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Add 3D conformer support and MolOps expansion#54

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sharifhsn wants to merge 14 commits intordkit-rs:mainfrom
sharifhsn:pr/conformers-molops
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Add 3D conformer support and MolOps expansion#54
sharifhsn wants to merge 14 commits intordkit-rs:mainfrom
sharifhsn:pr/conformers-molops

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@sharifhsn sharifhsn commented Mar 15, 2026

Note: This PR is stacked on #50. Unique files: conformer.{h,cc,rs}, mol_ops.{h,cc,rs} modifications, build.rs library links, test_conformer.rs, test_mol_ops_expanded.rs.

3D conformers

let mut mol = ROMol::from_smiles("CCO").unwrap();

// Generate 3D coordinates
let conf_id = mol.embed_molecule();
assert!(mol.conformer_is_3d(conf_id));

let (x, y, z) = mol.atom_position(conf_id, 0);

// Or 2D depiction coordinates
let conf_id = mol.compute_2d_coords();
assert!(!mol.conformer_is_3d(conf_id as i32));

// Multiple conformers for ensemble analysis
let ids = mol.embed_multiple_confs(10);
assert_eq!(mol.num_conformers(), 11); // 1 from before + 10 new

Links: DistGeomHelpers, Depictor, RDGeometryLib, EigenSolvers, ForceField, ForceFieldHelpers, PartialCharges.

MolOps expansion

// Split disconnected structures
let mol = ROMol::from_smiles("CCO.CC.[Na+].[Cl-]").unwrap();
let frags = get_mol_frags(&mol);
assert_eq!(frags.len(), 4);

// Formal charge
assert_eq!(get_formal_charge(&ROMol::from_smiles("[NH4+]").unwrap()), 1);

// Aromaticity and stereochemistry perception
set_aromaticity(&mut rw_mol);
assign_stereochemistry(&mut mol);

🤖 Generated with Claude Code

sharifhsn and others added 14 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>
Conformers: embed_molecule(), embed_multiple_confs(), compute_2d_coords(),
num_conformers(), conformer_is_3d(), atom_position(). Enables 3D-QSAR,
docking prep, and 2D depiction workflows.

MolOps: set_aromaticity(), assign_stereochemistry(), get_formal_charge(),
get_mol_frags() for splitting disconnected structures.

Links new RDKit libraries: DistGeomHelpers, Depictor, RDGeometryLib,
EigenSolvers, ForceField, ForceFieldHelpers, PartialCharges.

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