I am new to RDKit and have been going with the following lines of code to generate and then optimize structures from SMILES files. >>> m = Chem.MolFromSmiles('....') >>> m2 = Chem.AddHs(m) >>> m3 = m2 >>> AllChem.EmbedMolecule(m2, randomSeed=0xf00d) Then I try embedding multiple conformations: >>> cids10 = AllChem.EmbedMultipleConfs(m3,numConfs=10) I can optimize and print the embedded version of one molecule (m2): >>> AllChem.UFFOptimizeMolecule(m2) >>> print(Chem.MolToMolBlock(m2), file=open('file.mol','w+')) However, despite numerous attempts, I cannot figure out how to generate multiple conformers (make a proper ensembles), minimize and print out the pre-minimized and minimized versions of the ensemble.
Can you help me with this?
I hope you have found your answer.
If not, the link may be your want.
Anyway, the question of the code should be asked on other web sites.
https://www.programcreek.com/python/example/110776/rdkit.Chem.AllChem.EmbedMultipleConfs
- Badges
- Science topic
- Similar topics
- Filing