tag:blogger.com,1999:blog-7844526396210378482.post6879082202519387925..comments2024-01-31T09:23:26.925+00:00Comments on Noel O'Blog: cheminformatics.js: Open BabelNoel O'Boylehttp://www.blogger.com/profile/03288289351940689018noreply@blogger.comBlogger13125tag:blogger.com,1999:blog-7844526396210378482.post-29285471702702816472017-01-18T09:38:47.558+00:002017-01-18T09:38:47.558+00:00Hi Justin, nice to see you building on this furthe...Hi Justin, nice to see you building on this further. Also very interested to see the Molecular Design Toolkit and associated work.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-35217440134521263412017-01-17T18:01:02.712+00:002017-01-17T18:01:02.712+00:00Thanks for the article! I tried compiling Open Ba...Thanks for the article! I tried compiling Open Babel to Web Assembly and got it mostly working, but hopefully I'll be able to revisit it and actually build something with it in the browser when I have more time: http://autodeskbionano.blogspot.com/2016/12/a-look-at-web-assembly-and-molecular.htmlAnonymoushttps://www.blogger.com/profile/06721995176639873048noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-85898359045320673802017-01-17T17:59:43.599+00:002017-01-17T17:59:43.599+00:00Thanks for the article! I tried to compile Open B...Thanks for the article! I tried to compile Open Babel into Web Assembly and mostly got it working, but hopefully I'll be able to revisit it and actually build something with it in the browser at some point: http://autodeskbionano.blogspot.com/2016/12/a-look-at-web-assembly-and-molecular.htmlAnonymoushttps://www.blogger.com/profile/06721995176639873048noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-73648723328986984892016-05-29T10:21:38.512+01:002016-05-29T10:21:38.512+01:00Hey Noel! Thanks for the post. We’re playing aroun...Hey Noel! Thanks for the post. We’re playing around with OpenBabel (c#) on a web-page, but the dll’s are causing problems (I might have mentioned that before ; ). Anyways, we can solve that with php or js. So is there perhaps an openbabel.js package that we simply can be put in a folder on the web-server and call it from the website?Anonymoushttps://www.blogger.com/profile/14610787719360398368noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-65184234235351082432015-10-23T14:31:38.353+01:002015-10-23T14:31:38.353+01:00Sorry - I can't help beyond suggesting you try...Sorry - I can't help beyond suggesting you try using the version of CMake that I specified above.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-34994393449216653332015-10-23T06:52:10.895+01:002015-10-23T06:52:10.895+01:00Dear Noel,
I try to compile our modified sources ...Dear Noel,<br /><br />I try to compile our modified sources on a mac yosemite with cmake 3.3.2 using your command line but it failed any suggestion to solve this problem?<br /><br /><br />CMake Error at CMakeLists.txt:226 (export):<br /> export FILE option given filename "" which does not have an extension of<br /> ".cmake".<br /><br /><br /><br />CMake Error at CMakeLists.txt:228 (install):<br /> install TARGETS given no ARCHIVE DESTINATION for static library target<br /> "openbabel".<br /><br /><br />.....<br /><br />-- Configuring incomplete, errors occurred!<br /><br />Guillaume Godinhttps://www.blogger.com/profile/17207670669470073848noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-50215317408963035832015-02-20T11:18:32.267+00:002015-02-20T11:18:32.267+00:00Ah right. I'll look into it a bit more. I star...Ah right. I'll look into it a bit more. I started on integrating the smiley validation too, but I didn't finish.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-23053720603861070952015-02-20T03:18:11.634+00:002015-02-20T03:18:11.634+00:00Well, I was referring to the SMILES -> SVG feat...Well, I was referring to the SMILES -> SVG feature. Daylight depict doesn't exist, and this is better since it has live updating.<br /><br />(For example, hosting this service at openbabel.org/depict...)<br /><br />The interesting question for me is whether it's possible to have multiple JS files, e.g., one for InChI (shudder), one for CML, etc. You wouldn't expose the full API, but you could have load-on-demand JS files for various file conversion features.<br /><br />Very interesting possibilities. :-)Geoff Hutchisonhttps://www.blogger.com/profile/12183565052523203480noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-87689060819156952312015-02-13T21:25:51.975+00:002015-02-13T21:25:51.975+00:00@Dave: That's exactly right about the dead cod...@Dave: That's exactly right about the dead code elimination. I'm not sure that what you suggest is going to be too compact though if you include formats with additional dependencies (e.g. InChI, CML, etc.).<br /><br />OB has a JSON output format, so you might find it useful to write a convenience function FormatToJSON that takes a format identifier (e.g. "pdb"), the molecular file format text itself, and then returns it as JSON.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-17121571701422746752015-02-13T17:45:32.344+00:002015-02-13T17:45:32.344+00:00What I'd really like is to use openbabel's...What I'd really like is to use openbabel's format readers (all of them) in 3Dmol.js.<br /><br />Since you apparently get to decide which functions to expose, does enscripten do dead code elimination on everything that isn't needed for that function? That might make for a relatively compact general-purpose molecular file reader.Davehttps://www.blogger.com/profile/02271247487610773792noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-58001563702620346422015-02-13T17:18:00.598+00:002015-02-13T17:18:00.598+00:00@Dave: I haven't measured performance, but acc...@Dave: I haven't measured performance, but according to the emscripten folk, it should be between 2x and 10x slower than native code, which is good enough for most purposes.<br /><br />@Geoff: Whoa, let's not get carried away :-) I haven't exposed the OB API, except for a single function, SmilesToSVG, so I don't think this particular javascript is of general use. Exposing the API is alledgedly possible (embind) though.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-87568226929272113072015-02-13T16:36:04.585+00:002015-02-13T16:36:04.585+00:00I think you should put this up on GitHub and then ...I think you should put this up on GitHub and then add to JSdelivr.com or a similar JavaScript CDN. This way, people can use OB without needing to host on their server.Geoff Hutchisonhttps://www.blogger.com/profile/12183565052523203480noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-13230562484599069102015-02-13T14:29:24.327+00:002015-02-13T14:29:24.327+00:00That's just craziness... how's performance...That's just craziness... how's performance? Davehttps://www.blogger.com/profile/02271247487610773792noreply@blogger.com