Create desktop chemoinformatics application with JS #chemoinformatics #RDKit #JS

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 the

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 ;)

Try to use casperjs

CasperJS is navigation scripting and testing utility for the PhantomJS and SlimerJS written in Javascript. You know, PhantomJS, and SlimerJS are headless browsers. Some years ago, I used selenium for web scraping because selenium has python binding and easy to use. Today, I used CasperJS for test. Installation is very easy. Just use homebrew(for Mac

Use rdkitjs in local application

Electron is tool to build cross platform desktop apps with javascript, HTML, and CSS. http://electron.atom.io/ Users can develop their own app like web app. I think it’s interesting, because the developed application will run local environment. Today I tried to use electron. My code (index.js) is almost same as quick start. I installed browserfiy, rdkitjs,

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 highcharts

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 use

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 used

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 that

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! Step

nodejs-rdkit

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 can

rdkit in javascript-2

The day before yesterday, I posted short code about rdkitjs. Today I added some sample code in my github repo. RDKitjs can draw molecule as svg using Drawing2D function. So, I wrote javascript and embedded it to HTML. Following code… I used replace function in moldraw, because Drawing2D() function return svg:svg tag. does not work

rdkit in javascript

I think this project is very cooooooooool. ;-) https://github.com/thegodone/RDKitjs This project is trying to convert c++ to javascript using emscripten. Emscripten is an LLVM-based project that compiles C and C++ into highly-optimizable JavaScript in asm.js format. So, if rdkit.js works well, I can write chemoinformatic function using only javascript. It’s sounds nice. I tried it.

chem-redmine

I’m still playing with redmine. I want to embed structure editor in redmine, and store structural information. It’s good idea to make plugin, but it’s difficult to do ASAP. So, I embedded javascript directory in base code. At first, put javascript library JSME in $REDMINE_ROOT/public/javascripts/. JSME can get from following site. http://peter-ertl.com/jsme/ Then added javascript

Make Interactive Cluster Heatmap

Heat map is useful tool to visualise multi parameter not only biology, but also chemoinformatics. I often use spot-fire or R to make it. Last week I found cool javascript library “InCHlib(Interactive Cluster Heatmap library)”. There is good document in this link http://openscreen.cz/software/inchlib/home/ . I make simple test to use the library. At first, I

fisheye “GYOGAN”?

I’m newbei of javascript. There are lots of libraries. And I’m interested in D3.js. D3.js is a JavaScript library for manipulating documents based on data, and lots of plug-ins are. Today I made simple scatter plot with fisheye. Fisheye.js is plug-in of D3.js and it can distortion magnifies the local region around the mouse, OK

similarity network using cytoscape.js.

Lots of relationships are presented as graph. For example, if I set molecule as node, and similarity as edge, I could make molecular networks. Cytoscape.js is one of the good tool. It is an open-source JavaScript graph theory library for analysis and visualisation. And works on server side. So, Not depend on client machine. I

mol_prop_calc and Flask and Ajax

I build very simple portal site in my lab, that can predict some physchem value using structure designed by med chem. I used javascript library jQuery and python library flask , rdkit for main code. Ajax is very powerful because it can return results without screen translation. But,,,,,,, I’m not good at javascript ;-(…. (also