Sharing lists of molecular structures with associated chemical properties is a common task in computer-aided drug design and medicinal chemistry. WebChem Viewer is a simple, free, open-source program that generates HTML-formatted output that can be viewed in any modern web browser, on any operating system (including mobile), without requiring the installation of additional software. The output can also be easily incorporated into existing web pages. WebChem Viewer is released under the FreeBSD license can be downloaded from SourceForge. It was created by Jacob Durrant, a post-doc in the lab of Rommie E. Amaro.
WebChem Viewer should work on any operating system with Python/TKinter installed. Fortunately, Python comes installed by default on most Linux and Mac OSX systems. A version for Windows can be downloaded from the official Python website.
Users can launch the program by clicking on the WebChemViewer.LINUX executable script in Linux, the WebChemViewer.MacOSX Automator application in OSX, or the WebChemViewer.Windows.bat batch file in Windows. Advanced users can launch WebChem Viewer from the command line (i.e., "python WebChemViewer.py").
WebChem Viewer accepts two types of tabular input files: 1) comma separated values (CSV, e.g., the format used by Microsoft Excel), and 2) tab delimited. The first row of the input file must contain column labels, and subsequent rows must contain data in the same order. Each row represents a single molecule; row entries might include any molecule-associated data, such as the molecular name, weight, SMILES string, or a docking score.
Example of the CSV format:
ID Number,SMILES,Docking,Source,Synthesis Method PLZKL-OMM-71287,c1ccccc1,-5.2,"Pilzukil, Pharmaceuticals",Click Chemistry PLZKL-OMM-67790,CCOC,-9.3,Owen Moore Monet Pharma,Natural Product
Example of the tab-delimited format:
ID Number SMILES Docking Source Company Synthesis Method PLZKL-OMM-71287 c1cccc1 -5.2 Pilzukil Pharm Click Chemistry PLZKL-OMM-67790 CCOC -9.3 OwenMonet Drug Natural Product
Next, the user must indicate which of the data columns contains SMILES strings, from which 2D representations of each molecule are ultimately generated, with stereochemistry indicated when appropriate. The user next indicates which column to use to initially sort the data, either in ascending or descending order. Finally, the user can specify which columns to initially hide.
WebChem Viewer output is HTML formatted and so can be viewed in any modern web browser, on any computer operating system, including mobile. The user can choose to create a single HTML file with all the required dependencies embedded directly into the code (perfect for simple sharing), or the user can choose to save the HTML file and all dependencies as separate files in a directory.
Two-dimensional representations of the molecular structures are generated from the SMILES strings using the free programs Open Babel and the accompanying Cario 2D graphics library. Note that these programs are required dependencies for those using the WebChem-Viewer program, but not for those viewing the program’s HTML output. All the required HTML-output dependencies (JQuery and DataTables) are embedded in the output itself, so that the output can be viewed in any modern web browser without requiring additional plugins or programs.
For the user's convenience, WebChem Viewer provides a Tkinter-dependent graphical user interface. If Tkinter isn't installed or if the user wishes to run WebChem Viewer on a system without a graphical interface (e.g., a remote web server), the program can also be run using a command-line interface. The command-line parameters are: