I didn't test it extensively to see if this was because I'm using particularly complicated molecules or maybe strange molfiles? Chemspider also has a nice API that might help with this sort of thing, but it apparently uses OpenBabel as the backend, and when I put in my InChI string the resulting molfile is unparsable by both ChemDraw and Chemdoodle. OpenBabel looks like an extremely useful open source! OpenBabel generates InChI strings that are identical to those generated by ChemDraw, but when I convert them back into molfiles, it struggles, and does not output a molecule that looks the same as the one originally input I was getting carbons with 5 bonds because it was protonating quaternary carbons for some reasonit also crashes when I ask for it to generate 2d coordinates the -gen2d option. I then looked for ways to automate it, and came upon OpenBabel.
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I first tried this manually in ChemDraw which fortunately my university has a site license for, because I surely can't afford it on my own and it worked well. The solution: I found that by converting a molfile into an InChI string, and then back into a molfile seems to retain the important structural information while at the same time normalizing the coordinates, and losing extraneous information, so this seems to be a reasonable way to go. The problem: I want to take molfiles from multiple sources and normalize them so that they can be rendered with the same style settings by chemdoodle web components. Python is currently the language I do general purpose programming in, and pywin32 works quite well for COM scripting. This time, I'm using it to control ChemDraw to help me convert molecule formats.Īnytime I use COM scripts, it feels pretty clumsy, like it would be a lot slicker just to have a command line utility, but in this case I couldn't find anything that seemed like it would work well enough update: I later found out about ChemAxon Molconverter which is quite niceso COM scripts it is. Tuesday, March 18, Automating Chemdraw: win32 com scripting with python pywin Last time I tried, with mixed success. Pusha is a popular Swedish website, the best Swedish Reddit alternative. Everyone is treated equally with no special preference. With true democracy, no one is privileged here. It is operated by a simple tally of up-votes as well as downvotes. It uses a peer to peer network and personal identity are not shown. It can be used by Windows, Linux, and Mac. Originally this is not a website instead it is an app. Just after simply registering to it, you can post your links and images but the matter must be good.Īnother entry in the list is Aether. If you desire to discuss or vote for the current events, share a wide variety of images or create your own content of your favorite topic then Qetzl is the right place. So if you have extraordinary skills then this is the best place. Here everyone shares an equal opportunity to share their good articles. If your article is of great quality then no one can cheat you like the concept of downvote is omitted here. The article gets the top position only if it contains the appropriate and nicely written text. PushdUp is basically a news site and target mainly on quality articles.
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