Questions tagged [cheminformatics]

Synonym for chemoinformatics. For questions about applying informatics techniques to study chemical systems.

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1answer
24 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 ...
7
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1answer
152 views

How to create molecule image similar with molconvert using RDKit

I have the following molecule in SMILE format (saved as my_molecule.smi): ...
8
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1answer
336 views

Given the adjacency matrix of a molecule, how can I get a graphical representation using only open source software?

In Huckel Method, by numbering the sp2 carbons in a molecule with conjugated double bonds, we can assemble its secular determinant in a form similar to the adjacency matrix of a graph. Taking trans-...
8
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1answer
244 views

Functional group detection for group contribution methods

I would like to be able to parse a molecule into its functional groups, and, also, know the number of occurrences of each. A similar question was asked on matter modelling specifically for xyz files. ...
10
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2answers
848 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 ...
17
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6answers
371 views

What are the applications of chemical graph theory?

Graph theory was originally introduced in computer science to study data structure. Chemists also introduced graph theory to study the relation between structure and properties for molecular compounds....
15
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2answers
275 views

What are the best fingerprints to characterize molecules?

When working with libraries of thousand of molecules or with de novo design (using combinatorial chemistry), it is usual to filter the libraries using as a criterion the molecular similarity. The ...
15
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1answer
105 views

Types of Discrete molecular models

It is often assumed in cheminformatics that molecules with similar physical structure tend to have similar chemical properties [1]. Based on this, our group has used discrete graphs as a model for the ...