Long time ago, I wrote post about the same topic. The code used old version of rdkitjs and electron. Recently rdkitjs is maintained in official repository so I would like to re-test the approach. My old post is here. To do the following approach, I installed node.js, electron and npm at first. Then init theContinue reading “Create desktop chemoinformatics application with JS #chemoinformatics #RDKit #JS”
Embed molecular editor into Streamlit app #streamlit #chemoinformatics #RDKit
I wrote some posts about usage of combination chemoinformatics and streamlit. One was predictive model application which was used rdkit and scikit-learn. When I tweeted that, Jan Jansen (who is Great quantum chemist and I met him RDKit UGM!!!) commented me that it is useful that if molecular drawer can use in the app ;)Continue reading “Embed molecular editor into Streamlit app #streamlit #chemoinformatics #RDKit”
Try to use casperjs
Use rdkitjs in local application
Visualize chemical space using RDKit-Scikitlearn-Highchart
I often use Principle component analysis (PCA) to visualize chemical space. PCA is useful to describe chemical diversity. I wonder if I could project new designed molecules to reference current chemical space. I think that sci-kitlearn and rdkit is suitable to do that. Recently I often use seaborn to visualization, but today I used highchartsContinue reading “Visualize chemical space using RDKit-Scikitlearn-Highchart”
Interesting Web app Named ‘ChemTreeMap’ using RDKit.
I like web app because user does not need client soft to use it. I often use cytoscape to visualise molecular network. Network view is very informative. Yesterday, I found cool web app that using RDKit. URL is following. http://ajing.github.io/ChemTreeMap/ The app is an open source application for visualizing molecular networks. If user can useContinue reading “Interesting Web app Named ‘ChemTreeMap’ using RDKit.”
SAR visualization with RDKit ver2.
Somedays ago I posted SARviz test code using RDKit. It was based on command line type. So, I think it is easy to use for applying SDF etc but not familiar for chemist. Because almost of chemist, don’t like black command screen….;-) Next step, I tried to make very simple web-app using sarviz.py. I usedContinue reading “SAR visualization with RDKit ver2.”
Admin portal about MongoDB
I use mongodb to make MMP-DB. MongoDB is noSQL, and flexible database program. Also I use postgresSQL. PostgresSQL has pgAdmin to provide adminportal for administrator. It’s useful for me. I wonder if I could use Adminportal in mongDB too. I searched web, and I found it. You know, mongo-exporess is one of the app thatContinue reading “Admin portal about MongoDB”
Draw Molecular Matched Pair as SVG.
Somedays ago, I posted drawing molecule as SVG using RDKit. It works fine. So, I challenged draw MMP as SVG. My plan is … 1. Generate MMP using RDKit. 2. Store MMP data to MongoDB. 3. Provide MMP data to user using flask. 4. Draw structure on the fly using Ajax. OK, Let start! StepContinue reading “Draw Molecular Matched Pair as SVG.”
I often use flask for developing some web services. Because it’s very easy and powerful tool and python library. There are lot’s of extensions. Yesterday, @kzfm san gave me useful information for developing web services via node-js. I haven’t used node-js before, but I tried it. Node-js is very major tools and also it canContinue reading “nodejs-rdkit”
Make Interactive Cluster Heatmap
similarity network using cytoscape.js.
mol_prop_calc and Flask and Ajax