How to use the app :
Card 1 :Find out what this molecule is and write one sentence about the molecule's geometry ?
Card 2 to 6 : Try to explain the following molecule's geometry. (hint : use Lewis, electrons pairs, lone pairs...)
Card 7 to 11 : answers for cards 2 to 6, showing molecule's geometry, electrons pair and lone pairs.
Card 12 : final answer for cards 1, molecule showing molecule's geometry, electrons pair and lone pairs.
Once downloaded this one does not require an Internet connection.
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.
== 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 firstname.lastname@example.org
=== 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/>.
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!
The chemistry tutorial topics include:
Hybridization geometry and bond angles
Sigma bonds and Pi bonds
Drawing Lewis dot structures
Fatty Acid Structures, Saturated/Unsaturated
Polyatomic Ion Structures
Chirality (handedness) of drugs
Lattice Energy (Born-Haber Cycle)
Electronic and molecular geometry
This application displays and allows you to interact (using the touchscreen to rotate) with a 3D molecular model of your choice.
You can choose a 3D model of the available molecules and interact with it by hitting the screen.
Furthermore, for each molecular model, there is information about it, you can consult.
If you want to watch a 3D model of molecules such as O2, N2, Ozone ... Do not waste time and try it!
As moléculas apresentadas podem ser manipuladas pelos usuários, permitindo a visualização por diferentes ângulos, assim como ampliar ou reduzir as estruturas, para que seja dado destaque em áreas de interesse. Cada molécula possui um texto explicativo.
Apoio: Sociedade Brasileria de Química (SBQ), INCT Energia e Ambiente e INCT Inomat
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
Introducing Chem Pro, the chemistry tutor in your pocket, and the only resource you will need to excel in AP Chemistry or General Chemistry this year. Chem Pro features an exclusive lesson library containing a total of 80 videos that cover the entire course of AP and General Chemistry. See what thousands of high school and college students across the world have been raving about. This life saving app is now available on Android!
Lessons: Struggling in your current chemistry course? Perhaps you need to review some material for an upcoming exam? Chem Pro contains over 31 hours of lesson videos, which makes it the perfect companion to have after you step out of the classroom. These lessons are dedicated to teaching students how to solve problems, the most important skill to master in order to excel in chemistry. In the videos, students are shown problems that are solved stepwise at a slow and easy to follow pace. The lessons don't just cover one example problem per topic, they cover all the possible problem scenarios that you would encounter in your homework or in an exam. Every topic is covered, from calculating molar masses to drawing Lewis structures to equilibrium. The first 10 lessons are bundled with the app for free and if you wish to continue learning, you can purchase and download the next pack of topics. Lesson videos are downloaded and saved to your device so you don't have to stream anything on the go. You can truly learn whenever and wherever you go.
Flash Cards: Chem Pro contains nine sets of flash cards specifically designed for what any student needs to memorize for a standard chemistry course. With these flash cards, you can easily memorize the 40 basic elements, the 21 common polyatomic ions, the common acid names, chemical colors (specifically for the AP Exam), and the 13 VSEPR molecular geometries. Simply select what you would like to memorize from the list of flash cards to begin memorizing. Just tap on each flash card and it flips around to show you the answer. Swipe back and forth to go to the previous or next card. It's that simple! What's even better is that every time you go to a flash card set, it automatically shuffles the order of the cards so that you can quiz yourself to make sure you know the material. This great feature can save you hours of time making index cards to memorize tedious chemistry concepts.
Chem Pro will not only teach you chemistry in a way you won't find in the classroom, but also provide you with several time saving tools you will love to use. Download and find out for yourself today!
If you have any questions, comments, suggestions, or concerns please feel free to email us at firstname.lastname@example.org
This app provides a visual approach to organic chemistry. It is not meant to replace a textbook - it should be seen as a visual aid. The molecules and reactions are just briefly described. The main focus are the numerous animations of the molecules and reactions. Currently only alkanes, alkenes and alkynes are described. You can test your knowledge through a quiz of 40 questions.
IMPORTANT: Hardware requirements - SCREEN SIZE > 3.7 inches and DUAL-CORE CPU!
The animations are strongly compressed in order to keep the app size small. This is why the animations only run on newer smartphones!
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
In Atomify you are in charge of the universe. You are God. You can control the temperature and size of your system to see how this affects the behavior of the atoms.
Six different systems are available for study: crystal, diffusion, chamber, fracture, wall crash and bullets.
The simulation is performed with a high performance molecular dynamics model with the Lennard-Jones potential using standard parameters for argon.
Developed by Anders Hafreager and Svenn-Arne Dragly (PhD candidates at the University of Oslo).
Source code is available from https://github.com/computationalphysics/molecules (GPL v3).
This app is produced by Calistry. Visit calistry.org to use hundreds of similar tools in the field of chemistry.
I currently am a college student working in my free time on creating some apps. The goal of this one is to get the feel of drawing interfaces/ working on an AI.
NOTE: I know the comp is easy, right now it just places them at random, though I have been working on a harder AI, and hope to have it out some time.
Please feel free to email me with tips/ ideas, everything is appreciated! :-)
Future upgrades to layout, and save features are in process of being added.
Image from http://self-help.thehappyguy.com/wp-content/uploads/2011/05/Report-Card.jpg