Questions tagged [rdkit]

Questions about the RDkit software.

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4
votes
1answer
39 views

Change in RDKit's encoding of InChi?

Using RDKit (2020.09.5) I would like to assign InChi to molecules expressed as SMILES and fail to replicate this GitHub gist for initial training written about 2 years ago (RDKit 2019.03.2). I would ...
7
votes
2answers
119 views

RDkit and PySmiles results differ on some SMILES strings

I recently started using both pysmiles and RDkit to parse SMILES strings into molecules. ...
4
votes
0answers
45 views

RDkit parse zero-order bonds (python)

I'm a computer scientist, helping with a chemistry project in python. I have been working with the library pysmiles in order to parse ...
10
votes
2answers
124 views

How to canonicalize SMILES written with aromatic bond symbols (:)?

I am using a package called PySmiles and it is returning a dialect of SMILES for aromatic groups that uses aromatic bond symbols e.g. NC:1:N:N:C:[N]1N. RDKit does ...
9
votes
1answer
65 views

Excluding certain sp3-hybridized carbons with SMARTS

Let's say I have a compound shown above (SMILES: CCC(F)(F)F), and I want to exclude the trifluoromethyl group with SMARTS, how would I do that? I have tried ...
10
votes
1answer
120 views

Computing optimized 3D structures in python that take solvent into account

I have been using RDKit to generate 3D coordinates, cleaning-up the structures using a general-purpose force field as follows: ...
9
votes
1answer
290 views

Using OpenBabel or RDKIT Python API to generate conformers from a SMILES string

I have a bunch of monomers in the form of SMILES string and I want to generate conformers from them. At the moment, I am using RDKit to convert these SMILES strings to .sdf files, then using ...
11
votes
0answers
81 views

Bioisosteric replacement using SMARTS (KNIME and RDKit) [closed]

I am trying to create a KNIME workflow that would accept a list of compounds and carry out bioisosteric replacements (we will use the following example here: carboxylic acid to tetrazole) ...
10
votes
2answers
692 views

RDkit: While converting a *.sdf file to fingerprint, I'm facing several errors

suppl = Chem.SDMolSupplier('1.sdf') for mol in suppl: if mol is None: continue # print(mol.GetNumAtoms()) fps = [Chem.RDKFingerprint(x) for x in supply] I am ...