NDKmol - molecular viewer



NDKmol -- Molecular Viewer for Android

== About ==

NDKmol is a molecular viewer for Android. You can view three dimensional structures of proteins, nucleic acids and small molecules. NDKmol supports most of common representations for molecules, such as ribbon, trace, stick, sphere and line. NDKmol also supports symmetry operations; biological assemblies and crystal packing can be displayed. You can search and download structures from RCSB PDB and NCBI Pubchem.

NDKmol has almost same functionality as GLmol, which is written in
WebGL/Javascript and runs on Web browsers. You can try GLmol at http://webglmol.sourceforge.jp/index-en.html

== Features ==

* Read PDB or SDF/MOL file
* Rotate/Translate/Zoom model by finger
* Representations
- Line
- Stick
- Sphere(van der Waals radius)
- Alpha carbon trace
- Ribbon (Thin or Thick)
- 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 (a.k.a chainbow)
- B factor
- polar/nonpolar
* Crystallography
- Display unit cell
- Show crystal packing (when defined in REMARK section)
- Display biological assembly (when defined in REMARK section)

== How to Use ==

When launched, NDKmol automatically loads Porin (PDBID: 2POR) as an example. You can rotate the molecule by your finger.

To zoom or translate the molecule, press MENU button in your phone/tablet and select the mode. Two-finger gestures are also supported.

Everything else can be done from the MENU.

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.

== Contact ==

Project website is located at http://webglmol.sourceforge.jp/ . You can get source codes for this program from here.

Comments and suggestions are welcome at http://sourceforge.jp/projects/webglmol/forums/ or biochem_fan@users.sourceforge.jp

=== LICENSE notice ===

NDKmol itself is licensed under GNU Lesser General Public License as follows.

However, PDB files included as examples are under DIFFERENT conditions.
Please consult


NDKmol - Molecular Viewer for Android

(C) Copyright 2011, biochem_fan

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.

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