Questions tagged [smiles]
Questions about or relating to SMILES (simplified molecular-input line-entry system) or related things such as SMARTS.
7
questions
10
votes
1
answer
107
views
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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- 5,499
10
votes
2
answers
248
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How to convert SMILES to Amino Acids sequence using RDKit
I have the following SMILES, wrapped in Python RDKit:
...
- 225
7
votes
2
answers
451
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RDkit and PySmiles results differ on some SMILES strings
I recently started using both pysmiles and RDkit to parse SMILES strings into molecules. ...
- 213
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 ...
- 213
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 ...
- 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 ...
- 93