Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database

Journal of Cheminformatics
Miguel QuirósAntanas Vaitkus

Abstract

Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for predicting chemical properties from molecular structure. In this article, the ongoing work to describe the chemical connectivity of entries contained in the Crystallography Open Database (COD) in SMILES format is reported. This collection of SMILES is publicly available for chemical (substructure) search or for any other purpose on an open-access basis, as is the COD itself. The conventions that have been followed for the representation of compounds that do not fit into the valence bond theory are outlined for the most frequently found cases. The procedure for getting the SMILES out of the CIF files starts with checking whether the atoms in the asymmetric unit are a chemically acceptable image of the compound. When they are not (molecule in a symmetry element, disorder, polymeric species,etc.), the previously published cif_molecule program is used to get such image in many cases. The program package Open Babel is then applied to get SMILES strings from the CIF files (either those directly taken from the COD or those produced by cif_molecule when applicable). The results are then checked and/or fixed by a human editor,...Continue Reading

References

May 31, 2002·Acta Crystallographica. Section B, Structural Science·Peter S WhiteYvon Le Page
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Citations

Apr 24, 2020·The Journal of Chemical Physics·Paolo GiannozziStefano Baroni
Jan 13, 2021·Journal of Cheminformatics·Laurianne DavidOla Engkvist
Apr 15, 2021·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Katharina SchrautOleh Ivashko
Jun 1, 2021·ACS Omega·Michael T WallTim Ellis
Jul 3, 2021·Materials·Oleksandr ShtykaTomasz Maniecki
Aug 14, 2021·The Journal of Physical Chemistry. C, Nanomaterials and Interfaces·Bernhard M H WeningerFokko M Mulder

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Methods Mentioned

BETA
X-ray

Software Mentioned

SMILES
indigo
obgrep
OPSIN
SQUEEZE
CDK
MySQL
Make Makefile
allcod
fs

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