sdf structure loses 3D spatial information

mSorok / NaturalProductsOnline

Website code for COCONUT

https://coconut.naturalproducts.net/

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sdf structure loses 3D spatial information #90

Closed SynchronyML closed 2 years ago

SynchronyML commented 2 years ago

Hi, thank you very much for your work, he helped me a lot. But I still encountered some difficulties here. When I tried to download the entire dataset (https://coconut.naturalproducts.net/download) and used the sdf for analysis, I found that (download address: https://coconut.naturalproducts .net/download/sdf), each sdf structure has no three-dimensional space structure, what am I doing wrong?

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steinbeck commented 2 years ago

I don't think you are doing anything wrong. For most NP in COCONUT, we simply do not have 3D coordinates since they have not been determined experimentally. I do, however, think that the SDF should at least contain 2D coordinates for proper display. Furthermore, COCONUT has recently been deposited in PubChem, so you should be able to find (calculated/predicted) 3D coordinates there.

SynchronyML commented 2 years ago

Hi, what do you mean by ‘deposited in PubChem’? Does it mean that you can search through pubchempy through smiles?

Kohulan commented 2 years ago

Hi @SynchronyML ,

The whole COCONUT database is now available on pubchem under this link: https://pubchem.ncbi.nlm.nih.gov//#query=ZyDBP0YZI6UUjyGWo-5ouj_jHINwD96CpKfFzr-218-_r-s

Meanwhile, I now have updated the downloads, where you could download the SDF file with 2D coordinates generated using CDK . Hope it helps.

Kohulan

SynchronyML commented 2 years ago

Thank you very much！！！！！！