CGRtools

CGRtools provides Python utilities to represent, manipulate, and analyze condensed graphs of reactions (CGRs) for reaction-aware cheminformatics and structure–reactivity modeling.

Key Features:

• Condensed Graph of Reaction (CGR) Handling: Represents and processes condensed graphs of reactions (CGRs) to encapsulate detailed reaction changes in a single graph.
• Reaction descriptor calculation and structure–reactivity modeling: Calculates reaction descriptors and supports structure–reactivity modeling for reaction-centered analyses.
• Atom-to-Atom Mapping Comparison and Correction: Performs atom-to-atom mapping comparison and correction between reactants and products.
• Reaction Center Extraction: Identifies and extracts reaction centers involved in chemical transformations.
• Reaction Balancing: Performs automatic reaction balancing to ensure stoichiometric accuracy.
• Support for Common Structural Formats: Supports common structural formats for input and output.
• Native Python Integration: Provides native Python objects for molecules, reactions, and CGRs with standard comparison operators.

Scientific Applications:

• Reaction descriptor calculation and QSAR: Enables calculation of reaction descriptors used in quantitative structure–activity relationship (QSAR) studies.
• Mechanistic analysis and predictive modeling: Uses atom-to-atom mapping and reaction center information to support mechanistic studies and development of predictive models for chemical reactivity.

Methodology:

Represents reactions as condensed graphs of reactions (CGRs); performs atom-to-atom mapping comparison and correction; extracts reaction centers; balances reactions; computes reaction descriptors; implements molecule, reaction, and CGR as Python objects; and supports common structural formats.