Open Babel: An open chemical toolbox.

Area of Science:

• Computational chemistry and cheminformatics.
• Software development for scientific research.

Background:

• Computational modeling frequently encounters challenges with interconverting chemical structures between diverse formats.
• Existing standard and de facto interchange formats like Chemical Markup Language and SMILES are insufficient due to varying data types (0D vs. 3D) and lack of vendor-neutral options.

Purpose of the Study:

• To introduce Open Babel, an open-source chemical toolbox designed to address the widespread issue of chemical data format interconversion.
• To detail the implementation and recent advances in Open Babel version 2.3, highlighting its capabilities beyond simple format translation.

Main Methods:

• Development of an open-source chemical toolbox capable of handling a wide array of chemical data formats.
• Implementation of essential cheminformatics algorithms including partial charge assignment, aromaticity detection, bond order perception, and canonicalization.
• Extensive testing and validation of interconversion capabilities across over 110 formats.

Main Results:

• Open Babel version 2.3 successfully interconverts more than 110 chemical data formats.
• The toolbox incorporates a comprehensive suite of cheminformatics algorithms necessary for diverse molecular data representation.
• Demonstrated utility in various applications, including software products and scientific research, extending beyond basic format conversion.

Conclusions:

• Open Babel provides a robust solution to the challenge of numerous chemical file formats in computational chemistry.
• Offers valuable utilities such as conformer searching, 2D depiction, filtering, batch conversion, and substructure/similarity searching.
• Serves as a versatile programming library for developers in organic chemistry, drug design, materials science, and computational chemistry, available under an open-source license.