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7 votes
Accepted

How to convert SMILES to Amino Acids sequence using RDKit

openbabel could also be used to tackle this problem. Convert initial structure to PDB format. I suspect this can be done directly from whatever format you are using for the skeletal structure, but I ...
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7 votes

How to convert SMILES to Amino Acids sequence using RDKit

Based on your recent comment to want to assemble a protein from scratch, and assuming you want to stick to the naturally occurring $\alpha$-amino acids, I suggest to type the amino acids by their ...
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6 votes
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Convert SMILES format to Amino Acid masses using RDKit - Cyclopeptides

I'm not sure if it's improper to answer my own question, but I think I've cracked it. For each peptide bond match identified by GetSubstructMatches the index [1] is ...
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6 votes

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

Your best bet is to keep the molecule (e.g., as a .mol or .sdf file) around and then simply update the coordinates from the <...
4 votes

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

The representation of a molecular structure as SMILES string is a (very) reduced one, often with only implicit hydrogen atoms. Recreating a 3D molecular structure with either OpenBabel or RDKit not ...
  • 1,459
4 votes

How to compute the synthetic accessibility score in Python?

Ertl and Schuffenhauer, who developed the synthetic accessibility score, provide an implementation packaged with RDKit called sascorer.py. This is provided in the Contrib folder of the RDKit repo; ...
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4 votes

How to obtain fingerprint bits as SMARTS pattern in RDKit

Based on your code and the code found by Geoff. Additionally you have to find the neighbors and change their identity. ...
  • 411
4 votes

How to obtain fingerprint bits as SMARTS pattern in RDKit

I'm not entirely sure I understand your question. You want a SMARTS that matches DrawMorganBit but with an extra * added? If you ...
3 votes

How do you determine substitution patterns using RDKit?

You can get the corresponding indices of the two structures with GenerateDepictionMatching2DStructure. The code was made in a Jupyter notebook. ...
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