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Generated during and then after the workshop this summer for addition to OBI \(or IO\):
wk? is a data matrix file format specific for the 1-2-3 software
wb? is a data matrix file format specific f…
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I have noticed that for certain species, hydrogens appear to be incorrectly added to certain species containing oxygen or nitrogen during the InChI to SMILES conversion. It is possible that there is s…
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I have some SMILES from ZINC database, but it seems that some of them are invalid or RDKit is unable to parse (read + canonicalize) them. I collect them in this [file](https://gist.github.com/hsiaoyi0…
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[CHEBI:1604 - 3-methylguanine](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:1604) lacks any SMILES annotation and therefore also lacks an image of its structure.
It is also missing all the u…
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Parsing the script bellow results in multiple errors. Please check.
##
## -- PostgreSQL database dump
-- Dumped from database version 9.6beta1
-- Dumped by pg_dump version 9.6beta1
-- Started on 20…
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Given `CC(=O)[C@@]1(O)CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C`, the babel-generated 3d molecules differ at two stereocenters from the Schrodinger Ligprep-generated molecule.
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In working toward making OpenMM more friendly toward small molecules and nonstandard residues, we've run into some nontrivial difficulties with the representation in `Topology` that relies only on con…
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Currently, `SmallMoleculeSetProposalEngine` takes `receptor_topology` in the constructor.
Since the `current_topology` is passed into every `propose()` call, it would give us much more flexibility if…
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I set up a multitarget designer calculation using an edited form of the `Ablaffinitytestsystem` class. It looks like the systems are being set up appropriately, but I keep getting the following error:…
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Together with innovations in the database model, we may publish a new record format in order to make map the new database structure.
tsufz updated
8 years ago