== 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
== Features ==
* Read PDB or SDF/MOL file
* Rotate/Translate/Zoom model by finger
- Sphere(van der Waals radius)
- Alpha carbon trace
- Ribbon (Thin or Thick)
- B factor tube
- Nucleic acid ladder
- Nucleic acid line
- solvent 'stars'
* Smoothing of beta-sheets
- By chain
- By secondary structure(when defined in SHEET/HELIX records)
- By Elements
- Gradation (a.k.a chainbow)
- B factor
- 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 email@example.com
=== LICENSE notice ===
NDKmol itself is licensed under GNU Lesser General Public License as follows.
However, PDB files included as examples are under DIFFERENT conditions.
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
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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/>.
Users of the Jmol Molecular Visualization Activity can download and investigate on their Android tablet over 60,000 biomolecular structures directly from the Protein Data Bank (PDB) by keyword or PDB ID and over 40,000,000 unique structures from the National Institutes of Health National Cancer Institute (NIH/NCI) using a wide variety of chemical identifiers, including CAS registry numbers, InChI keys, trade names, common names, and IUPAC-format names, among others. (For a full list, see http://cactus.nci.nih.gov/chemical/structure.) Files from any other internet-available site that can be read by Jmol may also be loaded.
The Jmol Molecular Visualization Activity is a nearly full touch-screen implementation of Jmol allowing for command-line entry of Jmol commands (see http://chemapps.stolaf.edu/jmol/docs) as well as a variety of preset simple visualization modes. Additional renderings include a full range of visualizations for crystals (unit cells, symmetry operators, Miller planes, for example), a wide variety of surfaces including Van der Waals surfaces, solvent-accessible surfaces, cavities, and molecular surfaces, and atomic and molecular orbitals.
Special features of the Android version of Jmol include a connection to the gyroscope, allowing for initiating of spinning by simply moving the tablet in a natural fashion (see http://www.youtube.com/watch?v=JPwvCmD5IDg and http://www.youtube.com/watch?v=D7uOkhoJ0Oc).
This activity is under active development. Feedback is much appreciated.
Do you want to see different molecules such as adrenaline, cocaine, amino acids and etc. with real 3D stereoscopic mode?
With "Molecule 3D" you can look at them with several 3D stereoscopic modes: Anaglyth, Side by Side and Mirror separated.
"Molecule 3D" helps you to understand space structure of complex molecules.
For Anaglyph stereoscopic mode you must have Anaglyph stereo glasses having red/green-blue color division.
Some people can see stereoscopic image without special glasses using Side by Side or Mirror separated mode.
You can simply open any file in PDB(protein Data Bank) format or choose some molecules in the available list and interact with it by simple standard touch control.
File browser shows files only with *.pdb, *.ent, *.txt extensions and only not empty directories.
Some basic control features:
- main menu is called by clicking on the title of the main window(where molecule is displayed) or by context menu;
- grouping, search are available by context menu in the "Molecule List" window.
Interleaved stereoscopic mode for HTC Evo 3D mobile phone is supported. It is automatically detected and added in stereo mode list.
The trajectories of the particles are determined numerically. The well known Velocity Verlet integration of Newton's equation of motions is used for a system of interacting particles. Forces between particles are defined analytically using a "pair potential function" that depends on the distance between two particles.
In physics, MMD is used to examine the dynamics of atomic-level phenomena that cannot be observed directly. Within the mobile devices context, it can be used as a small mobile laboratory to understand the basics of the particle physics. Furthermore it can be used to produce nice dynamical pictures that are suitable as a live wallpaper.
- The application can be set as a live wallpaper that visualizes the current experimental set up.
- In the live wallpaper mode, the active “static” wallpaper can be used as a background. You can mix your favorite background picture with particles “flying” in front of it.
- The changes made in main application will be applied to live wallpaper daemon to make the wallpaper tuning easier.
- Generation of an initial structure of the particles use diagonal or square grids with given dimension
- Possibility to select a boundary condition (full energy is constant, kinetic energy is constant, or no constraints)
- If kinetic energy is constrained, it is possible to apply “thermal change” that simulates heating/cooling of the system
- Possibility to change the gravity value. The gravity vector can be also changed by rotating of the device.
- Possibility to select and visualize selected potential. Currently, three common potentials are available: Lennard-Jones, Morse and Born-Mayer.
- The particle skin can be selected from build-in clip art.
- Multi-touch interface is used to zoom and drag the experimental area.
Note: since the application implements a numerical integration method, it generates a significant CPU load. Therefore, the live wallpaper mode is not suitable for low-power devices.
Keywords: live wallpaper, HD wallpaper, physics, molecular dynamics, atom simulations, experiment
Please note that the app requires at least 50 MB of space for basic app installation plus a further 50 MB of storage for index files. The app will not install or function properly unless there is sufficient space for installation. Older devices running android versions below 4.0 may not have sufficient hardware resources to run the app efficiently.
The app provides many 3D features including rotating model with finger movement, zooming in/out, changing color, etc. You can view multiple files together.
3D data files can be added to the app's external storage folder called 'afanche'. Just connect your phone (or tablet) with a PC and copy your 3D models to the 'afanche' folder of the device. After that, you can use the app to load the models you saved in the directory. If you have files in system 'download' folder of your device, the app can open them as well. You can also use the app to open files from email(attachment) or web (by downloading). The app also supports third party file management app, for instance, DropBox.
The app provides you file sorting features so that you can find your model quickly. You can sort by file name or file creation time. If you don't need some of the files any more, you can use the app to delete them. If you need share 3D model with your friend, coworker, client or partner, you can use in-app email feature to send your model out as email attachment.
The app is not just a data file viewer. It is also a 3D data file organizer. With its help, it is so easy to keep your 3D data and other files orgainzied. The app provides native support for multimedia including image, video and audio.
If you need Android, iPhone, iPad, Windows app for other 3D file formats, please search 'Afanche' to find more 3D oriented apps. Afanche Technologies is a company specialized in 3D technologies. Afanche provides customized 3D programming solutions for mobile, web and desktop. For more info, please contact us. Our email address is firstname.lastname@example.org
The app is built on top of jmol library. It supports the following molecule data format well:
MOL MDL / Elsevier / Symyx structure (classic version V2000)
PDB Protein Data Bank - Research Collaboratory for Structural Bioinformatics
XYZ XYZ format, XMol file - Minnesota Supercomputer Institute
CTFile MDL / Elsevier / Symyx chemical table (generic)
CIF Crystallographic Information File - standard from the International Union of Crystallography
CML Chemical Markup Language
CSF Fujitsu Cache chemical structure, now Fujitsu Sygress
HIN HIN / HIV files from HyperChem - Hypercube, Inc.
Jaguar Schrodinger, LLC
GRO Gromos87 format from GROMACS
PQR Modified pdb format including charge and radius
JME Java Molecular Editor - Peter Ertl
VASP VASP / VAMP / Vienna ab-initio simulation package
ADF ADF output - Amsterdam Density Functional
XSD Accelrys Materials Studio
WebMO WebMO interface to computational chemistry packages
CRYSTAL Output files from CRYSTAL, a computational tool for solid state chemistry and physics.
The app might also support the following format:V3000,SDF, MDL / Elsevier / Symyx structure (multiple models)
mmCIF Macromolecular Crystallographic Information File
XYZ+vib XYZ format with added vibrational vector information
XYZ-FAH XYZ format for Folding@home
MOL2 Sybyl, Tripos
Cube Gaussian, Inc.
Ghemical The Ghemical computational chemistry package
MM1GP Ghemical molecular mechanics file
MOLPRO Molpro output
odydata Odyssey data
xodydata Odyssey XML data
QOUT Q-Chem, Inc.
SMOL Spartan data - Wavefunction, Inc.
spinput Spartan data - Wavefunction, Inc.
Amber The Amber package of molecular simulation programs
CASTEP The CASTEP software package, uses density functional theory
DGrid Miroslav Kohout, Max-Planck Institute
Molden Electron density / molecular orbitals
Make sure to check out my other chemistry app, Molecule Viewer 3D.
Note: ad supported
If you don't like ads there is an ad free version on the market for a dollar :)
Comment or email me with questions or concerns.
Initial ribbons support (no sheets yet)
Check the server news for HOWTOs and explanations.
Contribute your molecules to the library (share button) and enter our contributor ranking!
Please report any problems via mail! :-)
### NEXT ###
Complete ribbons support
The Atomdroid app is a computational chemistry tool for the Android platform. It can be used as a molecular viewer/builder and contains local optimization and Monte Carlo simulation features. Install now and experience mobile computational chemistry!
List of features:
* molecular viewing (compatible with xyz and pdb files)
* trajectory analysis and viewing
* molecular building (export to xyz)
* PDB downloader (requires the Internet permission, downloads compressed pdb to save on your data plan)
* Atomdroid molecular libraries (requires the Internet permission)
* local optimization (L-BFGS and Powell algorithms)
* Monte Carlo simulation and analysis
* Global optimization using a Monte Carlo with minimizations approach
* Universal Force Field (UFF) implementation (currently without electrostatics)
* communication with other Atomdroid users via bluetooth and share your molecules (requires bluetooth permission, we are VERY cautious with using it)
Future versions will contain:
* more force field implementations (including analytical gradients)
* molecular dynamics engine
* and more...
The application is currently in beta state. Please report any bugs to email@example.com, we will be pleased to solve them quickly.
Support for Atomdroid molecular libraries: If you want to create your own library (e.g. for courses) let us know via mail and we provide you with the necessary tools and information free of charge!
Includes Support For-
Molecular mass calculations
Mass percentage calculations
And much more!
Be sure to check out Molar Mass Calculator Pro if you like the app.
This app is produced by Calistry. Visit calistry.org to use hundreds of similar tools in the field of chemistry.
You do not have to know everything by heart! Chemist application will be enough!
Use the Periodic Table just like a computer keyboard.
The chemist will show you possible products and balance the chemical reaction! All you have to do is enter the reactants.
With the Chemist you will learn everything you need to know about the elements, compounds and chemical reactions.
Chemist contains names, designs, and many other options for more than 1,500 chemical compounds.
Chemist shows the reaction products of over 2,000 chemical reactions and balances them immediately .
Chemist balances all redox reactions .
Chemist includes lots of information about compounds, the elements and chemical reactions.
Exemplary compounds :
- Oxygen acids : HNO3 , H2SO 4 , H3PO4,H2CO3
- Anaerobic acids : HCl , HBr , H2S
- Hydroxides : NaOH , Ca(OH)2 Mg(OH)2 , Al(OH)3
- Acidic oxides : SO3 , Cl2O 7 , N2O5
- Basic oxides: Na2O, CaO , MgO
- Oxygen salts: Al(NO3)3 ,
- Anaerobic salts NaCl , KCl , LiF
Examples of chemical reactions :
For Salt :
- Zn + HCl ( metal + acid )
- MgO + HBr ( metal oxide + acid )
- CaO + HNO3 ( metal oxide + acid )
- Al 2O3 + SO3 ( metal oxide + nonmetal oxide )
- Zn (OH)2 + H2SO 4 ( hydroxide + acid )
- KOH + N2O5 ( + metalloid oxide hydroxide )
- Na + Cl 2 (metal + non-metal )
- Cl 2O7 + H2O ( acidic oxide + water )
- K + H 2O ( metal + water )
- K 2O + H2O ( metal oxide + water )
- KH + H2O ( metal hydride + water )
- Each element + oxygen
Options for compounds:
- Molecular weight
- Structural formula
- Molecular formula
- The ratio
- Atomic composition
- Chemical character
- Concentration rates
- Molar concentration
- Type of bond
Options for elements :
- General information
- Information about the atom
- The structure of the atom
Options for chemical reactions :
- Verbal record
- Ion record
This Lite version lets you check out a bit of the Learn, Interact, and Test section for each topic.
If you like what you see you can unlock the full version with an in-App purchase.
First Class Standing creates intuitive, interactive Science Apps for students. Each module guides you through a topic in three stages.
Stage 1: LEARN
In this section the topic is introduced to you through an animated tutorial.
Stage 2: INTERACT
Next, you get a chance to interact with the process by moving cellular components, selecting molecules, and initiating sequences.
Stage 3: TEST
Finally, we give you a topic test to see how much you've learned. Then you can share your results with friends and teachers.
Our Apps are designed to compliment most high school Biology curriculum expectations (IB, AP, US, Canada), but may also suitable for many first year post secondary programs.
Each App is built around the concept of spaced learning to help you study more efficiently and effectively.
- Base de datos. Se podrán buscar los compuestos más comunes en Química INORGÁNICA, por su fórmula o por alguno de sus nombres más comunes. Gracias a las búsquedas de los usuarios aumentará el número de compuestos químicos disponibles a diario.
- Ayuda. Cuenta con un resumen y ejemplos, que ayudan a comprender como se nombran y formulan los compuestos inorgánicos más comunes.
NOTE: ChemDoodle® Mobile is accessed with your ChemDoodle account that is provided to you for free when you purchase ChemDoodle desktop. You can use the Guest account to access this app without purchasing ChemDoodle, but you will not be able to save your drawings and some features may be restricted.
Full 3D graphics requires Android 5+, Lollipop.
Logging into your account enables the following:
1. IUPAC naming
2. Full 3D graphics (orthographic lines otherwise)
3. 1H NMR Spectra
4. Saving structures
Thank you for all the positive feedback! Please rate ChemDoodle Mobile 5 stars so we can continue to provide you with new and free features.
ChemDoodle Mobile is the Android companion to the popular chemical publishing desktop application, ChemDoodle. ChemDoodle Mobile is a calculator for drawn organic structures. There are five main windows: Draw, 3D, Calculate, Spectra and Help. The Draw window shows a typical ChemDoodle sketcher, where you can draw and store your structures. The 3D window allows you to view the drawn molecule in 3D. The Calculate page calculates properties and the Spectra page simulates NMR spectra. All spectra are interactive. The Help page contains a thorough help guide.
Please note that in the Android version, pinch gestures only work on platforms supporting Chrome for Android. Performance may vary depending on the Android device this app is run on. Recommended screen size of 320x480 pixels or greater.
1. IUPAC Name
2. Molecular Formula
3. Empirical Formula
4. Molecular Mass
5. Monoisotopic Mass
6. Degree of Unsaturation
7. Hydrogen Bond Acceptors
8. Hydrogen Bond Donors
9. Rotatable Bonds
10. Total Number of Electrons
11. Average Molecular Polarizability
12. Molar Refractivity
13. Polar Surface Area
14. van der Waals Volume
1. Mass Parent Peak (Isotopic Distribution)
2. 1H NMR
3. 13C NMR