Archive for the ‘Java’ Category

PaDEL-ADV

Monday, November 9th, 2009

Introducing another new software, PaDEL-ADV. This is a software to perform virtual screening using AutoDock Vina.

PaDEL-ADV reads a directory containing ligands files. For each ligand, the structural file is converted into a pdb file, if necessary, using The Chemistry Development Kit. The pdb file is then converted to pdbqt using the prepare_ligand4.py script provided by AutoDockTools. AutoDock Vina is then used to dock the ligand with the receptor. Individual binding modes are extracted from the output pdbqt file using vina_split. The pdbqt files are then converted to pdb files using the pdbqt_to_pdb.py script provided by AutoDockTools. Results for each binding modes are extracted from the log file and placed into the results CSV file. The log file and all the related pdb and pdbqt files are then compressed into a zip file.

PaDEL-Crypt

Saturday, October 25th, 2008

Announcing another product from my laboratory. PaDEL-Crypt is a portable software for encrypting and decrypting files. The encrypted files are stored in a vault and can only be viewed and decrypted using a correct password. The main intended use of PaDEL-Crypt is to encrypt files in portable devices like flash drives or portable hard disks, so as to maintain data confidentiality in the event of accidental loss of such devices. The targeted users are those who do not have much knowledge about encryption but wish to have a simple solution for adding encryption to their portable devices.

At the current moment, PaDEL-Crypt will run on any platform that have Java installed. Once I figure out how to run GCJ, I will make a native version for Windows so that Java will no longer need to be installed in the target machine. In the meantime, you can use the Java Portablizer to copy the Java JRE to your portable device and make a batch file to make PaDEL-Crypt use that version to run.

It might seem strange why my laboratory, which focuses on applying knowledge discovery and data mining techniques to pharmaceutical and biomedical areas, would produce a product like PaDEL-Crypt. Well, data confidentiality is an important issue in many areas, including the pharmaceutical and biomedical areas. Flash drives are so popular nowadays that most of us have at least one with us. However, most of us did not bother to encrypt the data that are stored in it, which is disturbing because flash drives are easily lost. Although most of the information that we put on flash drives are usually not confidential, there might be some that are confidential and it is important to protect these.

Before developing PaDEL-Crypt, I have looked at a few solutions in the market, including those that come with the flash drives. However, most of these solutions are usable only on Microsoft Windows and are not strictly portable (they leave behind information on the target machine). Thus I decided to develop my own using Java. PaDEL-Crypt is not meant to replace other encryption system for harddisks, like TrueCrypt. Rather, it is meant to complement these systems, which are not portable because they require administrative privileges on the target machine to run. PaDEL-Crypt will be an ideal solution to carry or distribute your encrypted files via portable devices or email. As PaDEL-Crypt can also create self-decrypting archives, the target machine does not even require PaDEL-Crypt to be present in order to decrypt the files.

PaDEL-Crypt is basically free for all to use, with the exception of one group of people. Please see the license conditions at its homepage to find out more.

PaDEL-Descriptor

Saturday, August 2nd, 2008

Introducing the first product from my laboratory, PaDEL-Descriptor. It is a software to calculate molecular descriptors and fingerprints. The software currently calculates 393 descriptors (290 1D, 2D descriptors and 103 3D descriptors) and 5 types of fingerprints. The descriptors and fingerprints are calculated using The Chemistry Development Kit with some in-house addition for electrotopological descriptors. All the different types of descriptors are calculated in parallel to take full advantage of the multi-core CPUs that are commonly found nowadays. The usage instructions can be found on the website itself. This software is free for all (e.g. personal, academic, non-profit, non-commercial, government, commercial, etc) to use.

The software is Java Web Start ready. What this means is that if you have Java JRE installed on your computer (which most people should have by now), you can just click on a link on the website to launch the software directly. A copy of the software will automatically be downloaded, stored on your computer and run. You can create a shortcut to this software on your desktop. When you click on this shortcut and if you are online, Java Web Start will automatically check if there is a new version of the software available. If there is, it will download it before running the software. If you are offline, Java Web Start will just run your local copy. The main advantage of Java Web Start is that it will always ensure that you are running the latest version of the software (if you are online). If I have the time, I will give a short writeup on how to make your own Java software Java Web Start ready. It is really very easy if you are using NetBeans.


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