Questions tagged [cheminformatics]

See [tag:chemoinformatics] for a description.

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7
votes
1answer
304 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
votes
1answer
170 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
votes
2answers
698 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
votes
6answers
338 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
votes
2answers
219 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
votes
1answer
103 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 ...