No description, website, or topics provided.
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.
Dockerfile First commit Oct 24, 2018 Update Jan 24, 2019

webMolCS: Visualizing Molecules in 3D Chemical Space

The concept of chemical space provides a convenient framework to analyze large collections of molecules by placing them in property spaces where distances represent similarities. Here we report webMolCS, a new type of web-based interface visualizing up to 5000 user-defined molecules in six different three-dimensional (3D) chemical spaces obtained by principal component analysis or similarity mapping of multidimensional property spaces describing composition (MQN: 42D molecular quantum numbers, SMIfp: 34D SMILES fingerprint), shapes and pharmacophores (APfp: 20D atom pair fingerprint, Xfp: 55D category extended atom pair fingerprint), and substructures (Sfp: 1024D binary substructure fingerprint, ECfp4:1024D extended connectivity fingerprint). Each molecule is shown as a sphere, and its structure appears on mouse over. The sphere is color-coded by similarity to the first compound in the list, by the list rank, or by a user-defined value, which reveals the relationship between any property encoded by these values and structural similarities. WebMolCS website is freely available at

Description of Files


Complete webMolCS web application


Netbeans project containing Java source code for Molecule Preprocessing, Principal component analysis and 3D-map generation. This Java Project is use by webMolCS application (see webMolCS/dist folder)


  1. Java
  2. tomcat server
  3. Chemaxon license file

Setting up the webMolCS in Dockerised container

Edit the path "ABSOLUTE_PATH_TO_WEBMOLCS" in file. run ./