Questions tagged [smiles]

Questions about or relating to SMILES (simplified molecular-input line-entry system) or related things such as SMARTS.

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10 votes
1 answer
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Node features matrix with Networkx

I built a function to generate graphs from smiles strings using networkx, inserting various features on the nodes. This is the code: ...
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8 votes
2 answers
705 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). ...
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10 votes
2 answers
248 views

How to convert SMILES to Amino Acids sequence using RDKit

I have the following SMILES, wrapped in Python RDKit: ...
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7 votes
2 answers
451 views

RDkit and PySmiles results differ on some SMILES strings

I recently started using both pysmiles and RDkit to parse SMILES strings into molecules. ...
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4 votes
0 answers
55 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 ...
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10 votes
2 answers
160 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 ...
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  • 7,744
9 votes
1 answer
82 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 ...
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