between_atoms().

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
New: RWMol::new(), add_atom(), add_bond(), remove_atom(), remove_bond(),
num_atoms(). Also adds sanitize_mol() and kekulize_mol() which are
essential for validating programmatically constructed molecules.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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