search

RBVI / chemViz2

Cheminformatics App for Cytoscape 3
6 stars 2 forks source link

TanimotoSimilarity missing in generated chemical similarity networks #5

Open dhimmel opened 7 years ago

dhimmel commented 7 years ago

When creating structural similarity networks using chemViz2, the resulting edges don't have an attribute for Tanimoto similirity. The only attribute I see is shared interaction which is set to simialirity. Is it possible to output the actual chemical similarity score (Tanimoto coefficient)?

I used the following menu options

Apps > Chemoinformatics Tools > Create Similarity Network > Using All Nodes

scootermorris commented 7 years ago

Hi Daniel, Actually it does create a column called TanimotoSimilarity although I've noticed a bug where if that column already exists, it just fails (it should just use it if it's the proper type). I'll try to get this fixed (probably by creating the attribute as a LOCAL attribute), but in the meantime, if you just import your nodes from an excel file into a new network collection, everything should work.

dhimmel commented 7 years ago

Ah makes sense... the first time I created a similarity network, I remember there being a TanimotoSimilarity column. But I deleted that network, and now new similarity networks I create in that session don't have TanimotoSimilarity.