Turning on --property flag leading to a smaller number of transformed structures #29

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opened 2025-10-14 17:01:26 -06:00 by navan · 0 comments

navan commented

2025-10-14 17:01:26 -06:00

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Originally created by @chengthefang on 4/25/2023

Hi all,

I recently found some unexpected outcomes when using "mmpdb transform" with or without the property flag. The mmpdb database was generated using ChEMBL database with calculated LogP as the property.

When I used the "--no-properties" flag, I got 4632 transformed structures.
mmpdb transform chembl.mmpdb --smiles "XXXXXX" --min-pairs 5 --min-variable-size 0 --max-variable-size 20 --no-properties -o results_noprop.csv &

However, when I turned on the "--property LogP" flag, I got 591 transformed structures.
mmpdb transform chembl.mmpdb --smiles "XXXXXX" --min-pairs 5 --min-variable-size 0 --max-variable-size 20 --property LogP -o results_prop.csv &

I would expect the code with "--property LogP" generates the same number of compounds but with more output info.

Any thoughts on that?

Thanks!
Cheng

*Originally created by @chengthefang on 4/25/2023* Hi all, I recently found some unexpected outcomes when using "mmpdb transform" with or without the property flag. The mmpdb database was generated using ChEMBL database with calculated LogP as the property. When I used the "--no-properties" flag, I got 4632 transformed structures. `mmpdb transform chembl.mmpdb --smiles "XXXXXX" --min-pairs 5 --min-variable-size 0 --max-variable-size 20 --no-properties -o results_noprop.csv &` However, when I turned on the "--property LogP" flag, I got 591 transformed structures. `mmpdb transform chembl.mmpdb --smiles "XXXXXX" --min-pairs 5 --min-variable-size 0 --max-variable-size 20 --property LogP -o results_prop.csv &` I would expect the code with "--property LogP" generates the same number of compounds but with more output info. Any thoughts on that? Thanks! Cheng