updating readme

README.md

@@ -8,8 +8,6 @@ AMAX is an open source dataset designed to assist machine learning models in sma
 
 This dataset is actively expanding with new experimental retention time values from the Coley Research Group at MIT, ensuring it remains a growing resource for optical property prediction.
 
-Additionally, AMAX includes ```.smi``` lists of 22,418 unique compounds and 356 unique solvents in the dataset for chemical descriptor calculations.
-
 AMAX is designed for use in:
 
 - Estimating retention times for new compound–environment combinations
@@ -20,8 +18,9 @@ AMAX is designed for use in:
 
 The AMAX dataset contains:
 
-- 40,016 unique molecule–environment combinations, the largest singular LC-MS retention time dataset of its kind to date
+- 40,013 unique molecule–environment combinations, the largest singular LC-MS retention time dataset of its kind to date
 - Experimentally measured λ<sub>max</sub> values in nm, curated from public datasets, benchmark papers, and literature
+- 160 calculated chemical descriptors for 22,415 unique compounds and 356 unique solvents
 
 Additionally, the AMAX dataset is divided into training, validation, and testing subsets in an 80:10:10 split. 
 

data/compounds/README.md

@@ -1,6 +1,6 @@
 # 🔬 AMAX Compound Desciptors
 
-Compound descriptors capture detailed structural, electronic, and topological features of the molecule, computed using RDKit.
+The AMAX dataset is accompanied with 160 descriptors for each compound, capturing detailed structural, electronic, and topological features for model training. Descriptors were computed using RDKit.
 
 ## Topological Descriptors
 
@@ -8,7 +8,7 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 |------------|---------|---------------|
 | 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 (0-4), Chi_n (1-4) Chi_v (1-4)  | Connectivity indices reflecting molecular topology, branching, and size | RDKit |
+| Chi (0-1), Chi_n (0-4) Chi_v (0-4)  | Connectivity indices reflecting molecular topology, branching, and size | RDKit |
 | Ipc  | Information content index representing structural complexity | RDKit |
 | Kappa (1-3) | Shape indices describing molecular flexibility and overall geometry | RDKit |
 
@@ -16,7 +16,6 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 
 | Descriptor | Summary | Software Used |
 |------------|---------|---------------|
-| MaxAbsEStateIndex | Maximum absolute E-state value in the molecule | RDKit |
 | MaxAbsPartialCharge | Maximum absolute atomic partial charge | RDKit |
 | MaxEStateIndex | Maximum E-state value in the molecule | RDKit |
 | MaxPartialCharge | Highest partial charge in the molecule | RDKit |
@@ -48,7 +47,7 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | NumSaturatedCarbocycles | Fully saturated carbon rings | RDKit |
 | NumSaturatedHeterocycles | Fully saturated heteroatom rings | RDKit |
 | NumSaturatedRings | Total saturated rings in the molecule | RDKit |
-| FractionCSP | Fraction of sp3 hybridized carbons (aliphatic character) | 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 |
@@ -66,7 +65,6 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | 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_COO2 | Count of additional carboxylic acid groups (possibly duplicates) | 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 |
@@ -76,8 +74,6 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | 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_Ndealkylation1 | Count of first type N-dealkylation fragments | RDKit |
-| fr_Ndealkylation2 | Count of second type N-dealkylation fragments | 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 |
@@ -86,7 +82,6 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | fr_allylic_oxid | Count of allylic oxidation sites | RDKit |
 | fr_amide | Count of amide groups | RDKit |
 | fr_amidine | Count of amidine groups | RDKit |
-| fr_aniline | Count of aniline groups (aromatic amines) | 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 |
@@ -109,7 +104,6 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | fr_isocyan | Count of isocyanate groups | RDKit |
 | fr_isothiocyan | Count of isothiocyanate groups | RDKit |
 | fr_ketone | Count of ketone groups | RDKit |
-| fr_ketone_Topliss | Count of ketone groups (Topliss definition) | RDKit |
 | fr_lactam | Count of lactam rings | RDKit |
 | fr_lactone | Count of lactone rings | RDKit |
 | fr_methoxy | Count of methoxy groups (-OCH3) | RDKit |
@@ -117,17 +111,12 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | 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_nitro_arom_nonortho | Count of non-ortho 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_para_hydroxylation | Count of para hydroxylation sites | RDKit |
 | fr_phenol | Count of phenol groups | RDKit |
-| fr_phenol_noOrthoHbond | Count of phenols without ortho hydrogen bonding | RDKit |
 | fr_phos_acid | Count of phosphoric acid groups | RDKit |
 | fr_phos_ester | Count of phosphoric ester groups | RDKit |
-| fr_piperdine | Count of piperidine rings | RDKit |
-| fr_piperzine | Count of piperazine rings | RDKit |
 | fr_priamide | Count of primary amides | RDKit |
 | fr_prisulfonamd | Count of primary sulfonamides | RDKit |
 | fr_pyridine | Count of pyridine rings | RDKit |
@@ -140,7 +129,6 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | fr_thiazole | Count of thiazole rings | RDKit |
 | fr_thiocyan | Count of thiocyanate groups | RDKit |
 | fr_thiophene | Count of thiophene rings | RDKit |
-| fr_unbrch_alkane | Count of unbranched alkane chains | RDKit |
 | fr_urea | Count of urea groups | RDKit |
 
 ## Constitutional Descriptors
@@ -164,4 +152,4 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 
 | Descriptor | Summary | Software Used |
 |------------|---------|---------------|
-| Morgan_Fingerprint | Circular fingerprints encoding molecular substructures up to a given radius, used for similarity and machine learning | RDKit |
+| Morgan_Fingerprint | Circular fingerprints encoding molecular substructures up to a given radius, used for similarity and machine learning | RDKit |

data/solvents/README.md

@@ -1,6 +1,6 @@
 # 🧪 AMAX Solvent Desciptors
 
-Compound descriptors capture detailed structural, electronic, and topological features of the molecule, computed using RDKit.
+The ReTiNA dataset is accompanied with 160 descriptors for each solvent, capturing detailed structural, electronic, and topological features for model training. Descriptors were computed using RDKit.
 
 ## Topological Descriptors
 
@@ -8,7 +8,7 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 |------------|---------|---------------|
 | 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 (0-4), Chi_n (1-4) Chi_v (1-4)  | Connectivity indices reflecting molecular topology, branching, and size | RDKit |
+| Chi (0-1), Chi_n (0-4) Chi_v (0-4)  | Connectivity indices reflecting molecular topology, branching, and size | RDKit |
 | Ipc  | Information content index representing structural complexity | RDKit |
 | Kappa (1-3) | Shape indices describing molecular flexibility and overall geometry | RDKit |
 
@@ -16,7 +16,6 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 
 | Descriptor | Summary | Software Used |
 |------------|---------|---------------|
-| MaxAbsEStateIndex | Maximum absolute E-state value in the molecule | RDKit |
 | MaxAbsPartialCharge | Maximum absolute atomic partial charge | RDKit |
 | MaxEStateIndex | Maximum E-state value in the molecule | RDKit |
 | MaxPartialCharge | Highest partial charge in the molecule | RDKit |
@@ -48,7 +47,7 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | NumSaturatedCarbocycles | Fully saturated carbon rings | RDKit |
 | NumSaturatedHeterocycles | Fully saturated heteroatom rings | RDKit |
 | NumSaturatedRings | Total saturated rings in the molecule | RDKit |
-| FractionCSP | Fraction of sp3 hybridized carbons (aliphatic character) | 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 |
@@ -66,7 +65,6 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | 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_COO2 | Count of additional carboxylic acid groups (possibly duplicates) | 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 |
@@ -76,8 +74,6 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | 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_Ndealkylation1 | Count of first type N-dealkylation fragments | RDKit |
-| fr_Ndealkylation2 | Count of second type N-dealkylation fragments | 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 |
@@ -86,7 +82,6 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | fr_allylic_oxid | Count of allylic oxidation sites | RDKit |
 | fr_amide | Count of amide groups | RDKit |
 | fr_amidine | Count of amidine groups | RDKit |
-| fr_aniline | Count of aniline groups (aromatic amines) | 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 |
@@ -109,7 +104,6 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | fr_isocyan | Count of isocyanate groups | RDKit |
 | fr_isothiocyan | Count of isothiocyanate groups | RDKit |
 | fr_ketone | Count of ketone groups | RDKit |
-| fr_ketone_Topliss | Count of ketone groups (Topliss definition) | RDKit |
 | fr_lactam | Count of lactam rings | RDKit |
 | fr_lactone | Count of lactone rings | RDKit |
 | fr_methoxy | Count of methoxy groups (-OCH3) | RDKit |
@@ -117,17 +111,12 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | 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_nitro_arom_nonortho | Count of non-ortho 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_para_hydroxylation | Count of para hydroxylation sites | RDKit |
 | fr_phenol | Count of phenol groups | RDKit |
-| fr_phenol_noOrthoHbond | Count of phenols without ortho hydrogen bonding | RDKit |
 | fr_phos_acid | Count of phosphoric acid groups | RDKit |
 | fr_phos_ester | Count of phosphoric ester groups | RDKit |
-| fr_piperdine | Count of piperidine rings | RDKit |
-| fr_piperzine | Count of piperazine rings | RDKit |
 | fr_priamide | Count of primary amides | RDKit |
 | fr_prisulfonamd | Count of primary sulfonamides | RDKit |
 | fr_pyridine | Count of pyridine rings | RDKit |
@@ -140,7 +129,6 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 | fr_thiazole | Count of thiazole rings | RDKit |
 | fr_thiocyan | Count of thiocyanate groups | RDKit |
 | fr_thiophene | Count of thiophene rings | RDKit |
-| fr_unbrch_alkane | Count of unbranched alkane chains | RDKit |
 | fr_urea | Count of urea groups | RDKit |
 
 ## Constitutional Descriptors
@@ -164,4 +152,4 @@ Compound descriptors capture detailed structural, electronic, and topological fe
 
 | Descriptor | Summary | Software Used |
 |------------|---------|---------------|
-| Morgan_Fingerprint | Circular fingerprints encoding molecular substructures up to a given radius, used for similarity and machine learning | RDKit |
+| Morgan_Fingerprint | Circular fingerprints encoding molecular substructures up to a given radius, used for similarity and machine learning | RDKit |