Unexpected results from Generate #18

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opened 2025-10-14 17:00:42 -06:00 by navan · 0 comments

navan commented

2025-10-14 17:00:42 -06:00

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Originally created by @lydiaauch on 9/29/2024

This may be related to #54 but it isn't limited to unexpected results with double cuts. After updating to the released V3, my results changed and I can't make sense of how these pairs are being formed. I've attached a smiles file that was used to build a test DB with the default commands and the resulting file from running a basic generate command (example below). I would expect many more rows using *c1ccccc1 as the constant smiles to generate something like Oc1ccccc1. Any thoughts would be appreciated!

mmpdb generate postgres_db --smiles CCc1ccccc1 -o generate.csv --radius 0

generate.csv
test_data.txt

*Originally created by @lydiaauch on 9/29/2024* This may be related to #54 but it isn't limited to unexpected results with double cuts. After updating to the released V3, my results changed and I can't make sense of how these pairs are being formed. I've attached a smiles file that was used to build a test DB with the default commands and the resulting file from running a basic generate command (example below). I would expect many more rows using `*c1ccccc1` as the constant smiles to generate something like `Oc1ccccc1`. Any thoughts would be appreciated! `mmpdb generate postgres_db --smiles CCc1ccccc1 -o generate.csv --radius 0` [generate.csv](https://github.com/user-attachments/files/17177066/generate.csv) [test_data.txt](https://github.com/user-attachments/files/17177067/test_data.txt)