CODCHEM+

CODCHEM+ was a project, carried out by the COD Vilnius team in 2023-2025 and funded by the Research Council of Lithuania under grant agreement No. MIP-23-87.

One of the aims of the CODCHEM+ project was to derive a set of atomic bonding radii from data in the Crystallography Open Database. This has been achieved by developing a fully automated, unsupervised method for derivation of bonding radii from interatomic distances observed in crystal structures. The derived radii values for the organogenic elements closely follow the values previously published by other authors. Radii for metal elements differ more significantly, mostly due to the scarcity of chemical environments in the COD where contacts between such elements are encountered. The derived radii set and tools for comparing it to other published bonding radii sets are publicly available at https://radii.crystallography.net.

Second aim of the project was to develop a free software program for the assignment of IUPAC chemical names for chemical compounds. This aim has been achieved by implementing the rules from the IUPAC Blue Book (2013 edition) in a program we have named ChemOnomatopist. The 0.11.5 version of this program achieved almost 40% correctness in reproducing the nearly 4000 compound names present in the IUPAC Blue Book. ChemOnomatopist has been released under BSD-3-Clause license and can either be downloaded from https://github.com/merkys/ChemOnomatopist, or used directly on the Web at https://scripts.crystallography.net/web-scriptlets/cgi-bin/chemonomatopist.pl.

Third aim of the project was to enhance the previously reported system for the comparison of chemical annotations, which is useful for the detection of irregularities between chemical annotations originating from different sources. During the course of the project a few major notation differences were identified and mitigated. Thus now the comparison is much less sensitive to the impact of different aromaticity notation (resolving 53% of annotation pairs previously detected as differing in aromaticity and/or bond orders) and metal bond notation (resolving 94% of pairs previously detected as different due to reasons unknown). Moreover, the comparison method now much better resolves annotations having superfluous molecular entities, resolving 98% of entries previously marked as having superfluous molecular entities. All the enhancements were implemented in the smiles-scripts v0.4.0 package, distributed under GPL-2 free software license at https://www.crystallography.net/cod/archives/2026/software/smiles-scripts/.

Fourth aim of the project was to create and publish an interactive Web platform for the access of command line tools created by the COD developers. This has been achieved by developing a Common Gateway Interface (CGI) based interface between a Web server and a command line utility. The created platform allowed wrapping the tools from cod-tools package, with an addition of aforementioned ChemOnomatopist. The platform is open for all Web users at https://scripts.crystallography.net/web-scriptlets/. Its source is accessible in a Subversion repository at svn://saulius.grazulis.lt/web-scriptlets/web-run/branches/andrius-dev/ and is distributed under GPL-3 free software license.