{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T00:39:54Z","timestamp":1777595994407,"version":"3.51.4"},"reference-count":17,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,5,23]],"date-time":"2024-05-23T00:00:00Z","timestamp":1716422400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,5,23]],"date-time":"2024-05-23T00:00:00Z","timestamp":1716422400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"European Research Council","award":["948770"],"award-info":[{"award-number":["948770"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Effective visualization of small molecules is paramount in conveying concepts and results in cheminformatics. Scalable vector graphics (SVG) are preferred for creating such visualizations, as SVGs can be easily altered in post-production and exported to other formats. A wide spectrum of software applications already exist that can visualize molecules, and customize these visualizations, in many ways. However, software packages that can output projected 3D models onto a 2D canvas directly as SVG, while being programmatically accessible from Python, are lacking. Here, we introduce CineMol, which can draw vectorized approximations of three-dimensional small molecule models in seconds, without triangulation or ray tracing, resulting in files of around 50\u2013300 kilobytes per molecule model for compounds with up to 45\u00a0heavy atoms. The SVGs outputted by CineMol can be readily modified in popular vector graphics editing software applications. CineMol is written in Python and can be incorporated into any existing Python cheminformatics workflow, as it only depends on native Python libraries. CineMol also provides programmatic access to all its internal states, allowing for per-atom and per-bond-based customization. CineMol\u2019s capacity to programmatically create molecular visualizations suitable for post-production offers researchers and scientists a powerful tool for enhancing the clarity and visual impact of their scientific presentations and publications in cheminformatics, metabolomics, and related scientific disciplines.<\/jats:p>\n                  <jats:p>\n                    <jats:bold>Scientific contribution<\/jats:bold>\n                  <\/jats:p>\n                  <jats:p>We introduce CineMol, a Python-based tool that provides a valuable solution for cheminformatics researchers by enabling the direct generation of high-quality approximations of two-dimensional SVG visualizations from three-dimensional small molecule models, all within a programmable Python framework. CineMol offers a unique combination of speed, efficiency, and accessibility, making it an indispensable tool for researchers in cheminformatics, especially when working with SVG visualizations.<\/jats:p>","DOI":"10.1186\/s13321-024-00851-y","type":"journal-article","created":{"date-parts":[[2024,5,23]],"date-time":"2024-05-23T11:02:34Z","timestamp":1716462154000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["CineMol: a programmatically accessible direct-to-SVG 3D small molecule drawer"],"prefix":"10.1186","volume":"16","author":[{"given":"David","family":"Meijer","sequence":"first","affiliation":[]},{"given":"Marnix H.","family":"Medema","sequence":"additional","affiliation":[]},{"given":"Justin J. J.","family":"van der Hooft","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2024,5,23]]},"reference":[{"key":"851_CR1","unstructured":"Jmol: an open-source Java viewer for chemical structures in 3D. http:\/\/www.jmol.org\/. Accessed 7 Jan 2024."},{"key":"851_CR2","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1093\/bioinformatics\/btu829","volume":"31","author":"N Rego","year":"2015","unstructured":"Rego N, Koes D (2015) 3Dmol.js molecular visualization with WebGL. Bioinformatics 31:1322\u20131324. https:\/\/doi.org\/10.1093\/bioinformatics\/btu829","journal-title":"Bioinformatics"},{"key":"851_CR3","unstructured":"Blender Foundation. https:\/\/www.blender.org\/. Accessed 7 Jan 2024."},{"key":"851_CR4","unstructured":"PyMOL. https:\/\/pymol.org\/2\/. Accessed 7 Jan 2024"},{"key":"851_CR5","unstructured":"RDKit: Open-source cheminformatics. https:\/\/www.rdkit.org\/. Accessed Jan 7 2024"},{"key":"851_CR6","unstructured":"OpenGL. https:\/\/www.opengl.org\/. Accessed 7 Jan 2024"},{"key":"851_CR7","unstructured":"Blender manual: Freestyle SVG exporter. https:\/\/docs.blender.org\/manual\/en\/latest\/addons\/render\/render_freestyle_svg.html. Accessed 7 Jan 2024"},{"key":"851_CR8","unstructured":"GL2PS: an OpenGL to PostScript printing library. https:\/\/www.geuz.org\/gl2ps\/. Accessed 7 Jan 2024."},{"key":"851_CR9","unstructured":"Greenfield JS (1990) A proof for a quickhull algorithm. Electrical Engineering and Computer Science-Technical Reports"},{"key":"851_CR10","unstructured":"Koltun WL (1965) Space filling atomic units and connectors for molecular models. US Patent. 3170246"},{"key":"851_CR11","unstructured":"National Center for Biotechnology and Information (2024) Atomic Radius in the Periodic Table of Elements. https:\/\/pubchem.ncbi.nlm.nih.gov\/periodic-table\/atomic-radius. Accessed Jan 7 2024"},{"key":"851_CR12","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1109\/MCSE.2007.55","volume":"9","author":"JD Hunter","year":"2007","unstructured":"Hunter JD (2007) Matplotlib: A 2D graphics environment. Comput Sci Eng 9:90\u201395","journal-title":"Comput Sci Eng"},{"key":"851_CR13","unstructured":"National Center for Biotechnology and Information (2024) PubChem compound summary for CID 5904, Penicillin G. https:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/Penicillin-G. Accessed Jan 7 2024"},{"key":"851_CR14","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1038\/282875a0","volume":"282","author":"JA Kelly","year":"1979","unstructured":"Kelly JA, Sielecki AR, Sykes BD, James MNG, Phillips DC (1979) X-ray crystallography of the binding of the bacterial cell wall trisaccharide NAM-NAG-NAM to lysozyme. Nature 282:875\u2013878","journal-title":"Nature"},{"issue":"17","key":"851_CR15","doi-asserted-by":"publisher","first-page":"2308","DOI":"10.1093\/bioinformatics\/btg299","volume":"19","author":"T Hamelryck","year":"2003","unstructured":"Hamelryck T, Manderick B (2003) PDB file parser and structure class implemented in Python. Bioinformatics 19(17):2308\u20132310","journal-title":"Bioinformatics"},{"key":"851_CR16","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1021\/acs.jcim.6b00613","volume":"57","author":"N-O Friedrich","year":"2017","unstructured":"Friedrich N-O, Meyder A, de Bruyn KC, Sommer K, Flachsenberg F, Rarey M, Kirchmair J (2017) High-Quality dataset of protein-bound ligand conformations and its application to benchmarking conformer ensemble generators. J Chem Inf Model 57:529\u2013539","journal-title":"J Chem Inf Model"},{"key":"851_CR17","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/s13321-023-00730-y","volume":"15","author":"CT Hoyt","year":"2023","unstructured":"Hoyt CT, Zdrazil RB, Guha R, Jeliazkova N, Martinez-Mayorga K, Nittinger E (2023) Improving reproducibility and reusability in the Journal of Cheminformatics. J Cheminf 15:62","journal-title":"J Cheminf"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-024-00851-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13321-024-00851-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-024-00851-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,23]],"date-time":"2024-05-23T11:07:17Z","timestamp":1716462437000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-024-00851-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,23]]},"references-count":17,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["851"],"URL":"https:\/\/doi.org\/10.1186\/s13321-024-00851-y","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv-2024-bvxr2","asserted-by":"object"}]},"ISSN":["1758-2946"],"issn-type":[{"value":"1758-2946","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,23]]},"assertion":[{"value":"1 February 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 May 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 May 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"JJJvdH is currently member of the Scientific Advisory Board of NAICONS Srl., Milano, Italy, and consults for Corteva Agriscience, Indianapolis, IN, USA. MHM is a member of the scientific advisory board of Hexagon Bio. The other author declares to have no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"58"}}