sodium 1.5.1
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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
Daisy 1.5.1
Daisy project consists of a CMS framework. more>>
Daisy project consists of a CMS framework.
Daisy is a content management application framework. It provides a standalone, HTTP/XML-accessible repository server and an Apache Cocoon-based, Wiki-like Web-based client application.
Daisy is a comprehensive content management application framework, consisting of a standalone repository server accessible through HTTP/XML (using the ReST style of WebServices) and/or a high-level (remote) Java API, and an extensive browsing and editing DaisyWiki application running inside Apache Cocoon.
Daisy is licensed under the commercially-friendly Apache License 2.0. Outerthought provides commercial services around Daisy.
Enhancements:
- Added characterEncoding=UTF-8 parameter to the MySQL JDBC URL, which is needed for correct UTF-8 support when UTF-8 is not the default character set of the MySQL server.
- Fixed a "NullPointerException" that occured when using a field with a static selection list with labels for the list items, but not for the language of the active user.
- Fixed the remaining issues that prevented installing Daisy in a directory containing spaces (such as c:Program Files)
<<lessDaisy is a content management application framework. It provides a standalone, HTTP/XML-accessible repository server and an Apache Cocoon-based, Wiki-like Web-based client application.
Daisy is a comprehensive content management application framework, consisting of a standalone repository server accessible through HTTP/XML (using the ReST style of WebServices) and/or a high-level (remote) Java API, and an extensive browsing and editing DaisyWiki application running inside Apache Cocoon.
Daisy is licensed under the commercially-friendly Apache License 2.0. Outerthought provides commercial services around Daisy.
Enhancements:
- Added characterEncoding=UTF-8 parameter to the MySQL JDBC URL, which is needed for correct UTF-8 support when UTF-8 is not the default character set of the MySQL server.
- Fixed a "NullPointerException" that occured when using a field with a static selection list with labels for the list items, but not for the language of the active user.
- Fixed the remaining issues that prevented installing Daisy in a directory containing spaces (such as c:Program Files)
Download (MB)
Added: 2007-01-22 License: The Apache License Price:
1010 downloads
AUSTRUMI 1.5.1
AUSTRUMI is a business card size (50MB) bootable Live CD Linux distribution. more>>
AUSTRUMI is a bootable Live CD Linux distribution with a business card size (50MB). Imagine the ability to boot your favorite Linux distribution whether you are at home, at school or at work.
Main features:
Graphic
- gqview - image browser
- gimp - Image Manipulation Program
- inkscape - SVG editor
Office
- gcalctool - graphical calculator
- abiword - word processor
- gnumeric - spreadsheet editor
- stardict - dictionary
- bluefish - html editor
- gv - a PostScript and PDF previewer
Network
- nmap - network scaner
- ettercap - sniffer/interceptor/logger for LAN
- airsnort - wireless LAN (WLAN) tool
- gspoof - sending tool of TCP/IP packets
- hydra - login cracker
- LinNeighborhood - samba client
- tsclient - frontend for rdesktop and vncviewer
- telnet - telnet client
- gputty - ssh client
- mtr - traceroute
Internet
- firefox - WWW browser
- gftp - ftp client
- skype - free internet telephony
- gitmail - mail client
- apache - Web server
- vsftpd - ftp server
- xmail - mail server
Multimedia
- mplayer - movie player
- simplecdrx - CD creation and audio manipulation program
Games
- ltris - classic Tetris clone
- atomix - logical game
- xboard:phalanx - chess
- gnomine - variation of minesweeper
- gtkballs - clone of well-known DOS game "Lines"
- gsoko - logical game
- icebreaker - clasic Xonix clone
Other
- emelfm - file manager
- rxvt - color VT102 terminal emulator
- htop - task manager
- xproc - system information
- partimage - partition imaging utility
- voarti - firewall/router
- gtkfind - graphical file finding program
- turma - search (and replace) text
- xfdiff4 - graphical diff frontend
- hexedit - shows/modify a file both in ASCII and in hexadecimal
- gcrontab - a crontab editor
<<lessMain features:
Graphic
- gqview - image browser
- gimp - Image Manipulation Program
- inkscape - SVG editor
Office
- gcalctool - graphical calculator
- abiword - word processor
- gnumeric - spreadsheet editor
- stardict - dictionary
- bluefish - html editor
- gv - a PostScript and PDF previewer
Network
- nmap - network scaner
- ettercap - sniffer/interceptor/logger for LAN
- airsnort - wireless LAN (WLAN) tool
- gspoof - sending tool of TCP/IP packets
- hydra - login cracker
- LinNeighborhood - samba client
- tsclient - frontend for rdesktop and vncviewer
- telnet - telnet client
- gputty - ssh client
- mtr - traceroute
Internet
- firefox - WWW browser
- gftp - ftp client
- skype - free internet telephony
- gitmail - mail client
- apache - Web server
- vsftpd - ftp server
- xmail - mail server
Multimedia
- mplayer - movie player
- simplecdrx - CD creation and audio manipulation program
Games
- ltris - classic Tetris clone
- atomix - logical game
- xboard:phalanx - chess
- gnomine - variation of minesweeper
- gtkballs - clone of well-known DOS game "Lines"
- gsoko - logical game
- icebreaker - clasic Xonix clone
Other
- emelfm - file manager
- rxvt - color VT102 terminal emulator
- htop - task manager
- xproc - system information
- partimage - partition imaging utility
- voarti - firewall/router
- gtkfind - graphical file finding program
- turma - search (and replace) text
- xfdiff4 - graphical diff frontend
- hexedit - shows/modify a file both in ASCII and in hexadecimal
- gcrontab - a crontab editor
Download (50MB)
Added: 2007-07-02 License: GPL (GNU General Public License) Price:
638 downloads
sdts++ 1.5.1
SDTS++ is a C++ toolkit that programmers can use to write applications that can read or write SDTS datasets. more>>
SDTS++ is a C++ toolkit that programmers can use to write applications that can read or write SDTS datasets.
Application developers can use SDTS++ library classes to work with the logical structure of these datasets without having to worry about the physical details of each dataset.
What compilers does it work with?
SDTS++ is known to work with:
- GNU g++ 2.8.x and 2.95.x
- egcs 1.x.y
- Microsoft Visual C++ 6.0 (Apply latest service pack!)
<<lessApplication developers can use SDTS++ library classes to work with the logical structure of these datasets without having to worry about the physical details of each dataset.
What compilers does it work with?
SDTS++ is known to work with:
- GNU g++ 2.8.x and 2.95.x
- egcs 1.x.y
- Microsoft Visual C++ 6.0 (Apply latest service pack!)
Download (0.88MB)
Added: 2006-05-24 License: Freeware Price:
1252 downloads
ModAssy 1.5.1
This is an advanced portable C++ library with 80 variations of the ASSERT macro, to add expressions, levels and optional actions. 48 are modular because they can also use Rich Boolies, allowing much more combinations than non-modular ASSERT macros. It is very flexible because it allows you to create custom loggers and assertion displayers, but you can also use the provided ones for Windows, wxWidgets or console applications. more>>
ModAssy - This is an advanced portable C++ library with 80 variations of the ASSERT macro, to add expressions, levels and optional actions. 48 are modular because they can also use Rich Boolies, allowing much more combinations than non-modular ASSERT macros. It is very flexible because it allows you to create custom loggers and assertion displayers, but you can also use the provided ones for Windows, wxWidgets or console applications. The loggers and displayers show extra information, like the date and time, the thread id, the current working directory, etc. and you can add infoprovider objects to ModAssy, to provide similar custom information.
It has eight basic assertions, that each have 16 variations, by adding four suffixes that add functionality.
It is very reliable and portable, as it has been tested with five different compilers (VC++ 6.0, .NET 2003, .NET 2005, gcc on Windows and Linux), with nearly all warnings enabled.
The Rich Boolies can do all kinds of checks and generate elaborate information:
* Relations between two objects: rbEQUAL, rbLESS, ...
* Bitwise comparisons: rbEQUAL_BITWISE, rbBITS_ON, rbBITS_OFF, ...
* Type checking (with RTTI): rbEQUAL_TYPES, rbHAS_TYPE, ...
* Working on ranges and containers: rbIN_RANGE, rbIN_RANGES, rbIN_CONTAINER, rbIN_CONTAINERS, ... These have an extra argument that tells what kind of check to do, e.g. Sorted, Compare, Has, Unique, ...
* String comparisons: rbSTRING, rbSTRING_BEGINS_WITH, rbSTRING_ENDS_WITH, rbSTRING_CONTAINS. These have an extra argument that tells what kind of check to do, e.g. case sensitive or not.
* Logical expressions: rbAND, rbOR, rbXOR. These can have Rich Boolies or plain boolean expressions as their arguments.
* Exceptions: rbEXCEPTION takes an exception as its argument, and uses the information in it.
Enhancements:
Version 1.5.1
System Requirements:<<less
Download (1000.7Kb)
Added: 2006-10-15 License: Free Price: Free
15 downloads
bksys 1.5.1
bksys is a framework based on scons for detecting the environment, compiling applications and installing them. more>>
bksys is a framework based on scons for detecting the environment, compiling applications and installing them.
It replaces the whole GNU autotool chain (automake, autoconf, aclocal, autoheader, libtool) and depends on python only. It features kde3, qt4 and wxwidgets examples.
The scripts are currently used by many kde projects like rosegarden, kdissert, codeine, kshaderdesigner or linpacker.
Enhancements:
- Split between builddir and srcdir
- New logging function to enable or disable the coloured output (enabled by default)
- Most of the generic code (dist, distclean) was moved to the modules
<<lessIt replaces the whole GNU autotool chain (automake, autoconf, aclocal, autoheader, libtool) and depends on python only. It features kde3, qt4 and wxwidgets examples.
The scripts are currently used by many kde projects like rosegarden, kdissert, codeine, kshaderdesigner or linpacker.
Enhancements:
- Split between builddir and srcdir
- New logging function to enable or disable the coloured output (enabled by default)
- Most of the generic code (dist, distclean) was moved to the modules
Download (0.15MB)
Added: 2005-08-18 License: BSD License Price:
1528 downloads
g3data 1.5.1
g3data is a program for extracting data from graphs. more>>
g3data is used for extracting data from graphs. In publications data is usually presented as graphs, while the actual data is often missing. The project makes the extracting process much easier. The commercially available alternative is called data thief.
Main features:
- Zoom windows for maximum accuracy
- Can handle logarithmic scales and non-ortogonal graphs
- Tabbed processing of multiple images consequetively
Enhancements:
- Added basic drag-n-drop support, current version only supports uri drops.
- Added preliminary basis for datapoint movement.
- Some of the graph properties are now hideable, to resolv issues on lower resolution screens.
<<lessMain features:
- Zoom windows for maximum accuracy
- Can handle logarithmic scales and non-ortogonal graphs
- Tabbed processing of multiple images consequetively
Enhancements:
- Added basic drag-n-drop support, current version only supports uri drops.
- Added preliminary basis for datapoint movement.
- Some of the graph properties are now hideable, to resolv issues on lower resolution screens.
Download (0.048MB)
Added: 2007-03-16 License: GPL (GNU General Public License) Price:
957 downloads
Meld 1.1.5.1
Meld is a GNOME 2 diff and merge tool. more>>
Meld is a visual diff and merge tool. Meld project integrates especially well with CVS. The diff viewer lets you edit files in place (diffs update dynamically), and a middle column shows detailed changes and allows merges.
The margins show location of changes for easy navigation, and it also features a tabbed interface that allows you to open many diffs at once.
Look at the screenshots page for more detailed features.
<<lessThe margins show location of changes for easy navigation, and it also features a tabbed interface that allows you to open many diffs at once.
Look at the screenshots page for more detailed features.
Download (0.63MB)
Added: 2007-06-13 License: GPL (GNU General Public License) Price:
867 downloads
GPLIGC 1.5.1
GPLIGC is a software package for glider* pilots. more>>
GPLIGC is a software package for glider* pilots. IGC flight data files can be analysed and visualised.
The package contains two components:
*and all others who want to view GPS track logs (para-glider pilots, hang-glider pilots and even pilots of radio-controlled (sail)planes.
- GPLIGC, analysation
- openGLIGCexplorer, 3d visualisation (can be used as a viewer for digital elevation data too)
GPLIGC can be used on Linux, Unix, Windows and Mac OS X.
GPLIGC application can be used under the terms of the GNU General Public License (GPL).
Enhancements:
- This release fixes a few bugs.
- Some options were added that allow you to specify a destination folder and filenames for screenshots.
- The background colors (including gradients) can be changed.
<<lessThe package contains two components:
*and all others who want to view GPS track logs (para-glider pilots, hang-glider pilots and even pilots of radio-controlled (sail)planes.
- GPLIGC, analysation
- openGLIGCexplorer, 3d visualisation (can be used as a viewer for digital elevation data too)
GPLIGC can be used on Linux, Unix, Windows and Mac OS X.
GPLIGC application can be used under the terms of the GNU General Public License (GPL).
Enhancements:
- This release fixes a few bugs.
- Some options were added that allow you to specify a destination folder and filenames for screenshots.
- The background colors (including gradients) can be changed.
Download (0.85MB)
Added: 2007-04-24 License: GPL (GNU General Public License) Price:
548 downloads
LyX 1.5.1
LyX is the first WYSIWYM document processor. more>>
LyX is an advanced open source document processor that encourages an approach to writing based on the structure of your documents, not their appearance. LyX lets you concentrate on writing, leaving details of visual layout to the software.
LyX runs on many Unix platforms, OS/2, and under Windows/Cygwin (this port requires an X server). LyX project can also run natively on Mac OS X, thanks to the Qt/Mac library.
LyX produces high quality, professional output -- using LaTeX, an industrial strength typesetting engine, in the background; LyX is far more than a front-end to LaTeX, however. No knowledge of LaTeX is necessary to use LyX, although it will give a user more power.
LyX is stable and fully featured. It has been used for documents as large as a thesis, or as small as a business letter. Despite its simple GUI interface (available in many languages), it supports tables, figures, and hyperlinked cross-references, and has a best-of-breed math editor.
<<lessLyX runs on many Unix platforms, OS/2, and under Windows/Cygwin (this port requires an X server). LyX project can also run natively on Mac OS X, thanks to the Qt/Mac library.
LyX produces high quality, professional output -- using LaTeX, an industrial strength typesetting engine, in the background; LyX is far more than a front-end to LaTeX, however. No knowledge of LaTeX is necessary to use LyX, although it will give a user more power.
LyX is stable and fully featured. It has been used for documents as large as a thesis, or as small as a business letter. Despite its simple GUI interface (available in many languages), it supports tables, figures, and hyperlinked cross-references, and has a best-of-breed math editor.
Download (9.8MB)
Added: 2007-08-07 License: GPL (GNU General Public License) Price:
515 downloads
XAR 1.5.1
XAR stands for eXtensible ARchiver. more>>
XAR application aims to provide an easily extensible archive format.
Important design decisions include an easily extensible XML table of contents for random access to archived files, storing the toc at the beginning of the archive to allow for efficient handling of streamed archives, the ability to handle files of arbitrarily large sizes, the ability to choose independent encodings for individual files in the archive, the ability to store checksums for individual files in both compressed and uncompressed form, and the ability to query the table of contents rich meta-data.
The ultimate goal of the XAR project is to provide an archive format suitable for packaging software created by DarwinPorts. (Note it is a work in progress, so please feel free to make suggestions and report bugs in the xar Bugzilla product.)
Installation:
cd xar/src
./configure
make
sudo make install
<<lessImportant design decisions include an easily extensible XML table of contents for random access to archived files, storing the toc at the beginning of the archive to allow for efficient handling of streamed archives, the ability to handle files of arbitrarily large sizes, the ability to choose independent encodings for individual files in the archive, the ability to store checksums for individual files in both compressed and uncompressed form, and the ability to query the table of contents rich meta-data.
The ultimate goal of the XAR project is to provide an archive format suitable for packaging software created by DarwinPorts. (Note it is a work in progress, so please feel free to make suggestions and report bugs in the xar Bugzilla product.)
Installation:
cd xar/src
./configure
make
sudo make install
Download (0.10MB)
Added: 2007-08-13 License: BSD License Price:
811 downloads
Jxp 1.5.1
Jxp (Java scripted page) is a script-processor/template-engine that can execute template files containing text + java code. more>>
Jxp (Java scripted page) is a script-processor/template-engine that can execute template files containing text + java code. Jxp contains a parser to parse the script file into an abstract syntax tree and a tree processor (JxpProcessor) that will process the syntax tree to execute the code using reflection API to produce output.
Main features:
- Java as template language. Why learn another one? ;)
- support common java language 1.4 constructs (partial 1.5 syntax support on jdk 1.4)
- practical template sources management framework
- support caching of parsed syntax tree to eliminate reparse of template
- a servlet implementation to enable web-scripting
- extensible processing context for defining built-in function on the scripts
Below is an example of a script file:
This is normal text
This is text with variable
This is another text with variable `var1`
This is yet another text with expression `var1.toString()`
< %
import java.util.*;
//print
println("This text is printed by jxp");
//populate the list with 1 to 10
var i = 0;
List l = new ArrayList();
for (int i = 0; i
Enhancements:
- This release fixes a small dependency problem.
- A syntax was added for specifying text which should not be parsed.
- The plus operator for strings was fixed.
- A default package was added in class lookup.
- Method lookup was improved in ReflectUtils (common-java) using a best match strategy (scoring) instead of first match.
- The ability to lookup a class in the default package was added.
<<lessMain features:
- Java as template language. Why learn another one? ;)
- support common java language 1.4 constructs (partial 1.5 syntax support on jdk 1.4)
- practical template sources management framework
- support caching of parsed syntax tree to eliminate reparse of template
- a servlet implementation to enable web-scripting
- extensible processing context for defining built-in function on the scripts
Below is an example of a script file:
This is normal text
This is text with variable
This is another text with variable `var1`
This is yet another text with expression `var1.toString()`
< %
import java.util.*;
println("This text is printed by jxp");
//populate the list with 1 to 10
var i = 0;
List l = new ArrayList();
for (int i = 0; i
Enhancements:
- This release fixes a small dependency problem.
- A syntax was added for specifying text which should not be parsed.
- The plus operator for strings was fixed.
- A default package was added in class lookup.
- Method lookup was improved in ReflectUtils (common-java) using a best match strategy (scoring) instead of first match.
- The ability to lookup a class in the default package was added.
Download (1.7MB)
Added: 2006-08-04 License: LGPL (GNU Lesser General Public License) Price:
1178 downloads
libgmail 0.1.5.1
ibgmail is a pure Python binding to provide access to Googles Gmail Webmail service. more>>
libgmail project is a pure Python binding to provide access to Googles Gmail web-mail service.
Please note: Always download and test the CVS version of libgmail if you are having problems. The most recent packaged version no longer works correctly. The current development status means critical errors caused by changes at Gmail will be corrected as soon as possible in CVS, if the author is notified about the issue.
Archive Gmail messages to mbox format
The library currently ships with one demonstration utility to archive messages from an Gmail account into mbox files, suitable for importing into a local email client.
Use your Gmail account as a SMTP server
The library now includes a demonstration utility gmailsmtp.py that sets up a SMTP proxy on port 8025 of your computer to enable you to use a standard mail client (e.g. Mozilla, Mail.app) to send messages. (Attachments are now supported.)
Use your Gmail account as a POP server
The library now includes a demonstration utility gmailpopd.py that sets up a POP3 proxy on port 8110 of your computer to enable you to use a standard mail client (e.g. Mozilla, Mail.app) to retrieve messages.
Use your Gmail account as a FTP server!
The included demonstration gmailftpd.py sets up a download-only FTP proxy on port 8021 of your computer to enable you to use a standard ftp client to retrieve message attachments that have the label ftp.
Enhancements:
- Minor bugfix -- before, if you logged in with an incorrect password, the program would exit poorly instead of throwing the appropriate exception.
<<lessPlease note: Always download and test the CVS version of libgmail if you are having problems. The most recent packaged version no longer works correctly. The current development status means critical errors caused by changes at Gmail will be corrected as soon as possible in CVS, if the author is notified about the issue.
Archive Gmail messages to mbox format
The library currently ships with one demonstration utility to archive messages from an Gmail account into mbox files, suitable for importing into a local email client.
Use your Gmail account as a SMTP server
The library now includes a demonstration utility gmailsmtp.py that sets up a SMTP proxy on port 8025 of your computer to enable you to use a standard mail client (e.g. Mozilla, Mail.app) to send messages. (Attachments are now supported.)
Use your Gmail account as a POP server
The library now includes a demonstration utility gmailpopd.py that sets up a POP3 proxy on port 8110 of your computer to enable you to use a standard mail client (e.g. Mozilla, Mail.app) to retrieve messages.
Use your Gmail account as a FTP server!
The included demonstration gmailftpd.py sets up a download-only FTP proxy on port 8021 of your computer to enable you to use a standard ftp client to retrieve message attachments that have the label ftp.
Enhancements:
- Minor bugfix -- before, if you logged in with an incorrect password, the program would exit poorly instead of throwing the appropriate exception.
Download (0.025MB)
Added: 2006-08-09 License: GPL (GNU General Public License) Price:
1173 downloads
pong_curses 1.5.1
pong_curses is an implementation of pong in glorious text mode. more>>
pong_curses is an implementation of pong in glorious text mode.
INSTALLATION
$ tar -xzf pong_curses.tar.gz
$ make
$ su
# make install
Enhancements:
- preferences file
- color, score
- visual improvements
<<lessINSTALLATION
$ tar -xzf pong_curses.tar.gz
$ make
$ su
# make install
Enhancements:
- preferences file
- color, score
- visual improvements
Download (0.010MB)
Added: 2006-12-08 License: GPL (GNU General Public License) Price:
1055 downloads
Rextile 1.5.1
Rextile project allows you to build XHTML documents and entire Web sites with ease. more>>
Rextile project allows you to build XHTML documents and entire Web sites with ease.
You write text using Textile (a format much more concise than XHTML), automate document parts with Ruby scripting, and generate the site offline (the server gets static XHTML).
Rextile was inspired by Xilize. It uses RedCloth to convert Textile to XHTML, erb to run script blocks, and Hpricot for DOM manipulation.
Enhancements:
- Support for dt tags was added.
- Support for Debian-based Ruby (without gems) was improved.
- Minor fixes required by newer versions of RedCloth were made.
<<lessYou write text using Textile (a format much more concise than XHTML), automate document parts with Ruby scripting, and generate the site offline (the server gets static XHTML).
Rextile was inspired by Xilize. It uses RedCloth to convert Textile to XHTML, erb to run script blocks, and Hpricot for DOM manipulation.
Enhancements:
- Support for dt tags was added.
- Support for Debian-based Ruby (without gems) was improved.
- Minor fixes required by newer versions of RedCloth were made.
Download (0.042MB)
Added: 2007-06-13 License: GPL (GNU General Public License) Price:
863 downloads
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