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http://www.crystallography.net/cod/: "Open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers."
Would be very neat to incorpo…
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**Describe the behavior you would like added to mBuild**
Openbabel has a [huge variety of supported file formats](http://openbabel.org/wiki/Category:Formats) ( #430 uses pybel to convert a smiles str…
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Hello there,
First of all, thanks for your great work, I just stumbled over this great package recently.
Unfortunately I observed some strange behaviour, when I tried to create a Chemical object for…
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I installed the pybel on python3.7 by pip, tried python 32bit and 64bit both. The result is the same.
Error:AttributeError: module 'pybel' has no attribute 'readstring'
How to install pybel correctl…
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**Describe the behavior you would like added to mBuild**
Not something that needs to be done right now, but once #555 is merged, we need another PR to update`mb.load()` to be able to take in and conv…
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Currently, each corpus comes with the original .bel file containing the raw BEL script, and a .pickle file containing the processed PyBEL Graph, but for programmatic access over the web, loading pickl…
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We should try to keep unique bonds only. Seems like if we read a PSF and a PDB we store each bond twice. While this is not an issue in most of moleculekit it trips off pybel which then detects wrong a…
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**Submitting author:** @loftytopping (David Topping)
**Repository:** https://github.com/loftytopping/PyBox
**Version:** v1.0.0
**Editor:** @lheagy
**Reviewer:** @dvalters, @highendcompute
**Archive:**…
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While I was testing the new Open Babel flask images, I started noticing that, despite running the Open Babel bond perception, the psi4 output for water would not have bonds.
I investigated it furth…
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If you import something larger, such as caffeine, using the import_structure API the request thread times out. We probably need to move the generation of 3D coordinates to something asynchronous to av…
cryos updated
5 years ago