Update README.md

README.md

@@ -1,17 +1,41 @@
-# QM9 Molecular Data Preprocessing and ML Pipeline
+---
+language:
+- en
+pretty_name: Bioactivity Report QM9 - Molecular Data Preprocessing and ML Pipeline
+size_categories:
+- 100K<n<1M
+---
+# Bioactivity Report QM9 - Molecular Data Preprocessing and ML Pipeline
+
 
-This repository contains a series of scripts for processing the QM9 dataset, computing molecular descriptors (e.g., ECFP4), cleaning and organizing molecular data, and preparing it for machine learning (ML) tasks.
+This data set provides a comprehensive set of quantum chemical properties for a relevant and consistent chemical space of small organic molecules. 
+The dataset consists of computed geometric, energetic, electronic, and thermodynamic properties for 134k stable small organic molecules made up of CHONF, corresponding to the subset of all 133,885 species with up to nine heavy atoms (CONF) out of the GDB-17 chemical universe the properties were calculated at the B3LYP/6-31G(2df,p) level of quantum chemistry. 
 
+## Format
+
+| Property Group (Column Range)                         | Columns                                                                                                                                                             |
+|--------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| Identifier (1–1)                                       | `ID`                                                                                                                                                                 |
+| Chemical descriptors (2–9)                             | `MolWt`, `ClogP`, `TPSA`, `HBD`, `HBA`, `NumRotatableBonds`, `RingCount`, `FractionCSP3`                                                                             |
+| Quantum-chemical & thermodynamic properties (10–24)    | `Rotational_Constant_A`, `Rotational_Constant_B`, `Rotational_Constant_C`, `Dipole_Moment`, `Isotropic_polarizability`, `Energy_of_HOMO`, `Energy_of_LUMO`, `LUMO_HOMO_GAP`, `Electronic_spatial_extent`, `Zero_point_vibrational_energy`, `Internal_energy_at_0_K`, `Internal_energy_at_298.15_K`, `Enthalpy_at_298.15_K`, `Free_energy_at_298.15_K`, `Heat_capacity_at_298.15_K` |
+| Structural fingerprint (25–25)                         | `Ecfp_4` (2,048-bit Morgan fingerprint, radius 2)                                                                 
+
+## Sources: 
+
+    L. Ruddigkeit, R. van Deursen, L. C. Blum, J.-L. Reymond, Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17, J. Chem. Inf. Model. 52, 2864–2875, 2012.
+    R. Ramakrishnan, P. O. Dral, M. Rupp, O. A. von Lilienfeld, Quantum chemistry structures and properties of 134 kilo molecules, Scientific Data 1, 140022, 2014. 
+
+## Data processing
 
 This pipeline transforms raw .xyz molecular files into a structured ML-ready format by:
-	1.	Extracting properties
-	2.	Calculating ECFP4 fingerprints
-	3.	Cleaning and filtering problematic entries
-	4.	Organizing columns and unpacking features
-	5.	Finalizing the dataset for ML
-	6.	Splitting it into training, validation, and test sets
+    1. Extracting properties
+    2. Calculating ECFP4 fingerprints
+    3. Cleaning and filtering problematic entries
+    4. Organizing columns and unpacking features
+    5. Finalizing the dataset for ML
+    6. Splitting it into training, validation, and test sets
 
-# Scripts
+### Scripts
 
 | File                     | Description |
 |--------------------------|-------------|
@@ -26,42 +50,9 @@ This pipeline transforms raw .xyz molecular files into a structured ML-ready for
 | `08_organize_columns.py` | Reorganizes column order, drops unnecessary columns, and prepares a clean structure. |
 | `09_unpack_ecfp4.py`     | Unpacks the ECFP4 bit vectors into individual binary columns for ML input. |
 | `10_finalize_ml_data.py` | Final checks and formatting to ensure the data is ready for ML training. |
-| `11_split_ml_data.py`    | Splits the final dataset into train/val/test sets using fixed proportions (e.g., 80/10/10). |
-
-
-
-
-
-
----
-
- # Output
-
-
-
-- Clean .parquet file containing ECFP4 + molecular properties, Split files for ML training: train.parquet, val.parquet, test.parquet
-
-### output format
-
-| Property Group (Column Range)                         | Columns                                                                                                                                                             |
-|--------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Identifier (1–1)                                       | `ID`                                                                                                                                                                 |
-| Chemical descriptors (2–9)                             | `MolWt`, `ClogP`, `TPSA`, `HBD`, `HBA`, `NumRotatableBonds`, `RingCount`, `FractionCSP3`                                                                             |
-| Quantum-chemical & thermodynamic properties (10–24)    | `Rotational_Constant_A`, `Rotational_Constant_B`, `Rotational_Constant_C`, `Dipole_Moment`, `Isotropic_polarizability`, `Energy_of_HOMO`, `Energy_of_LUMO`, `LUMO_HOMO_GAP`, `Electronic_spatial_extent`, `Zero_point_vibrational_energy`, `Internal_energy_at_0_K`, `Internal_energy_at_298.15_K`, `Enthalpy_at_298.15_K`, `Free_energy_at_298.15_K`, `Heat_capacity_at_298.15_K` |
-| Structural fingerprint (25–25)                         | `Ecfp_4` (2,048-bit Morgan fingerprint, radius 2)                                                                                                                    |
-
-
-
-
-# Sources: 
-
-    L. Ruddigkeit, R. van Deursen, L. C. Blum, J.-L. Reymond, Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17, J. Chem. Inf. Model. 52, 2864–2875, 2012.
-    R. Ramakrishnan, P. O. Dral, M. Rupp, O. A. von Lilienfeld, Quantum chemistry structures and properties of 134 kilo molecules, Scientific Data 1, 140022, 2014. 
+| `11_split_ml_data.py`    | Splits the final dataset into train/val/test sets using fixed proportions (e.g., 80/10/10).
 
 
 # License
 
-This project is licensed under CC0 (for use with QM9 which is public domain). Attribution is appreciated but not required.
-
-
-
+This project is licensed under CC0 (for use with QM9 which is public domain). Attribution is appreciated but not required.