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Algorithms, data structures, and utilities for processing chemical information

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There's a been some papers using the RDKit for synthesis planning. If you're writing a paper and use the term "Reaction SMARTS" make sure you mean what everyone else thinks it means.The SMILES, SMARTS, and SMIRKS line notations were created* by Daylight for...
I'm currently refactoring parts of the CDK core classes. As part of this I often need to find specific patterns/idioms that need to be changed. Whilst source code inspections and an IDE can make this task easy sometimes the tools aren't quite sharp enough....
The core class for molecule representation in CDK is the AtomContainer. The AtomContainer uses an edge-list data structure for storing the underlying connection table (see The Right Representation for the Job). Essentially this edge-list representation is efficient...

Most popular posts

There's a been some papers using the RDKit for synthesis planning. If you're writing a paper and use the term "Reaction SMARTS" make sure you mean what everyone else thinks it means.The SMILES, SMARTS, and SMIRKS line notations were created* by Daylight for...
I'm currently refactoring parts of the CDK core classes. As part of this I often need to find specific patterns/idioms that need to be changed. Whilst source code inspections and an IDE can make this task easy sometimes the tools aren't quite sharp enough....
The core class for molecule representation in CDK is the AtomContainer. The AtomContainer uses an edge-list data structure for storing the underlying connection table (see The Right Representation for the Job). Essentially this edge-list representation is efficient...