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**Configuration:**
- RDKit Version:
- Operating system:
- Python version (if relevant):
- Are you using conda?
- If you are using conda, which channel did you install the rdkit from?
…
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[terminal-imine.pdb.txt](https://github.com/rdkit/rdkit/files/13278105/terminal-imine.pdb.txt)
Assigning bond orders to the attached PDB with SMILES:` [H]/N=C\CC(=O)N1CC[C@@H](C)[C@@H](N(C)c2ncnc3[…
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Hi, I'm trying to run the command: polygon generate \
--model_path ../data/pretrained_vae_model.pt \
--scoring_definition scoring_definition.csv \
--max_len 100 \
--n_epochs 200 \
…
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**Configuration:**
- RDKit Version: 2020.03
- Operating system: linux
- Python version (if relevant): 3.7
- Are you using conda? yes
- If you are using conda, which channel did you i…
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**Bug summary**
Trying to fix an issue in GMSO with loading benzene molecules from different sources. The `print_hierarchy` method and `children` attribute seem to raise an error whenever they're a…
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**Configuration:**
- RDKit Version: 2019.09.1
- Operating system: Mac
- Python version (if relevant): 3.7.4
- Are you using conda? Yes
- If you are using conda, which channel did you install th…
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Is there any way to match names and/or order of ligand's atoms in the output structure to CIF or SDF format of the ligand file?
Output:
```
ATOM 1949 N N_1 . LIG . 1 ? B 1.644 -8.467 17.946 1.000 2…
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# A more comprehensive PyTest pipeline
Below I copy-paste some items we have listed together with @Abellegese on today's 1-on-1 meeting (04/11/2024).
## Wishlist
- [ ] Test a predefined set o…
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The current data preprocessing module only supports SMILES strings as input and generates a limited set of molecular descriptors. Is it possible to expand the module to support other molecular input f…
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**Describe the bug**
A `rdkit` molecule is created from a SMILES whose atom order is specified by the order of coordinate lines in a structure file (using `reordered_smiles_100` from [(this website)…