ESmol & NDKmol - Molecular Viewer for Android

About ESmol & NDKmol

ESmol and NDKmol are open-source molecular viewers for Android. You can view three dimensional structures of proteins and small molecules on your Android phone/tablet. Both are licensed under LGPL3.

ESmol is written in Java while NDKmol is written in C++ using Android NDK. ESmol is more portable and runs on almost all Android phones/tablets. NDKmol runs faster and supports bigger molecules than ESmol. NDKmol can even open GroES-EL complex! (try PDBID: 1AON)

ESmol and NDKmol have almost same functionality as GLmol, which is written in WebGL/Javascript and runs on Web browsers. You can try GLmol online.

Features

Currently ESmol/NDKmol has following features. More is coming...

• Read PDB file (ESmol supports PDB file up to 3MB. NDKmol can load bigger PDB files as far as system memory permits.)
• Read SDF/MOL file.
• Search and Download structures from RCSB PDB and NCBI PubChem
• Rotate/Translate/Zoom model by finger
• Representations
  • Line
  • Stick
  • Sphere(van der Waals radius)
  • Alpha carbon trace
  • Thick ribbon
  • Thin ribbon
  • Strand
  • B factor tube
  • Nucleic acid ladder
  • Nucleic acid line
  • Solvent 'stars'
• Smoothing of beta sheets
• Coloring
  • By chain
  • By secondary structure (when defined in SHEET/HELIX records)
  • By Elements
  • Gradation (chainbow)
  • Temperature factor (B factor)
  • Polar/Nonpolar
• Crystallography
  • Display unit cell
  • Show crystal packing (when defined in REMARK section)
  • Display biological assembly (when defined in REMARK section)

System requirements

Android 1.6 and newer is supported. NDKmol runs on most of modern devices.

How to use

When launched, NDKmol automatically loads Porin (PDBID: 2POR) as an example. You can rotate the molecule by your finger. (Two-finger gestures such as pinch-zoom is not supported yet.)

To zoom or translate the molecule, press MENU button in your phone/tablet and select the mode.

Everything can be done from the menu; changing representation of protein or ligand (non protein molecules), changing colors, showing biological assembly, crystal packing and/or unit cell.

To load other PDB files, please put the file in "PDB" directory of the SD card and select "Open" command in the menu. You can also download structures directly from RCSB PDB and NCBI PubChem web server. Select "Search and Download" in the menu.

Download

You can download ESmol and NDKmol from Android Market. If your device doesn't support Market, you can also download from this server. In this case, you may have to change setting by checking Settings>>Applications>>Unknown sources.

• ESmol: from Android Market, from this server (apk)
• NDKmol: from Android Market, from this server (apk)

For source codes, follow the link below.

Interaction with other softwares

ESmol and NDKmol have handlers for file extension pdb/sdf/mol. Once NDKmol or ESmol are installed, when users click(tap) a link to these files on Web browser, the viewer will be launched. If you are writing an application and want to invoke ESmol/NDKmol, the following code is enough.

To open local files,
startActivity(new Intent(Intent.ACTION_VIEW, Uri.parse("file:///sdcard/test.pdb"))));

To download files from network,
startActivity(new Intent(Intent.ACTION_VIEW, Uri.parse("http://some.server/pdbfile.pdb"))));