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Dear author:
Hello,
I read the article code you provided, but I see that the model name you are using on the ESP prediction code is "xgboost_model_production_mode_gnn_esm1b_ts.dat".
Your code in ju…
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I have noticed that my MACCS fingerprints generated in python using scyjava were actually 192 long, when they should be only 166bit long according to documentation at [CDK Java Docs](http://cdk.github…
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**The bug**
After applying refineGEMs.polish to several models containing InChI-Strings in the annotations, I realised that COBRApy gave warnings that some of the URIs containing InChI-Strings were w…
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I would like to use a method other than molecular fingerprints to represent the substrate molecule, could you please provide the SMILES string of the substrate molecule used in the paper, only the ChE…
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I would love to see additional feature, where I could just assign `GENERATE="smiles_or_inchi_string_here"` command along with other parameters, such as `PM7 ADD-H OPT GNORM=0.0` so that mopac would ge…
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**Describe the bug**
Hello! I've been working to integrate `rdkit-js` in a new React project and found that passing an InChI string to `get_mol` will not return an RDKit Molecule.
**To Reproduc…
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I went ahead and took all the entries that had a `wikipedia.pageId` property and queried to see if they have a WikiData page.
Results
```
java Q251
javascript Q2005
c Q15777
python Q28865…
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I came across your Twitter post today and had some notes kicking around on my laptop that might be relevant background literature to your project...and perhaps a connection to a broader literature.
…
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In this thread, I answer some relevant questions from the GDI team @ersilia-os/gdi-volunteers
**Q1: What is the maximum acceptable level of latency for predictions to be returned to a user?**
A1. A…
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I find that it would takes up to 30s to run just `import dpdata` on the login node of HPC. I did some investigation myself and find that it would load almost all the modules into memory when importi…