-
This document outlines the rationale, requirements, and proposed technical implementation of the “DB Properties” feature.
# Context and Goals
Datagrok has a concept of entities. Among other featur…
-
## Purpose
Because it's a complicated topic, and to maintain the ability to restart this discussion in the future, I think it's important to record our design decisions with regard to stereochemistry…
-
I want to run torsion scans with Parsley and OpenMM on the OpenFF Substituted Phenyl Set 1. The JSON for the inputs are here:
https://github.com/openforcefield/qca-dataset-submission/blob/master/20…
-
Hi Pat,
Thanks for providing these cheminformatics tutorials and blog posts, I've been learning a lot from them. I was going through the classification notebook (classification_model.ipynb) and had…
-
**Describe the bug**
A clear and concise description of what the bug is.
~Checking molecule equality for molecules with dummy atoms raises an error because the equality check first checks the hill…
-
I am looking to recruit some help to generate image files from a code base I haven't opened since 2017.
Please see this script:
https://github.com/USEPA/CompTox-ToxCast-EDSPsteroidogenesis/blob/mast…
-
In common cheminformatics practice, molecules with (sp3) stereoatoms, e.g. made from SMILES with '@/@@', are intended by the originator as **stereochemically pure**.
Similarly, in molecules with 'a…
-
Add support for temporary graphs with behavior similar to that of temporary tables in many popular relational database management systems such as MS SQL Server or Oracle. For example, an extension of …
-
OpenMM's topology objects and readers/writers don't provide enough chemical information to actually parameterize small molecules nonstandard biopolymers, post-translational modifications, glycosylatio…
-
**Hello All:**
--
I am computing descriptors for a set of compounds using a code similar to the one shown below:
```
# create descriptor calculator with ALL descriptors
suppl = Chem.SmilesMol…