sodium in water
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SODIUM 1.5.1
SODIUM it arranges ions around biological macromolecules. more>>
This program places the required number of sodium ions around a system of electric charges, e.g., the atoms of a biological macromolecule (protein, DNA, protein/DNA complex).
The ions are placed in the nodes of a cubic grid, in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula is used for the energy:
Energy(R) = Sum(i_atoms,ions) Q_i / |R-R_i|
All the constants are dropped out from this formula, resulting in some weird energy units; that doesnt matter for the purpose of energy comparison. To speed the program up, the atoms of the macromolecule are re-located to the grid nodes, closest to their original locations.
The resulting error is believed to be minor, compared to that resulting from the one-by-one ions placement, or from using the simplified energy function. The coordinates of the placed ions are printed out in the PDB format for further usage.
It is recommended that the placed ions are equilibrated in a separate Monte Carlo or Molecular Dynamics simulation. Trivial modifications to the program should allow the placement of any combination of multivalent ions of different charges.
<<lessThe ions are placed in the nodes of a cubic grid, in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula is used for the energy:
Energy(R) = Sum(i_atoms,ions) Q_i / |R-R_i|
All the constants are dropped out from this formula, resulting in some weird energy units; that doesnt matter for the purpose of energy comparison. To speed the program up, the atoms of the macromolecule are re-located to the grid nodes, closest to their original locations.
The resulting error is believed to be minor, compared to that resulting from the one-by-one ions placement, or from using the simplified energy function. The coordinates of the placed ions are printed out in the PDB format for further usage.
It is recommended that the placed ions are equilibrated in a separate Monte Carlo or Molecular Dynamics simulation. Trivial modifications to the program should allow the placement of any combination of multivalent ions of different charges.
Download (0.40MB)
Added: 2005-04-01 License: Free To Use But Restricted Price:
1699 downloads
Dirty Water 0.1.0
Dirty Water project is a custom MUD server. more>>
Dirty Water project is a custom MUD server.
Dirty Water is an original MUD server/engine written in OCaml.
It is designed to be much more advanced and realistic and to encourage role playing more than Diku-style MUDs.
We are using a higher level language which we feel will yield a code-base that is significantly easier to modify, maintain and understand.
We felt that OCaml would make a good choice for this language, though we have since decided Scheme would be a better choice.
All of our code is licensed under the GNU GPL.
Enhancements:
- can pick up items
- can view inventory
- you can specify 1st, 2nd, etc when refering to items
- cant pick up buildings or yourself
- dont see yourself in room descriptions
<<lessDirty Water is an original MUD server/engine written in OCaml.
It is designed to be much more advanced and realistic and to encourage role playing more than Diku-style MUDs.
We are using a higher level language which we feel will yield a code-base that is significantly easier to modify, maintain and understand.
We felt that OCaml would make a good choice for this language, though we have since decided Scheme would be a better choice.
All of our code is licensed under the GNU GPL.
Enhancements:
- can pick up items
- can view inventory
- you can specify 1st, 2nd, etc when refering to items
- cant pick up buildings or yourself
- dont see yourself in room descriptions
Download (0.085MB)
Added: 2006-12-19 License: GPL (GNU General Public License) Price:
1041 downloads
run in xterm 0.9.1
run in xterm is an servcie menu which adds run in xterm & run in xterm as root to action menu on binary files, scripts etc. more>>
run in xterm is an servcie menu which adds "run in xterm" & "run in xterm as root" to action menu on binary files, scripts etc.
It has 2 languages: english and polish.
Installation:
copy/save this file in
~/.kde/share/apps/konqueror/servicemenus
<<lessIt has 2 languages: english and polish.
Installation:
copy/save this file in
~/.kde/share/apps/konqueror/servicemenus
Download (MB)
Added: 2006-06-12 License: GPL (GNU General Public License) Price:
1230 downloads
Easiest Edit In Place 1.2
Easiest Edit In Place enables Web (2.0) developers to generate any number of edit in place widgets. more>>
Easiest Edit In Place enables Web (2.0) developers to generate any number of edit in place widgets with only one line of script code.
Using stylesheets and spans, any piece of text can be edited by any type of widget. Easiest Edit In Place features CSS customization and automatic caret positioning.
Main features:
- It requires only 1 line of javascript to make any number of widgets editable.
- Caret positioning. When editing inline, the caret is positioned at the point the user clicked, to make it more intuitive.
- Editor can be anything, from ordinary text input to text areas or custom widgets.
- Everything can be styled using CSS.
Eeip has been tested on Firefox and IE.
Enhancements:
- A bug that could lead to the accidental display of placeholder text when dealing with empty fields in some circumstances was fixed.
<<lessUsing stylesheets and spans, any piece of text can be edited by any type of widget. Easiest Edit In Place features CSS customization and automatic caret positioning.
Main features:
- It requires only 1 line of javascript to make any number of widgets editable.
- Caret positioning. When editing inline, the caret is positioned at the point the user clicked, to make it more intuitive.
- Editor can be anything, from ordinary text input to text areas or custom widgets.
- Everything can be styled using CSS.
Eeip has been tested on Firefox and IE.
Enhancements:
- A bug that could lead to the accidental display of placeholder text when dealing with empty fields in some circumstances was fixed.
Download (0.013MB)
Added: 2007-03-08 License: BSD License Price:
962 downloads
Open Source in Tab 1.5
Open Source in Tab is an extension which opens the pages source file in a new tab. more>>
Open Source in Tab is an extension which opens the pages source file in a new tab.
Opens the pages source file in a new tab. Has a preference to either open source in a new tab or existing tab.
<<lessOpens the pages source file in a new tab. Has a preference to either open source in a new tab or existing tab.
Download (0.008MB)
Added: 2007-04-19 License: MPL (Mozilla Public License) Price:
550 downloads
Set photo in Kopete 0.1
Set photo in Kopete is a really simple service menu that just sets the current photo as your photo in Kopete. more>>
Set photo in Kopete is a really simple service menu that just sets the current photo as your photo in Kopete, nothing more, nothing less.
It doesnt handle directories containing space yet, if someone have a workaround so that KURL dont escapes all characters that would be nice=)
Just put this file in ~/.kde/share/apps/konqueror/servicemenus or use http://www.kde-look.org/content/show.php?content=11435 to install it.
<<lessIt doesnt handle directories containing space yet, if someone have a workaround so that KURL dont escapes all characters that would be nice=)
Just put this file in ~/.kde/share/apps/konqueror/servicemenus or use http://www.kde-look.org/content/show.php?content=11435 to install it.
Download (MB)
Added: 2007-02-05 License: GPL (GNU General Public License) Price:
993 downloads
Cookie Button in the status bar0.8.9
Cookie Button in the status bar is a Firefox button for easy access to cookie permissions in the status bar. more>>
Cookie Button in the status bar is a Firefox button for easy access to cookie permissions in the status bar. For those who have been asking for cookie button in the status bar.
Some features are optional. See Tools -> Extensions/Addons, select Cookie button in the status bar, press Options/Preference Button.
Please post more info about the context menu bug to http://bugzilla.mozdev.org/show_bug.cgi?id=15011
<<lessSome features are optional. See Tools -> Extensions/Addons, select Cookie button in the status bar, press Options/Preference Button.
Please post more info about the context menu bug to http://bugzilla.mozdev.org/show_bug.cgi?id=15011
Download (0.025MB)
Added: 2007-07-28 License: MPL (Mozilla Public License) Price:
820 downloads
Ghost In The Mail 0.5
Ghost In The Mail is an anonymous e-mail client for linux written in C and designed in GTK+ 2. more>>
Ghost In The Mail is an anonymous e-mail client for linux written in C and designed in GTK+ 2. Look at the screenshots below to have a better idea of how does it works.
This piece of software allows to send e-mails to any person over the net with a fake email address, and also a fake name. Obviously you can use your true identity. gitmail can also send attached files. Ghost In The Mail uses MIME and Base64 technologies.
Enhancements:
- Full review of the code in order to improve stability and performances.
- Rewrite of all functions that contained malloc(CONST_VAL).
- Added functions gitm_malloc & gitm_realloc that check pointers after allocating them.
- Added some commentaries to describe functions.
- New sources files: functions are distributed into files in a more logical way.
- Files cbbentries.* removed (functions in cbbentries.* are now in history.*) Better core/gui splitting.
- Created a constant GITM_VERSION to hold the version number.
- MIME boundary is now randomly generated.
- Server errors are fully displayed.
<<lessThis piece of software allows to send e-mails to any person over the net with a fake email address, and also a fake name. Obviously you can use your true identity. gitmail can also send attached files. Ghost In The Mail uses MIME and Base64 technologies.
Enhancements:
- Full review of the code in order to improve stability and performances.
- Rewrite of all functions that contained malloc(CONST_VAL).
- Added functions gitm_malloc & gitm_realloc that check pointers after allocating them.
- Added some commentaries to describe functions.
- New sources files: functions are distributed into files in a more logical way.
- Files cbbentries.* removed (functions in cbbentries.* are now in history.*) Better core/gui splitting.
- Created a constant GITM_VERSION to hold the version number.
- MIME boundary is now randomly generated.
- Server errors are fully displayed.
Download (0.37MB)
Added: 2006-02-20 License: GPL (GNU General Public License) Price:
1347 downloads
Sidebar in a Can 1.0.1
Sidebar in a Can is a tool for webmasters to take a large amount of static content and turn it into a dynamic content. more>>
Sidebar in a Can is a simple and powerful tool for webmasters to take a large amount of static content (intimidating to new users) and turn it into a quite manageable amount of dynamic content. The result showcases your sites material.
Sidebar in a Can is built on Snippets technology.
Sidebar in a Can is designed to be run as a straightforward web application, with much administrative activity performed on-web. Rather than trying to explain how to use it, I simply encourage you to explore.
Security
The present release of Sidebar in a Can has not been closely scrutinized for security, and should be treated as such by security-conscious administrators. If you examine the code and discover a vulnerability that could compromise the server, please contact the author at jshayward@pobox.com. The script is intended to have light security and not to compromise a server, but it is not intended to store credit card numbers or other sensitive information.
The default installation sets < the private sidebar data directory > and contents to mode 777. Administrators are encouraged to set directory and contents to mode 700, owned by the effective user ID that Snippets will be running under.
<<lessSidebar in a Can is built on Snippets technology.
Sidebar in a Can is designed to be run as a straightforward web application, with much administrative activity performed on-web. Rather than trying to explain how to use it, I simply encourage you to explore.
Security
The present release of Sidebar in a Can has not been closely scrutinized for security, and should be treated as such by security-conscious administrators. If you examine the code and discover a vulnerability that could compromise the server, please contact the author at jshayward@pobox.com. The script is intended to have light security and not to compromise a server, but it is not intended to store credit card numbers or other sensitive information.
The default installation sets < the private sidebar data directory > and contents to mode 777. Administrators are encouraged to set directory and contents to mode 700, owned by the effective user ID that Snippets will be running under.
Download (0.056MB)
Added: 2007-02-23 License: GPL (GNU General Public License) Price:
973 downloads
Ogrian Carpet 0.9
Ogrian Carpet is a 3D fantasy action/strategy game. more>>
Ogrian Carpet project is a 3D fantasy action/strategy game.
Ogrian Carpet is an outdoor first person shooter game with real time strategy elements, inspired by the game Magic Carpet.
It uses Ogre3D as the renderer and allows you to fly around an island casting spells, summoning monsters, collecting mana, and building castles.
The object of the game is to build a castle, collect mana, and destroy your enemies. To build a castle, select a location, look at the ground, and cast the build spell. Note, you cannot build castles very close to water or other castles.
Your castle starts out small, with only one turret. As more mana is added to your castle, it will gain more turrets. Each turret adds another crane to your castles defense and another spell to your arsenal.
Basically, the game consists of fighting for control of mana. Whenever you encounter another wizard, shoot them with fireballs. If you hit them enough, they will "die" and be sent back to their castle. You are then free to claim all the mana in the area for yourself.
Once all the mana has been claimed, attack your enemys castle to get mana out of it so you can claim it for yourself. Once you enemys castle is out of mana, you can eliminate it by killing its heart. When all of your opponents have been banished, youve won.
Enhancements:
- AI bot player for skirmish
- things can now be loaded from an image, rather then randomly
- option for old randomized maps
- trees can now always bee seen
- made castle mana drops aggregate more
- loosened the restrictions on summoning
- made the config menu better
- added victory conditions to skirmish: kill all enemy towers/castles
- made ticks and gnomes stay in the formation you put them in
- made monsters and towers drop less then their cost when they have no wizard
- made mana float higher
- made towers cheaper (50)
- made sentinels drop much less (3)
- changed speed behavior on lava maps
- added victory music
- new music
<<lessOgrian Carpet is an outdoor first person shooter game with real time strategy elements, inspired by the game Magic Carpet.
It uses Ogre3D as the renderer and allows you to fly around an island casting spells, summoning monsters, collecting mana, and building castles.
The object of the game is to build a castle, collect mana, and destroy your enemies. To build a castle, select a location, look at the ground, and cast the build spell. Note, you cannot build castles very close to water or other castles.
Your castle starts out small, with only one turret. As more mana is added to your castle, it will gain more turrets. Each turret adds another crane to your castles defense and another spell to your arsenal.
Basically, the game consists of fighting for control of mana. Whenever you encounter another wizard, shoot them with fireballs. If you hit them enough, they will "die" and be sent back to their castle. You are then free to claim all the mana in the area for yourself.
Once all the mana has been claimed, attack your enemys castle to get mana out of it so you can claim it for yourself. Once you enemys castle is out of mana, you can eliminate it by killing its heart. When all of your opponents have been banished, youve won.
Enhancements:
- AI bot player for skirmish
- things can now be loaded from an image, rather then randomly
- option for old randomized maps
- trees can now always bee seen
- made castle mana drops aggregate more
- loosened the restrictions on summoning
- made the config menu better
- added victory conditions to skirmish: kill all enemy towers/castles
- made ticks and gnomes stay in the formation you put them in
- made monsters and towers drop less then their cost when they have no wizard
- made mana float higher
- made towers cheaper (50)
- made sentinels drop much less (3)
- changed speed behavior on lava maps
- added victory music
- new music
Download (20.0MB)
Added: 2006-12-11 License: GPL (GNU General Public License) Price:
1049 downloads
Gnome Play Video in Totem 0.1
Gnome Play Video in Totem allows Gnome Users to view video or audio externally in Totem. more>>
Many users prefer Gnome Window Manager but cant go without Amarok. Gnome Play Video in Totem allows Gnome Users to view video or audio externally in Totem.
This is very useful for Video Podcasts.
<<lessThis is very useful for Video Podcasts.
Download (MB)
Added: 2006-07-17 License: GPL (GNU General Public License) Price:
1200 downloads
Filesystem in Userspace 2.7.0
Filesystem in Userspace is an interface for filesystems implemented in userspace. more>>
FUSE can implement a fully functional filesystem in a userspace program.
Main features:
- Simple library API
- Simple installation (no need to patch or recompile the kernel)
- Secure implementation
- Userspace - kernel interface is very efficient
- Usable by non privileged users
- Runs on Linux kernels 2.4.X and 2.6.X
- Has proven very stable over time
Installation
Some projects include the whole FUSE package (for simpler installation). In other cases or just to try out the examples FUSE must be installed first. The installation is simple, after unpacking enter:
./configure
make
make install
If this produces an error, please read on.
The configure script will try to guess the location of the kernel source. In case this fails, it may be specified using the --with-kernel parameter. Building the kernel module needs a configured kernel source tree matching the running kernel. If you build your own kernel this is no problem. On the other hand if a precompiled kernel is used, the kernel headers used by the FUSE build process must first be prepared. There are two possibilities:
1. A package containing the kernel headers for the kernel binary is available in the distribution (e.g. on Debian its the kernel-headers-X.Y.Z package for kernel-image-X.Y.Z)
2. The kernel source must be prepared:
- Extract the kernel source to some directory
- Copy the running kernels config (usually found in /boot/config-X.Y.Z) to .config at the top of the source tree
- Run make menuconfig, then make dep at the top of the source tree (only needed on 2.4 kernels)
If using the 2.6 kernel, then write access is needed to some files in the kernel source tree. Usually it is enough if you make .tmp_versions and .__modpost.cmd writable.
Enhancements:
- Stacking support for the high level API
- Add filename charset conversion module
- Improved mounting
<<lessMain features:
- Simple library API
- Simple installation (no need to patch or recompile the kernel)
- Secure implementation
- Userspace - kernel interface is very efficient
- Usable by non privileged users
- Runs on Linux kernels 2.4.X and 2.6.X
- Has proven very stable over time
Installation
Some projects include the whole FUSE package (for simpler installation). In other cases or just to try out the examples FUSE must be installed first. The installation is simple, after unpacking enter:
./configure
make
make install
If this produces an error, please read on.
The configure script will try to guess the location of the kernel source. In case this fails, it may be specified using the --with-kernel parameter. Building the kernel module needs a configured kernel source tree matching the running kernel. If you build your own kernel this is no problem. On the other hand if a precompiled kernel is used, the kernel headers used by the FUSE build process must first be prepared. There are two possibilities:
1. A package containing the kernel headers for the kernel binary is available in the distribution (e.g. on Debian its the kernel-headers-X.Y.Z package for kernel-image-X.Y.Z)
2. The kernel source must be prepared:
- Extract the kernel source to some directory
- Copy the running kernels config (usually found in /boot/config-X.Y.Z) to .config at the top of the source tree
- Run make menuconfig, then make dep at the top of the source tree (only needed on 2.4 kernels)
If using the 2.6 kernel, then write access is needed to some files in the kernel source tree. Usually it is enough if you make .tmp_versions and .__modpost.cmd writable.
Enhancements:
- Stacking support for the high level API
- Add filename charset conversion module
- Improved mounting
Download (0.47MB)
Added: 2007-07-04 License: GPL (GNU General Public License) Price:
845 downloads
Filler in Java 1.02
Filler in Java project is a graphical game where you occupy coloured hexes by changing colours. more>>
Filler in Java project is a graphical game where you occupy coloured hexes by changing colours.
Its strengths are better computer players, internationalisability, and cross-platform deployability.
Installing
In the top directory (same directory as this file), run make. That will build a jar file for you. You then need to be super-user (root), and run make install. If you cant be super-user, just do java -jar filler.jar instead.
The executable program is called filler, and will be installed in /usr/local/bin. Since release 1.01, filler will use your shell variable LANG to set the language that it runs in.
Enhancements:
- Added inc to other directory. This is the code header you include to say that the code is released under GPL.
- Removed resources_de.properties, resources_fr.properties, as I wrote them and they were pretty bad.
- Added sortByRandom() to PlayerWrappers.
- Added build.xml to other. This is for use with ant.
- Cleaned up some access privileges on some fields, cleaned up some bad identifiers.
- Added Kris Verbeecks RemotePlayer.
<<lessIts strengths are better computer players, internationalisability, and cross-platform deployability.
Installing
In the top directory (same directory as this file), run make. That will build a jar file for you. You then need to be super-user (root), and run make install. If you cant be super-user, just do java -jar filler.jar instead.
The executable program is called filler, and will be installed in /usr/local/bin. Since release 1.01, filler will use your shell variable LANG to set the language that it runs in.
Enhancements:
- Added inc to other directory. This is the code header you include to say that the code is released under GPL.
- Removed resources_de.properties, resources_fr.properties, as I wrote them and they were pretty bad.
- Added sortByRandom() to PlayerWrappers.
- Added build.xml to other. This is for use with ant.
- Cleaned up some access privileges on some fields, cleaned up some bad identifiers.
- Added Kris Verbeecks RemotePlayer.
Download (0.37MB)
Added: 2006-12-27 License: GPL (GNU General Public License) Price:
1034 downloads
Claros In Touch 2.0
Claros In Touch is a webmail, address book, calendar, and notebook application. more>>
Claros In Touch is a webmail, address book, calendar, and notebook application. Claros In Touch aims to fulfill the need for a stable, full featured messaging application.
Main features:
- Bayesian Spam protection (no need to do setting on mail server, it is bundled with the webmail)
- Message Filtering (custom filters can be applied to the incoming mail)
- Its is developed using Apache Struts, Apache Commons, Claros Commons, JSP and Servlet technology.
- Folder support on the POP3 protocol. (It simulates the IMAP folders by database)
- No need to do database setup (indeed it supports any JDBC compliant database engine), it comes bundled with a ready to run database engine. (Look: http://www.hsqldb.org)
- It is compatible with any standarts compliant POP3 and SMTP server. (No IMAP)
- Operating system independent. Written with regular JSP and servlets.
- Can send HTML e-mail (DHTML based HTML editor included)
- Fully MIME compatible (can read any HTML e-mail)
- An address book aplication
- An advanced notebook application
- A calendar application, with daily, weekly, monthly views and reminder facilities etc...
Enhancements:
- The UI was improved.
- A preference window was added.
- More languages were added.
- Internet Explorer compatibility problems were fixed.
- POP3 mode was re-engineered. List titles were fixed.
- Attachment handling and the drag-drop system were improved.
- Message headers are now shown correctly.
- Message arrived (sound) notification was added.
- A paging system was introduced.
- Inline HTML messages are now shown correctly.
- A HTML sanitizer was added to prevent hacking.
- An address book was added.
- A chat module was added.
- Performance was improved.
- Less system resources are used.
<<lessMain features:
- Bayesian Spam protection (no need to do setting on mail server, it is bundled with the webmail)
- Message Filtering (custom filters can be applied to the incoming mail)
- Its is developed using Apache Struts, Apache Commons, Claros Commons, JSP and Servlet technology.
- Folder support on the POP3 protocol. (It simulates the IMAP folders by database)
- No need to do database setup (indeed it supports any JDBC compliant database engine), it comes bundled with a ready to run database engine. (Look: http://www.hsqldb.org)
- It is compatible with any standarts compliant POP3 and SMTP server. (No IMAP)
- Operating system independent. Written with regular JSP and servlets.
- Can send HTML e-mail (DHTML based HTML editor included)
- Fully MIME compatible (can read any HTML e-mail)
- An address book aplication
- An advanced notebook application
- A calendar application, with daily, weekly, monthly views and reminder facilities etc...
Enhancements:
- The UI was improved.
- A preference window was added.
- More languages were added.
- Internet Explorer compatibility problems were fixed.
- POP3 mode was re-engineered. List titles were fixed.
- Attachment handling and the drag-drop system were improved.
- Message headers are now shown correctly.
- Message arrived (sound) notification was added.
- A paging system was introduced.
- Inline HTML messages are now shown correctly.
- A HTML sanitizer was added to prevent hacking.
- An address book was added.
- A chat module was added.
- Performance was improved.
- Less system resources are used.
Download (9.1MB)
Added: 2007-06-08 License: MPL (Mozilla Public License) Price:
924 downloads
Open Directory in VLC 1.0
Open Directory in VLC is just a modified version of the Open in Kaffeine service menu. more>>
Open Directory in VLC is just a modified version of the Open in Kaffeine service menu.
I use it to open DVD/VIDEO_TS folders. VLC plays them with menus in tact.
<<lessI use it to open DVD/VIDEO_TS folders. VLC plays them with menus in tact.
Download (MB)
Added: 2007-06-06 License: GPL (GNU General Public License) Price:
891 downloads
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