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I've just completed my first run of Babel on Sterling (on a container with 500GB of memory!) using the changes in draft PR https://github.com/TranslatorSRI/Babel/pull/37. The results I've obtained (on…
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Not sure if this is an issue but just creating one to check later with @SteffenHeu
In BioTransformerTask.run there is a map of Smiles -> FeatureListRow to make the smiles unique.
`final Map un…
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Is there a way to retrieve the PubChem id from the ChemblApi Drug-Request. To be precise: does the data contain the id?
If not: is there any other way to retrieve this information via the API?
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**Is your feature request related to a problem? Please describe.**
Currently, the compounds listed as having the same connectivity encompass a broad range of different things including isotopomers
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Looking a the following content I note that the chemical formula, InChI and InChIKey cannot be right:
![image](https://user-images.githubusercontent.com/26721/30001564-0619756e-9092-11e7-9c1b-308c4…
egonw updated
7 years ago
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There are valid molecules that have no CID (they have usually either never been synthesized or at least never characterized in public literature). In the PubChem data you've worked with, there are fi…
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Just wanted to jot down an idea for speeding up RMG runs using QMTP (implementation and testing of this is currently low on my priority list). For certain problematic molecules where QMTP does not su…
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For instance, `HMDB`, `InchiKey`, `CASNO`, etc.
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- [x] Do we need to ask for better API access from MCule & Enamine? **NO**
- [ ] Rate-limiting?
- [ ] Implement bulk exact search
- [ ] **Resolve intermittent 504 errors**
- [x] Implement bulk sim…
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The number of compounds in MassBank is not available anywhere ... we should have basic stats on how many compounds by unique InChIKeys and a number of records without InChIKeys (for instance).
A tot…