Axel Drefahl - CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

Version 1

      Publication Details (including relevant citation   information):

      Journal of Cheminformatics 2011, 3:1 (7   January 2011).

      Additional file 1:

      Related content: CurlySMILES   project.


      CurlySMILES is a chemical line notation which   extends SMILES with annotations for storage, retrieval and   modeling of interlinked, coordinated, assembled and adsorbed   molecules in supramolecular structures and nanodevices.   Annotations are enclosed in curly braces and anchored to an   atomic node or at the end of the molecular graph depending on the   annotation type. CurlySMILES includes predefined annotations for   stereogenicity, electron delocalization charges, extra-molecular   interactions and connectivity, surface attachment, solutions, and   crystal structures and allows extensions for domain-specific   annotations. CurlySMILES provides a shorthand format to encode   molecules with repetitive substructural parts or motifs such as   monomer units in macromolecules and amino acids in peptide   chains. CurlySMILES further accommodates special formats for   non-molecular materials that are commonly denoted by composition   of atoms or substructures rather than complete atom   connectivity.

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