{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2010/12/11/supramolecular-chemistry.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/5wjex-vtd55", "url": "https://chem-bla-ics.linkedchemistry.info/2010/12/11/supramolecular-chemistry.html", "title": "Supramolecular chemistry", "content_html": "

Some smart software developer once said to not optimize your code too early. However, not caring about it at all does not help either.\nSome basic knowledge of memory management can keep you going. That is, I just ran into the limits of Oscar\nand ChemicalTagger. As I blogged earlier today, I am analyzing the BJOC literature ,\nbut Lezan and I are running into a reproducible out-of-memory exception. At first I thought it was a memory leak, as it was the 95th\npaper if fell over on, but after we optimized our code a bit, by reusing classes, the problem remained and turned out to be not in\nrecreating objects (though the code is significantly faster now), but in a single BJOC paper being too large.

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The particular paper is not even ridiculously large, though it has an amazing 800 references! The paper, Molecular recognition of\norganic ammonium ions in solution using synthetic receptors (doi:10.3762/bjoc.6.32), is in\nfact an interesting review paper on supramolecular chemistry. The molecules I worked on (see one below) in my own supramolecular chemistry\ntime (doing a M.Sc. minor (6 month practical) with Peter Buijnsters in organic chemistry in the\ngroup of Prof. Nolte), are actually of the type they review, though surfactants are\nnot really covered in it particularly.

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Yeah, supramolecular chemistry has this nice level complexity; it is so supramolecular, that it is currently outside the scope\nof the molecular analysis of Oscar and ChemicalTagger ;)

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References

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Späth, A., & König, B. (2010). Molecular recognition of organic ammonium ions in solution using synthetic receptors. Beilstein Journal of Organic Chemistry, 6. https://doi.org/10.3762/bjoc.6.32 CrossRef Scholia
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", "summary": "Some smart software developer once said to not optimize your code too early. However, not caring about it at all does not help either. Some basic knowledge of memory management can keep you going. That is, I just ran into the limits of Oscar and ChemicalTagger. As I blogged earlier today, I am analyzing the BJOC literature , but Lezan and I are running into a reproducible out-of-memory exception. At first I thought it was a memory leak, as it was the 95th paper if fell over on, but after we optimized our code a bit, by reusing classes, the problem remained and turned out to be not in recreating objects (though the code is significantly faster now), but in a single BJOC paper being too large.", "date_published": "2010-12-11T00:20:00+00:00", "date_modified": "2026-04-19T00:00:00+00:00", "tags": ["oscar","beilstein","chemistry"], "_references": [ { "url": "https://doi.org/10.3762/bjoc.6.32", "doi": "10.3762/bjoc.6.32" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }