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This sim requires that all possible molecules and molecule structures are defined prior to being built. This data is stored in `js/data` and was derived from [PubChem](https://pubchem.ncbi.nlm.nih.gov…
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**Describe the bug**
Generating a conformer for this SMILES fails in both OE/RD, but it seems like all stereocenters are specified:
```
from openforcefield.topology.molecule import Molecule
mol =…
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**Configuration:**
- RDKit Version: **2019.09.2**
- Operating system: **Ubuntu Linux 18.04**
- Python version (if relevant): **3.7.5**
- Are you using conda? **Yes**
- If you are using…
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Installing gt4sd currently only works on M1 Macs through the use of Rosetta (an x86 emulator). When trying to install on an M1 mac natively I ran into the following issues:
- pytorch-scatter v2.0.9…
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Hello, everyone!
I'm working with two molecules, 6LFR and 7LFR, provided to me in the `*.mol` format. They consist of 236 and 275 atoms, respectively.
To check the consistency of the results obt…
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Greetings,
The make3D function for molecules appears to be failing with some metals. It does not happen with every metal in my data set but I have attached an example metal of where is does fail.
…
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I'm trying to use `UnimolConfGModel` for molecular conformation generation because my molecules are hard to generate initial conformations with `rdkit`, so I'm trying to hack into the model `forward` …
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Currently, we collect the torsion QM data using the CLI interface to torsiondrive and we run each grid point optimisation in series which can be quite slow even for simple small molecules. Here I want…
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```
What steps will reproduce the problem?
1. In the attached BNGL file, call generate_network() before simulate_nf().
What is the expected output? What do you see instead?
NFsim throws the following…
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Introduction
(i) compound standardisation, (ii) descriptor calculation, (iii) preprocessing, model training and validation, and (iv) bioactivity/property prediction for new molecules.
Description
(…