Expand description
chematic-chem — molecular descriptors for chematic.
All descriptor functions take a &Molecule reference.
Values are approximate; calibrated against RDKit defaults.
Re-exports§
pub use cip::CipAssignment;pub use cip::assign_cip;pub use cip::tetrahedral_stereo_neighbors;pub use descriptors::Bcut2D;pub use descriptors::CarbonTypes;pub use descriptors::InformationContent;pub use descriptors::RingBundle;pub use descriptors::aromatic_ring_count;pub use descriptors::autocorr_2d;pub use descriptors::balaban_j;pub use descriptors::bcut2d;pub use descriptors::calc_mol_formula;pub use descriptors::carbon_types;pub use descriptors::cns_mpo_from_parts;pub use descriptors::cns_mpo_score;pub use descriptors::egan_passes;pub use descriptors::exact_mass;pub use descriptors::formal_charge_per_atom;pub use descriptors::formal_charge_sum;pub use descriptors::fraction_rotatable_bonds;pub use descriptors::fsp3;pub use descriptors::geary_autocorr;pub use descriptors::ghose_passes;pub use descriptors::hall_kier_alpha;pub use descriptors::hba_count;pub use descriptors::hba_count_lipinski;pub use descriptors::hbd_count;pub use descriptors::heavy_atom_count;pub use descriptors::hybridization_per_atom;pub use descriptors::implicit_hcount_per_atom;pub use descriptors::information_content;pub use descriptors::ipc;pub use descriptors::lead_like_passes;pub use descriptors::lipinski_passes;pub use descriptors::logp_and_mr;pub use descriptors::logp_crippen;pub use descriptors::logp_crippen_per_atom;pub use descriptors::mcf_passes;pub use descriptors::mde_carbon;pub use descriptors::mmff94_charges;pub use descriptors::molar_refractivity;pub use descriptors::molecular_weight;pub use descriptors::moran_autocorr;pub use descriptors::mqn;pub use descriptors::mr_per_atom;pub use descriptors::num_aliphatic_heterocycles;pub use descriptors::num_aliphatic_rings;pub use descriptors::num_amide_bonds;pub use descriptors::num_aromatic_heterocycles;pub use descriptors::num_bridgehead_atoms;pub use descriptors::num_bromines;pub use descriptors::num_carbons;pub use descriptors::num_chlorines;pub use descriptors::num_ester_bonds;pub use descriptors::num_fluorines;pub use descriptors::num_heteroatoms;pub use descriptors::num_hydrogens;pub use descriptors::num_iodines;pub use descriptors::num_nitrogens;pub use descriptors::num_oxygens;pub use descriptors::num_phosphorus;pub use descriptors::num_saturated_heterocycles;pub use descriptors::num_saturated_rings;pub use descriptors::num_spiro_atoms;pub use descriptors::num_stereocenters;pub use descriptors::num_sulfurs;pub use descriptors::num_unspecified_stereocenters;pub use descriptors::pfizer_3_75_passes;pub use descriptors::reos_passes;pub use descriptors::ring_bundle;pub use descriptors::ring_count;pub use descriptors::ring_system_count;pub use descriptors::ro3_passes;pub use descriptors::rotatable_bond_count;pub use descriptors::tpsa;pub use descriptors::tpsa_per_atom;pub use descriptors::usrcat;pub use descriptors::veber_passes;pub use iupac_stereo::iupac_name_stereo;pub use abbreviations::abbreviations;pub use abbreviations::expand_abbreviation;pub use activity_cliff::ActivityCliff;pub use activity_cliff::activity_cliffs;pub use admet::AdmetProfile;pub use admet::BoiledEggProfile;pub use admet::ClearanceClass;pub use admet::admet_profile;pub use admet::ames_alerts;pub use admet::ames_passes;pub use admet::ames_risk_score;pub use admet::bbb_passes;pub use admet::bbb_score;pub use admet::bbb_score_from_parts;pub use admet::boiled_egg;pub use admet::boiled_egg_from;pub use admet::caco2_permeability;pub use admet::caco2_precomputed;pub use admet::clearance_class;pub use admet::clearance_score;pub use admet::cyp3a4_inhibition_risk;pub use admet::cyp3a4_precomputed;pub use admet::herg_risk_precomputed;pub use admet::herg_risk_score;pub use admet::ppb_percent;pub use alerts::brenk_matches;pub use alerts::brenk_matches_detailed;pub use alerts::brenk_passes;pub use alerts::brenk_passes_and_matches;pub use alerts::pains_matches;pub use alerts::pains_matches_detailed;pub use alerts::pains_passes;pub use alerts::pains_passes_and_matches;pub use atropisomer::AtropisomerType;pub use atropisomer::assign_atropisomer_chirality;pub use atropisomer::detect_atropisomers;pub use brics::BricsConfig;pub use brics::brics_bonds;pub use brics::brics_fragments;pub use brics::brics_fragments_with_config;pub use cache::DescriptorCache;pub use cache::DescriptorEntry;pub use canonical::CanonicalMode;pub use canonical::canonical_smiles_mode;pub use condensed::CondensedError;pub use condensed::parse_condensed;pub use diversity::butina_cluster;pub use diversity::maxmin_picks;pub use drug_score::drug_score;pub use esol::esol_solubility;pub use estate::estate_all;pub use estate::estate_indices;pub use estate::max_estate;pub use estate::min_estate;pub use estate::sum_estate;pub use formula::FormulaParseError;pub use formula::parse_formula;pub use gasteiger::gasteiger_charges;pub use hash::are_identical;pub use hash::mol_hash;pub use hydrogen::add_hydrogens;pub use hydrogen::remove_hydrogens;pub use ifg::FunctionalGroup;pub use ifg::identify_functional_groups;pub use isotope_distribution::isotope_distribution;pub use logd::logd_from_logp;pub use logd::logd_profile;pub use logd::logd_simple;pub use mlp::MLP_SOLUBILITY_TRAINED;pub use mlp::mlp_solubility;pub use mmff94_bci::MmffType;pub use mmff94_bci::assign_mmff94_type;pub use mmff94_bci::mmff94_charges_bci;pub use mmff94_bci::mmff94_charges_typed;pub use mmp::MmpPair;pub use mmp::MmsMember;pub use mmp::MmsSeries;pub use mmp::find_mmp;pub use mmp::find_mms;pub use named_groups::NamedGroup;pub use named_groups::detect_named_functional_groups;pub use pka::PkaSite;pub use pka::PkaSiteType;pub use pka::pka_acid;pub use pka::pka_base;pub use pka::pka_both;pub use pka::predict_pka;pub use qed::qed;pub use qed::qed_with_bundle;pub use recap::recap_breakable_bond_count;pub use recap::recap_fragment;pub use rgroup::RGroupError;pub use rgroup::RGroupResult;pub use rgroup::rgroup_decompose;pub use sa_score::sa_score;pub use sa_score::sa_score_with_bundle;pub use scaffold::ScaffoldNetwork;pub use scaffold::generic_murcko_scaffold;pub use scaffold::murcko_scaffold;pub use scaffold::scaffold_network;pub use scaffold::scaffold_network_with_counts;pub use scaffold::schuffenhauer_parents;pub use standardize::MoleculeSnapshot;pub use standardize::PipelineStatus;pub use standardize::StandardizationPipeline;pub use standardize::StandardizationReport;pub use standardize::StandardizationStep;pub use standardize::StandardizationStepReport;pub use standardize::StandardizationWarning;pub use standardize::StandardizeOptions;pub use standardize::ZwitterionHandling;pub use standardize::has_zwitterion;pub use standardize::largest_fragment;pub use standardize::neutralize_charges;pub use standardize::normalize_groups;pub use standardize::normalize_zwitterion;pub use standardize::prefer_organic;pub use standardize::reionize;pub use standardize::remove_isotopes;pub use standardize::remove_stereo;pub use standardize::standardize;pub use standardize::uncharge;pub use stereo::assign_complete_stereochemistry;pub use stereo::enumerate_stereoisomers;pub use stereo::invert_stereocenter;pub use tautomer::TautomerConfig;pub use tautomer::canonical_tautomer;pub use tautomer::canonical_tautomer_with_config;pub use tautomer::enumerate_tautomers;pub use tautomer::enumerate_tautomers_with_config;pub use topo_descriptors::bertz_ct;pub use topo_descriptors::chi_all;pub use topo_descriptors::chi0;pub use topo_descriptors::chi0v;pub use topo_descriptors::chi1;pub use topo_descriptors::chi1v;pub use topo_descriptors::chi2;pub use topo_descriptors::chi2v;pub use topo_descriptors::chi3;pub use topo_descriptors::chi3v;pub use topo_descriptors::chi4;pub use topo_descriptors::chi4v;pub use topo_descriptors::eccentric_connectivity_index;pub use topo_descriptors::graph_diameter;pub use topo_descriptors::graph_eccentricities;pub use topo_descriptors::graph_radius;pub use topo_descriptors::gravitational_index;pub use topo_descriptors::gutman_mti;pub use topo_descriptors::hosoya_index;pub use topo_descriptors::kappa_all;pub use topo_descriptors::kappa1;pub use topo_descriptors::kappa2;pub use topo_descriptors::kappa3;pub use topo_descriptors::labute_asa;pub use topo_descriptors::labute_asa_per_atom;pub use topo_descriptors::num_valence_electrons;pub use topo_descriptors::padmakar_ivan_index;pub use topo_descriptors::petitjean_index;pub use topo_descriptors::randic_index;pub use topo_descriptors::schultz_mti;pub use topo_descriptors::topological_distance_matrix;pub use topo_descriptors::vabc;pub use topo_descriptors::wiener_index;pub use topo_descriptors::zagreb_index_m1;pub use topo_descriptors::zagreb_index_m2;pub use vsa::estate_vsa;pub use vsa::peoe_vsa;pub use vsa::slogp_vsa;pub use vsa::smr_vsa;pub use workflow::CompareOptions;pub use workflow::DescriptorDelta;pub use workflow::DescriptorSummary;pub use workflow::FilterSummary;pub use workflow::FunctionalGroupSummary;pub use workflow::MoleculeComparison;pub use workflow::MoleculeReport;pub use workflow::NamedGroupSummary;pub use workflow::PairwiseComparison;pub use workflow::ReportOptions;pub use workflow::ScreenOptions;pub use workflow::ScreeningRecord;pub use workflow::ScreeningReport;pub use workflow::SimilaritySummary;pub use workflow::WorkflowError;pub use workflow::WorkflowLimits;pub use workflow::compare_molecules;pub use workflow::compare_molecules_with_options;pub use workflow::molecule_report;pub use workflow::molecule_report_with_options;pub use workflow::screen_smiles;pub use workflow::screen_smiles_with_options;pub use xlogp3::xlogp3;pub use xlogp3::xlogp3_per_atom;
Modules§
- abbreviations
- Chemical abbreviation expansion.
- activity_
cliff - Activity cliff detection for SAR analysis.
- admet
- ADMET property prediction — absorption, distribution, metabolism, excretion, toxicity.
- alerts
- PAINS (Pan Assay Interference Compounds) structural alert filtering. 480 SMARTS patterns from Baell & Holloway 2010 (J. Med. Chem. 53, 2719–2740) as distributed in the RDKit FilterCatalog (pains_a/b/c.in).
- atropisomer
- Atropisomer detection and axial stereochemistry assignment.
- brics
- BRICS — Breaking of Retrosynthetically Interesting Chemical Substructures.
- cache
- Descriptor caching for improved performance.
- canonical
- Multi-mode canonical SMILES — analogous to OCL’s 5-mode IDcode canonicalization.
- cip
- CIP (Cahn–Ingold–Prelog) stereochemistry assignment.
- condensed
- Condensed formula parsing — converts text like “CH3COOH” to Molecule.
- descriptors
- Molecular descriptor functions for drug-likeness and physical property estimation.
- diversity
- Diversity picking and clustering algorithms.
- drug_
score - DrugScore — composite drug-likeness score.
- esol
- ESOL aqueous solubility prediction (Delaney 2004).
- estate
- EState indices (Hall & Kier, 1991).
- formula
- Chemical formula parsing: convert Hill-notation strings to element count maps.
- gasteiger
- Gasteiger-Marsili PEOE partial charges.
- hash
- Fast molecular structure hashing for duplicate detection.
- hydrogen
- Explicit hydrogen management.
- ifg
- Functional group identification using the Ertl (2017) algorithm.
- isotope_
distribution - Isotope distribution (isotope envelope) calculation.
- iupac_
stereo - IUPAC naming with CIP stereo prefix.
- logd
- LogD — pH-dependent apparent lipophilicity (distribution coefficient).
- mlp
- ECFP4-based linear model for aqueous solubility prediction (logS).
- mmff94_
bci - MMFF94 partial charges — element-pair BCI (legacy) and atom-typed BCI (improved).
- mmp
- Matched Molecular Pair (MMP) analysis.
- named_
groups - Named functional group detection via SMARTS patterns.
- pka
- Rule-based pKa prediction from functional group SMARTS patterns.
- qed
- QED — Quantitative Estimate of Druglikeness.
- recap
- RECAP (Retrosynthetic Combinatorial Analysis Procedure) fragmentation.
- rgroup
- R-group decomposition: split molecules into a common scaffold core and variable R-group substituents.
- sa_
score - Synthetic Accessibility Score (SA Score).
- scaffold
- Murcko scaffold decomposition.
- standardize
- Molecular standardization routines.
- stereo
- Stereochemistry manipulation — inversion, enumeration, and CIP/atropisomer integration.
- tautomer
- Tautomer enumeration and canonical tautomer selection.
- topo_
descriptors - Topological molecular descriptors.
- vsa
- VSA (van der Waals surface area) binned descriptors.
- workflow
- High-level, MCP-ready workflows built from the lower-level chematic APIs.
- xlogp3
- XLogP3 lipophilicity prediction.