PIKAChU

PIKAChU constructs detailed molecular graphs from SMILES for computational modeling and analysis of chemical structures, properties, and reaction mechanisms.

Key Features:

• Molecular Graph Construction: Constructs comprehensive molecular graphs from SMILES encoding aromaticity, chirality, charge, hybridisation, and electron orbital information.
• Downstream Analysis Capabilities: Provides Morgan fingerprinting, similarity scoring, substructure matching, and molecular visualization capabilities.
• Reaction Mechanism Implementation: Includes functions to simplify implementation and representation of reaction mechanisms for computational chemical modeling.

Scientific Applications:

• Computational Simulations of Chemical Processes: Enables simulation and analysis of chemical processes using graph-based molecular representations and reaction mechanism functions.
• Drug Discovery and Molecular Design: Supports fingerprinting, similarity scoring, and substructure analyses to assist compound prioritization and design.
• Molecular Biology: Facilitates analysis of molecular interactions and properties relevant to molecular biology studies.
• Materials Science: Assists studies in materials science that require representation, comparison, and analysis of molecular structures.

Methodology:

Implemented in Python and using SMILES strings as standardized input, with design for compatibility with other Python-based bioinformatics tools and databases.