data/compounds/README.md

# 🔬 AMAX Compound Desciptors

The AMAX 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 |