search

NREL / m2p

BSD 3-Clause "New" or "Revised" License
26 stars 12 forks source link

Get 3D structure of polymer chain from smile #10

Closed iuhgnor closed 1 year ago

iuhgnor commented 1 year ago

After generating SMILES of a polymer chain by m2p, is there an easy way to embed the 3D structure for the polymer chain from SMILES? I have tried to embed a polymer chain with about two thousand atoms by rdkit, but it takes too long time. Could you give me some suggestions? Thanks in advance.

wilsoa6 commented 1 year ago

I don't have a suggestion for 3D structure generation. I would rely on rdkit or some other package. You could try creating many small polymer chains in m2p using the DP (decrease) and replicates (increase) that might converge faster in the 3D algorithms, but this may impact whatever your results are as end group contributions will become larger for small chains.

iuhgnor commented 1 year ago

Thanks for your help.