Crate smiles_rs 

smiles-rs

Parses SMILES strings into molecular graphs, following the OpenSMILES specification. no_std with alloc, no unsafe code.

Beyond parsing it canonicalizes molecules through canonicalize and canonical_labeling, perceives aromaticity under the RDKit default, MDL and simple models, and kekulizes back to alternating bonds. It computes symmetrized SSSR rings and ring membership, fragments and connected components, radius-bounded atom environments for MAP4-style fingerprints, and the maximum common edge subgraph of two molecules through geometric-traits. Tetrahedral and double bond stereochemistry survive canonicalization, formulas convert into molecular-formulas types, and WildcardSmiles accepts * atoms with a fallible conversion back into Smiles.

Example

use core::str::FromStr;

use molecular_formulas::prelude::ChemicalFormula;
use smiles_rs::prelude::Smiles;

let ethanol = Smiles::from_str("CCO")?;

assert_eq!(ethanol.nodes().len(), 3);
assert_eq!(ethanol.number_of_bonds(), 2);
assert_eq!(ethanol.render(), "CCO");

let formula: ChemicalFormula<u32, i32> = ChemicalFormula::from(&ethanol);
assert_eq!(formula.to_string(), "C₂H₆O");

Features

Feature	Effect
datasets	Streams PubChem, ZINC20, COCONUT, LOTUS and MassSpecGym from a local cache, requires std. See datasets.
fuzzing	Exposes the parser internals the fuzz targets drive.

Re-exports

pub use crate::datasets::ArchiveMode;

pub use crate::datasets::CacheMode;

pub use crate::datasets::DatasetArtifact;

pub use crate::datasets::DatasetCollectionArtifact;

pub use crate::datasets::DatasetCollectionSource;

pub use crate::datasets::DatasetCompression;

pub use crate::datasets::DatasetError;

pub use crate::datasets::DatasetFetchOptions;

pub use crate::datasets::DatasetFile;

pub use crate::datasets::DatasetSmilesIter;

pub use crate::datasets::DatasetSmilesRecord;

pub use crate::datasets::DatasetSmilesRecordIter;

pub use crate::datasets::DatasetSource;

pub use crate::datasets::LOTUS_SMILES;

pub use crate::datasets::LotusSmiles;

pub use crate::datasets::MASS_SPEC_GYM_SMILES;

pub use crate::datasets::MassSpecGymSmiles;

pub use crate::datasets::PUBCHEM_SMILES;

pub use crate::datasets::PubChemSmiles;

pub use crate::datasets::SmilesDatasetRecordSource;

pub use crate::datasets::SmilesDatasetSource;

pub use crate::datasets::ZINC20_EXPECTED_RECORD_COUNT;

pub use crate::datasets::ZINC20_SMILES;

pub use crate::datasets::Zinc20Smiles;

pub use crate::datasets::default_dataset_cache_dir;

pub use crate::errors::RootError;

pub use crate::errors::SmilesError;

pub use crate::errors::SmilesErrorWithSpan;

pub use crate::errors::SubgraphError;

pub use crate::smiles::AromaticityAssignment;

pub use crate::smiles::AromaticityAssignmentApplicationError;

pub use crate::smiles::AromaticityDiagnostic;

pub use crate::smiles::AromaticityModel;

pub use crate::smiles::AromaticityPerception;

pub use crate::smiles::AromaticityPolicy;

pub use crate::smiles::AromaticityRingFamilyKind;

pub use crate::smiles::AromaticityStatus;

pub use crate::smiles::AtomEnvironment;

pub use crate::smiles::DoubleBondStereoConfig;

pub use crate::smiles::Fragment;

pub use crate::smiles::KekulizationError;

pub use crate::smiles::KekulizationMode;

pub use crate::smiles::RdkitDefaultAromaticity;

pub use crate::smiles::RdkitMdlAromaticity;

pub use crate::smiles::RdkitSimpleAromaticity;

pub use crate::smiles::RingAtomMembership;

pub use crate::smiles::RingAtomMembershipScratch;

pub use crate::smiles::RingMembership;

pub use crate::smiles::Smiles;

pub use crate::smiles::SmilesComponents;

pub use crate::smiles::SmilesMces;

pub use crate::smiles::SymmSssrResult;

pub use crate::smiles::SymmSssrStatus;

pub use crate::smiles::WildcardAromaticityPerception;

pub use crate::smiles::WildcardMolecularFormulaConversionError;

pub use crate::smiles::WildcardSmiles;

pub use crate::smiles::WildcardSmilesComponents;

Modules

atom

Atom storage and helpers.

bond

Module for specifying the bond between two atoms in a SMILES string

datasets

Programmatic dataset downloads with local caching.

errors

Defines errors used in the SMILES parser.

prelude

Common imports for working with this crate.

smiles

Represents a parsed SMILES graph.

token

Represents tokens used in parsing SMILES strings.

Structs

McesBuilder

Builder for MCES computation with typestate generics.

McesResult

Result of an MCES computation.

Enums

InitialProductVertexOrdering

Initial ordering policy for modular-product vertices before clique search.

LargestFragmentMetric

Fragment-size metric used by LargestFragmentMetricRanker.

McesSearchMode

Search mode for the clique stage of MCES.

Traits

GraphSimilarities

Trait for types that carry graph comparison results and can compute similarity metrics.