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.

Hi,

I am working on a research project which entails collecting SMILES data of polymers, however, the databases where I extracted this information from do not provide the SMILES of the polymer rather only the monomer SMILES. There is not much information in the examples folder that depicts this kind of functionality in this package but I was wondering if I can use this package to perform the task of converting monomer SMILES to polymer SMILES.

Hi makers from m2p,

Hopefully you can help me with an error I don't understand. I want to polymerize random co-polyesters with a given distribution. In order to do that, I used smiles from their corresponding hydroxyacid monomers and a given distribution. Thus, I model these polymers by monomer 1=A-B and monomer 2=A-C, where A is the diol and B & C are the diacids. Strangely, this gives an error if the length of the diol A is the same for both monomers. See sample code below:

data = pd.DataFrame({'smiles':[
'OCOC(C1=CC=C(C(O)=O)C=C1)=O.OCCOC(C1=CC=CC(C(O)=O)=C1)=O', #works
'OCCOC(C1=CC=C(C(O)=O)C=C1)=O.OCCOC(C1=CC=CC(C(O)=O)=C1)=O', #ERROR:Ester_ReactionFailed
'OCCCOC(C1=CC=C(C(O)=O)C=C1)=O.OCCOC(C1=CC=CC(C(O)=O)=C1)=O', #works
'OCCCCOC(C1=CC=C(C(O)=O)C=C1)=O.OCCOC(C1=CC=CC(C(O)=O)=C1)=O' #works
],
'distribution':[[1,1],[1,1],[1,1],[1,1]]
})
data['monomers'] = data.smiles.apply(lambda s: pm.get_monomers(s))
data = pm.thermoplastic(data,DP=5,mechanism='ester',replicate_structures=1)

If I don't specify the distribution, it works fine. Do you have any idea where things go wrong?

Thank you for your response.

Kind regards,
Evelien

Hi, I was wondering if your package can be used to find the polymerization points on the smiles strings represented by *. I am aware that the package returns the polymer SMILES to the degree of polymerization specified but for my purposes I need to have values with the polymerization points of the SMILES.