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⚛️ ReTiNA Table of Compound Desciptors

The ReTiNA dataset is accompanied with 157 descriptors for each compound, capturing detailed structural, electronic, and topological features for model training. Descriptors were computed using RDKit.

Topological Descriptors

Descriptor Summary Software Used
BalabanJ Quantifies molecular complexity based on average distance connectivity and graph branching RDKit
BertzCT Calculates molecular complexity based on graph connectivity and atomic contributions RDKit
Chi (0-1), Chi_n (0-4) Chi_v (0-4) Connectivity indices reflecting molecular topology, branching, and size RDKit
Kappa (1-3) Shape indices describing molecular flexibility and overall geometry RDKit

Electronic Descriptors

Descriptor Summary Software Used
MaxEStateIndex Maximum E-state value in the molecule RDKit
NumValenceElectrons Total number of valence electrons in the molecule RDKit
NumRadicalElectrons Total number of unpaired electrons (radicals) RDKit
HallKierAlpha Atom-type electrotopological descriptor modeling polarity and hybridization RDKit

Surface Area Descriptors

Descriptor Summary Software Used
EState_VSA (1-9) Binned E-state values mapped over atomic surface areas RDKit
LabuteASA Approximate surface area calculated by Labute’s method RDKit
PEOE_VSA (1-9) Partial equalization of orbital electronegativities across molecular surface area bins RDKit
SMR_VSA (1-9) Molar refractivity contributions binned by surface area RDKit
SlogP_VSA (1-12) SlogP contributions mapped to molecular surface area bins RDKit
TPSA Topological polar surface area related to hydrogen bonding potential RDKit

Structural Descriptors

Descriptor Summary Software Used
NumAliphaticCarbocycles Aliphatic (non-aromatic) carbon-only rings RDKit
NumAliphaticHeterocycles Aliphatic rings with at least one heteroatom RDKit
NumAliphaticRings Number of rings without aromaticity RDKit
NumAromaticCarbocycles Number of aromatic rings with only carbon atoms RDKit
NumAromaticHeterocycles Aromatic rings containing heteroatoms RDKit
NumAromaticRings Number of rings with aromatic character RDKit
NumSaturatedCarbocycles Fully saturated carbon rings RDKit
NumSaturatedHeterocycles Fully saturated heteroatom rings RDKit
NumSaturatedRings Total saturated rings in the molecule RDKit
FractionCSP3 Fraction of sp3 hybridized carbons (aliphatic character) RDKit
NumRotatableBonds Number of freely rotatable single bonds RDKit
NumHAcceptors Number of hydrogen bond acceptors (e.g. O, N atoms) RDKit
NumHDonors Number of hydrogen bond donors (e.g. -OH, -NH) RDKit

Functional Group Descriptors

Descriptor Summary Software Used
fr_Al_COO Count of aliphatic carboxylic acid groups (-COOH) RDKit
fr_Al_OH Count of aliphatic alcohol groups (-OH) RDKit
fr_Al_OH_noTert Count of non-tertiary aliphatic alcohol groups RDKit
fr_ArN Count of aromatic amines RDKit
fr_Ar_COO Count of aromatic carboxylic acid groups RDKit
fr_Ar_N Count of aromatic nitrogen atoms (excluding amines) RDKit
fr_Ar_NH Count of aromatic amines (-NH- groups) RDKit
fr_Ar_OH Count of phenol groups (aromatic alcohols) RDKit
fr_COO Count of carboxylic acid groups (-COOH) RDKit
fr_C_O Count of carbonyl groups (C=O) RDKit
fr_C_O_noCOO Count of carbonyls excluding carboxylic acids RDKit
fr_C_S Count of carbon-sulfur bonds RDKit
fr_HOCCN Count of hydroxyl connected to carbon connected to nitrogen RDKit
fr_Imine Count of imine groups (C=NH or C=NR) RDKit
fr_NH0 Count of nitrogen with zero attached hydrogens (e.g., quaternary) RDKit
fr_NH1 Count of nitrogen with one attached hydrogen RDKit
fr_NH2 Count of nitrogen with two attached hydrogens RDKit
fr_N_O Count of nitrogen-oxygen bonds RDKit
fr_Nhpyrrole Count of nitrogen atoms in pyrrole rings RDKit
fr_SH Count of thiol groups (-SH) RDKit
fr_aldehyde Count of aldehyde groups (-CHO) RDKit
fr_alkyl_carbamate Count of alkyl carbamate groups RDKit
fr_alkyl_halide Count of alkyl halide groups RDKit
fr_allylic_oxid Count of allylic oxidation sites RDKit
fr_amide Count of amide groups RDKit
fr_amidine Count of amidine groups RDKit
fr_aryl_methyl Count of methyl groups attached to aromatic rings RDKit
fr_azide Count of azide groups (-N3) RDKit
fr_azo Count of azo groups (-N=N-) RDKit
fr_barbitur Count of barbituric acid-like groups RDKit
fr_benzene Count of benzene rings RDKit
fr_benzodiazepine Count of benzodiazepine rings RDKit
fr_bicyclic Count of bicyclic ring systems RDKit
fr_diazo Count of diazo groups RDKit
fr_dihydropyridine Count of dihydropyridine rings RDKit
fr_epoxide Count of epoxide rings RDKit
fr_ester Count of ester groups RDKit
fr_ether Count of ether groups RDKit
fr_furan Count of furan rings RDKit
fr_guanido Count of guanidine groups RDKit
fr_halogen Count of halogen atoms (F, Cl, Br, I) RDKit
fr_hdrzine Count of hydrazine groups RDKit
fr_hdrzone Count of hydrazone groups RDKit
fr_imidazole Count of imidazole rings RDKit
fr_imid Count of imide groups RDKit
fr_isocyan Count of isocyanate groups RDKit
fr_isothiocyan Count of isothiocyanate groups RDKit
fr_ketone Count of ketone groups RDKit
fr_lactam Count of lactam rings RDKit
fr_lactone Count of lactone rings RDKit
fr_methoxy Count of methoxy groups (-OCH3) RDKit
fr_morpholine Count of morpholine rings RDKit
fr_nitrile Count of nitrile groups (-C≡N) RDKit
fr_nitro Count of nitro groups (-NO2) RDKit
fr_nitro_arom Count of aromatic nitro groups RDKit
fr_nitroso Count of nitroso groups (-NO) RDKit
fr_oxazole Count of oxazole rings RDKit
fr_oxime Count of oxime groups (=NOH) RDKit
fr_phenol Count of phenol groups RDKit
fr_phos_acid Count of phosphoric acid groups RDKit
fr_phos_ester Count of phosphoric ester groups RDKit
fr_priamide Count of primary amides RDKit
fr_prisulfonamd Count of primary sulfonamides RDKit
fr_pyridine Count of pyridine rings RDKit
fr_quatN Count of quaternary nitrogen atoms RDKit
fr_sulfide Count of sulfide groups (thioethers) RDKit
fr_sulfonamd Count of sulfonamide groups RDKit
fr_sulfone Count of sulfone groups RDKit
fr_term_acetylene Count of terminal acetylene groups RDKit
fr_tetrazole Count of tetrazole rings RDKit
fr_thiazole Count of thiazole rings RDKit
fr_thiocyan Count of thiocyanate groups RDKit
fr_thiophene Count of thiophene rings RDKit
fr_urea Count of urea groups RDKit

Constitutional Descriptors

Descriptor Summary Software Used
ExactMolWt Monoisotopic molecular weight of the compound RDKit
HeavyAtomCount Number of non-hydrogen atoms in the molecule RDKit
HeavyAtomMolWt Molecular weight of non-hydrogen atoms only RDKit
MolWt Molecular weight based on average atomic masses RDKit
NumHeteroatoms Number of non-carbon and non-hydrogen atoms RDKit

Physiochemical Descriptors

Descriptor Summary Software Used
MolLogP Partition coefficient (logP) estimating hydrophobicity RDKit
MolMR Molar refractivity related to volume and polarizability RDKit

Fingerprint Descriptors

Descriptor Summary Software Used
Morgan_Fingerprint Circular fingerprints encoding molecular substructures up to a given radius, used for similarity and machine learning RDKit