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Analysis of Complex Networks by Frank Emmert-Streib, Matthias Dehmer

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9.7 Chemical Software Packages

Popular chemical software packages useful for processing molecular graphs are as follows:

  1. CACTVS: a chemical package in C++ with a TCL-based scripting interface that is free for academic use.
  2. Daylight: commercial software package that introduced smiles. It is ideal for chemical databases with very efficient subgraph and similarity capabilities and specialized indexing.
  3. BABEL/OpenBabel: open-source package for converting chemical files but also incorporates a lot of chemical algorithms such as aromaticity detection.
  4. OpenEyes: commercial package with Java interface and low-level support for most of the operations required by chemical databases and processing applications.
  5. Chemistry Development Kit [105] (CDK): open-source package implemented in Java, useful also as a reference point for understanding chemical algorithms.

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