Deepen RDKit tutorial notebooks

[suneelbvs]

Summary

• expand each advanced RDKit tutorial notebook with detailed markdown guidance and step-by-step code cells
• add conformer analysis outputs, reaction enumeration scaffolds, standardisation workflows, QSAR evaluation, and richer visualisation examples
• demonstrate chemical format round-tripping while preserving metadata in the format conversion tutorial

Testing

• pytest

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https://chatgpt.com/codex/tasks/task_e_68ec9aeddc9883248ca529afd46970a4

[Copilot]

Pull Request Overview

This PR expands the RDKit tutorial collection by adding six new advanced Jupyter notebooks covering topics like conformer analysis, reaction enumeration, standardization workflows, QSAR modeling, and visualization techniques. The README is also updated to provide better structure and navigation for the enhanced tutorial catalog.

• Adds six new tutorial notebooks (5-10) covering advanced RDKit workflows
• Updates README with improved structure, table of contents, and tutorial catalog
• Includes practical examples of 3D conformer generation, reaction SMARTS, molecule standardization, and format conversion

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
README.md	Enhanced with table of contents, tutorial catalog table, and updated environment file reference
5_Conformer_Generation_and_3D_Analysis.ipynb	New notebook demonstrating 3D conformer generation with ETKDG and force field optimization
6_Reaction_Enumeration_and_Scaffolds.ipynb	New notebook showing reaction SMARTS usage and Bemis-Murcko scaffold analysis
7_Molecule_Standardization_and_Sanitization.ipynb	New notebook covering molecule cleanup, desalting, and charge neutralization
8_QSAR_Modeling_with_Scikit_Learn.ipynb	New notebook building a toy QSAR classifier using Morgan fingerprints
9_Visualization_and_Drawing_Options.ipynb	New notebook exploring RDKit's molecule visualization and drawing capabilities
10_Chemical_Format_Conversion_and_Metadata.ipynb	New notebook demonstrating format conversion while preserving metadata

Comments suppressed due to low confidence (2)

6_Reaction_Enumeration_and_Scaffolds.ipynb:1

• The reaction SMARTS pattern is incorrect. The product pattern maps atom [C:2] to the wrong position - it should connect to [C:3] from the acyl chloride, not directly replace it. The correct pattern should be: [NH:4]([C:2](=O)[C:3])[c:5]1ccccc[c:6]1

{

9_Visualization_and_Drawing_Options.ipynb:1

• This code appears in the wrong notebook. The SDWriter code belongs in the format conversion notebook (Tutorial 10), not the visualization notebook (Tutorial 9).

{

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[Copilot]

The environment file reference was changed from environment.yml to rdkit.yml, but the command on line 28 still references rdkit.yml. This is inconsistent with typical conda environment naming conventions which use environment.yml.