Questions tagged [rdkit]

Questions about using RDKit in matter modeling workflows.

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6 votes
2 answers
83 views

How to obtain fingerprint bits as SMARTS pattern in RDKit

I am using RDKit to generate Morgan Fingerprints (similar to ECFP) and then obtaining the bit information. I need the bit information in order to generate a statistics of substructures for each ...
  • 5,834
5 votes
1 answer
109 views

How do you determine substitution patterns using RDKit?

So I have a list of molecules. They all have a common substructure, but different substitution patterns. For example, in the figure below, the leftmost molecule is the base, and the center and ...
5 votes
1 answer
114 views

Convert SMILES format to Amino Acid masses using RDKit - Cyclopeptides

This is a variation of a question asked on October 30, 2021 here, but it is different enough that I think it warrants a new post. I'm also trying to use RDKit. Is it possible to convert a SMILES ...
  • 111
8 votes
1 answer
827 views

How to compute the synthetic accessibility score in Python?

I come from a mainly computer science background, but have become involved in a project related to artificial intelligence-based drug discovery. I made a model that generates novel molecules, for ...
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9 votes
2 answers
2k views

How to input 3D coordinates from xyz file and connectivity from SMILES in rdkit?

I am working on a QSAR project where the 3D structural descriptors are an input to a machine learning model. I am generating the descriptors using the python Mordred API (which uses rdkit). ...
  • 5,834
10 votes
2 answers
449 views

How to convert SMILES to Amino Acids sequence using RDKit

I have the following SMILES, wrapped in Python RDKit: ...
5 votes
1 answer
317 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 ...
  • 1,459
7 votes
2 answers
677 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
0 answers
57 views

RDkit parse zero-order bonds (python) [closed]

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
2 answers
199 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 ...
  • 7,794
9 votes
1 answer
94 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
1 answer
267 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: ...
  • 103
9 votes
1 answer
834 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 ...
  • 3,957
11 votes
0 answers
117 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
2 answers
1k 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 ...