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Placid 2.1
Placid comes from Phil Loathes ACID and was created as a replacement for CMUs ACID. more>>
Placid comes from Phil Loathes ACID and was created as a replacement for CMUs ACID. Acid was too big, too slow, and had too many requirements for me.
So I rewrote almost the entire thing(as well as added a few new features) using Python.
<<lessSo I rewrote almost the entire thing(as well as added a few new features) using Python.
Download (0.028MB)
Added: 2006-01-13 License: GPL (GNU General Public License) Price:
1380 downloads
Gabedit 2.0.9 Pre
Gabedit is a GUI for Gaussian and Molpro. more>>
Gabedit is a Graphical User Interface to Gaussian, Molcas, Molpro and MPQC computational chemistry packages.
Gabedit includes graphical facilities for generating keywords and options, molecule specifications and ther input sections for even the most advanced calculation types Gabedit includes an advanced Molecule Builder.
You can use it to rapidly sketch in molecules and examine them in three dimensions. You can build molecules by atom, ring, group, amino acid and nucleoside. You can also read geometry from a file. Most major molecular file formats are supported.
Gabedit includes a Gaussian, Molcas, Molpro and MPQC Calculation Setup window which allows you to set up Gaussian, Molcas, Molpro and MPQC jobs in a simple and straightforward manner.
Gabedit includes a text editor for editing Molcas, Molpro, Gaussian and MPQC input files.
Gabedit can graphically display a variety of Gaussian, Molcas, Molpro, MPQC and (partially) ADF calculation results, including the following:
- Molecular orbitals.
- Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties.
- Surfaces may be displayed in solid, translucent and wire mesh modes.
- Surfaces can be colored by a separate property.
- Contours (colorcoded).
- Planes (colorcoded).
- Dipole
- XYZ axes and the principal axes of the molecule.
- Animation of the normal modes corresponding to vibrational frequencies.
- Animation of the rotation of geometry, surface, dipole, xyz and the principal axes of the molecule.
- Animation of contours.
- Animation of colorcoded planes.
Gabedit can display IR and Raman computed spectra. Gabedit can generate a povray file for geometry (atoms + bonds, including hydrogens bond), surfaces (including colorcoded surfaces), contours, colorcoded planes.
Gabedit can save picture in PPM, BMP , (JPEG) and PS format. Gabedit can generate automatically a series of pictures for animation (vibration, geometry convergence, rotation, contours, colorcoded planes).
<<lessGabedit includes graphical facilities for generating keywords and options, molecule specifications and ther input sections for even the most advanced calculation types Gabedit includes an advanced Molecule Builder.
You can use it to rapidly sketch in molecules and examine them in three dimensions. You can build molecules by atom, ring, group, amino acid and nucleoside. You can also read geometry from a file. Most major molecular file formats are supported.
Gabedit includes a Gaussian, Molcas, Molpro and MPQC Calculation Setup window which allows you to set up Gaussian, Molcas, Molpro and MPQC jobs in a simple and straightforward manner.
Gabedit includes a text editor for editing Molcas, Molpro, Gaussian and MPQC input files.
Gabedit can graphically display a variety of Gaussian, Molcas, Molpro, MPQC and (partially) ADF calculation results, including the following:
- Molecular orbitals.
- Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties.
- Surfaces may be displayed in solid, translucent and wire mesh modes.
- Surfaces can be colored by a separate property.
- Contours (colorcoded).
- Planes (colorcoded).
- Dipole
- XYZ axes and the principal axes of the molecule.
- Animation of the normal modes corresponding to vibrational frequencies.
- Animation of the rotation of geometry, surface, dipole, xyz and the principal axes of the molecule.
- Animation of contours.
- Animation of colorcoded planes.
Gabedit can display IR and Raman computed spectra. Gabedit can generate a povray file for geometry (atoms + bonds, including hydrogens bond), surfaces (including colorcoded surfaces), contours, colorcoded planes.
Gabedit can save picture in PPM, BMP , (JPEG) and PS format. Gabedit can generate automatically a series of pictures for animation (vibration, geometry convergence, rotation, contours, colorcoded planes).
Download (1.2MB)
Added: 2007-05-25 License: BSD License Price:
886 downloads
Domino on Acid 1.2
Domino on Acid project is a weird colorful solitaire variant of dominoes that visualizes natural deduction. more>>
Domino on Acid project is a weird colorful solitaire variant of dominoes that visualizes natural deduction.
Superficially, Dominoes on Acid is a solitaire variant of Dominoes with weird colorful tiles (and this view is enough to play the game).
But on a deeper level it is a GUI for natural deduction.
Every completed domino is equivalent to a proof of a tautology in classical propositional logic.
The game can be played online as an applet or offline as an application.
It is built on a simple isometric engine that can be used independent of the game.
<<lessSuperficially, Dominoes on Acid is a solitaire variant of Dominoes with weird colorful tiles (and this view is enough to play the game).
But on a deeper level it is a GUI for natural deduction.
Every completed domino is equivalent to a proof of a tautology in classical propositional logic.
The game can be played online as an applet or offline as an application.
It is built on a simple isometric engine that can be used independent of the game.
Download (0.36MB)
Added: 2006-10-27 License: GPL (GNU General Public License) Price:
1092 downloads
Atomorun 1.1_pre2
Atomorun project is an OpenGL Jump&Run clone. more>>
Atomorun project is an OpenGL Jump&Run clone.
In Atomorun, the character "Atomio" has to escape from an exploding nuclear bomb. The shockwave tries to catch you, so run as fast as you can!
It uses 3D OpenGL for the graphics, while the gameplay is 2D (just jump and run as fast as you can, left to right)
Enhancements:
- Forgot to put the body in a displaylist also...
- The glasses are black again (ooops)
- It is now possible to leave the "game over"-screen with a press on ENTER
- The level is now generated randomly and a little bit larger. Makes it much more difficult :)
- Redesigned the menu.
- Some code cleanup
- Added the acid fog, from which Atomio has to run away.
- Fixed bug, where you could change the direction of Atomio in the menu.
- Sound support added. (New dependency: SDL_mixer with ogg support)
- Textures are now stored in smaller and better PNGs. (New dependency: SDL_image with png support)
- If loading a PNG (or OGG) fails, it tries to load a BMP (or WAV). See docsINSTALL.win32, why. Grrr, why do I have to make a win32 build?
- Fixed menu bug. It was possible to press Escape in the menu after playing the game.
- Its now possible to change resolution and fullscreen mode with commandline arguments. Start "atomorun -h" for more help.
<<lessIn Atomorun, the character "Atomio" has to escape from an exploding nuclear bomb. The shockwave tries to catch you, so run as fast as you can!
It uses 3D OpenGL for the graphics, while the gameplay is 2D (just jump and run as fast as you can, left to right)
Enhancements:
- Forgot to put the body in a displaylist also...
- The glasses are black again (ooops)
- It is now possible to leave the "game over"-screen with a press on ENTER
- The level is now generated randomly and a little bit larger. Makes it much more difficult :)
- Redesigned the menu.
- Some code cleanup
- Added the acid fog, from which Atomio has to run away.
- Fixed bug, where you could change the direction of Atomio in the menu.
- Sound support added. (New dependency: SDL_mixer with ogg support)
- Textures are now stored in smaller and better PNGs. (New dependency: SDL_image with png support)
- If loading a PNG (or OGG) fails, it tries to load a BMP (or WAV). See docsINSTALL.win32, why. Grrr, why do I have to make a win32 build?
- Fixed menu bug. It was possible to press Escape in the menu after playing the game.
- Its now possible to change resolution and fullscreen mode with commandline arguments. Start "atomorun -h" for more help.
Download (1.9MB)
Added: 2006-11-14 License: GPL (GNU General Public License) Price:
1074 downloads
ADODB 4.95a
ADOdb is a PHP database abstraction layer. more>>
ADOdb is a database abstraction library for PHP.
The PHP version currently supports an amazing number of databases, thanks to the wonderful ADOdb community: MySQL, PostgreSQL, Interbase, Firebird, Informix, Oracle, MS SQL, Foxpro, Access, ADO, Sybase, FrontBase, DB2, SAP DB, SQLite, Netezza, LDAP, and generic ODBC, ODBTP. The Sybase, Informix, FrontBase and PostgreSQL, Netezza, LDAP, ODBTP drivers are community contributions.
Many popular web applications such as ACID, PostNuke, Xaraya, phpWiki, Mambo, PHP GACL, TikiWiki, eGroupWare and phpLens App Server are using ADOdb as their database abstraction layer.
Main features:
- Designed for speed. It is probably the fastest open source database abstraction library available for PHP. See benchmarks.
- Provides extensive portability support such as date and type-handling and portable schema creation. See portable sql tips
- Support many enterprise features such as database backed sessions (with session expiry notification), SQL code generation, pivot tables, SELECT LIMIT emulation for all databases, performance monitoring.
- Easy to learn, especially if you have Windows programming experience, as it uses many ADO conventions.
- Extensive QA, every release is unit-tested on Access, MySQL, PostgreSQL, MS SQL, Oracle 9.
- Mature, continiously developed since August 2000. Has a large community of users.
- Very reasonable licensing terms (BSD). This means that you can incorporate (and even compile) it into your software applications royalty-free without asking the authors permission, provided you include license.txt in your release. Also dual-licensed (Lesser GPL).
<<lessThe PHP version currently supports an amazing number of databases, thanks to the wonderful ADOdb community: MySQL, PostgreSQL, Interbase, Firebird, Informix, Oracle, MS SQL, Foxpro, Access, ADO, Sybase, FrontBase, DB2, SAP DB, SQLite, Netezza, LDAP, and generic ODBC, ODBTP. The Sybase, Informix, FrontBase and PostgreSQL, Netezza, LDAP, ODBTP drivers are community contributions.
Many popular web applications such as ACID, PostNuke, Xaraya, phpWiki, Mambo, PHP GACL, TikiWiki, eGroupWare and phpLens App Server are using ADOdb as their database abstraction layer.
Main features:
- Designed for speed. It is probably the fastest open source database abstraction library available for PHP. See benchmarks.
- Provides extensive portability support such as date and type-handling and portable schema creation. See portable sql tips
- Support many enterprise features such as database backed sessions (with session expiry notification), SQL code generation, pivot tables, SELECT LIMIT emulation for all databases, performance monitoring.
- Easy to learn, especially if you have Windows programming experience, as it uses many ADO conventions.
- Extensive QA, every release is unit-tested on Access, MySQL, PostgreSQL, MS SQL, Oracle 9.
- Mature, continiously developed since August 2000. Has a large community of users.
- Very reasonable licensing terms (BSD). This means that you can incorporate (and even compile) it into your software applications royalty-free without asking the authors permission, provided you include license.txt in your release. Also dual-licensed (Lesser GPL).
Download (0.40MB)
Added: 2007-05-24 License: GPL (GNU General Public License) Price:
889 downloads
SIGOF 0.9 RC1
SIGOF is a Security Information Graphics Oriented Forensic application. more>>
SIGOF (Security Information Graphics Oriented Forensic) has been developped as a complement of ACID or BASE project by implementing useful and detailed graphical presentation of security information/events.
SIGOF is a web-based project, written in PHP, and it can exploit any secuity information stored in a ACID/BASE database schema (for example, SIGOF can exploit OSSIM project events, because it is based on the acid/base schema).
SIGOF introduces another way to manage security forensic and analysis by providing statistical and security trend thanks to very customizable graphics generation.
This approach provide the capability to manage large amount of security events.
<<lessSIGOF is a web-based project, written in PHP, and it can exploit any secuity information stored in a ACID/BASE database schema (for example, SIGOF can exploit OSSIM project events, because it is based on the acid/base schema).
SIGOF introduces another way to manage security forensic and analysis by providing statistical and security trend thanks to very customizable graphics generation.
This approach provide the capability to manage large amount of security events.
Download (0.021MB)
Added: 2006-04-27 License: GPL (GNU General Public License) Price:
1276 downloads
Basic Analysis and Security Engine 1.2
BASE is the Basic Analysis and Security Engine. more>>
BASE is the Basic Analysis and Security Engine. It is based on the code from the Analysis Console for Intrusion Databases (ACID) project.
This application provides a web front-end to query and analyze the alerts coming from a SNORT IDS system.
BASE is a web interface to perform analysis of intrusions that snort has detected on your network. It uses a user authentication and role-base system, so that you as the security admin can decide what and how much information each user can see. It also has a simple to use, web-based setup program for people not comfortable with editing files directly.
BASE is supported by a group of volunteers. They are available to answer any questions you may have or help you out in setting up your system. They are also skilled in intrusion detection systems and make use of that knowledge in the development of BASE.
Enhancements:
- This release fixes a number of bugs with PHP 5.
- It also adds a number of new features.
<<lessThis application provides a web front-end to query and analyze the alerts coming from a SNORT IDS system.
BASE is a web interface to perform analysis of intrusions that snort has detected on your network. It uses a user authentication and role-base system, so that you as the security admin can decide what and how much information each user can see. It also has a simple to use, web-based setup program for people not comfortable with editing files directly.
BASE is supported by a group of volunteers. They are available to answer any questions you may have or help you out in setting up your system. They are also skilled in intrusion detection systems and make use of that knowledge in the development of BASE.
Enhancements:
- This release fixes a number of bugs with PHP 5.
- It also adds a number of new features.
Download (0.33MB)
Added: 2005-10-10 License: GPL (GNU General Public License) Price:
1482 downloads
Isotopic Pattern Calculator 1.4
Isotopic Pattern Calculator is a calculates isotopic distributions. more>>
IPC is a program that calculates the isotopic distribution of a given chemical formula. It gives the rel. intensities and the propability of the masses belonging to a molecule ion, fragment or whatever is represented by the given chemical formula.
Furthernmore it can use GNUPlot to visualize the result. Only masses with a rel. Intensity bigger then 0.009% are shown. Additionaly ipc prints the overall number of peaks and the needed computation time.
The program uses an algorithm which computes the exact isotopic distribution. This leads to a large number of peaks which have very low rel. abundances. Even for a small molecule as Acetylsalicylic acid ( C9H8O4, Mr=180.15) there are 1350 peaks but only nine of them have a rel. abundance higher then 0.01%.
Enhancements:
- A complete list of elements and isotopes is now used.
- The list of elements is taken from the NIST.
<<lessFurthernmore it can use GNUPlot to visualize the result. Only masses with a rel. Intensity bigger then 0.009% are shown. Additionaly ipc prints the overall number of peaks and the needed computation time.
The program uses an algorithm which computes the exact isotopic distribution. This leads to a large number of peaks which have very low rel. abundances. Even for a small molecule as Acetylsalicylic acid ( C9H8O4, Mr=180.15) there are 1350 peaks but only nine of them have a rel. abundance higher then 0.01%.
Enhancements:
- A complete list of elements and isotopes is now used.
- The list of elements is taken from the NIST.
Download (0.070MB)
Added: 2005-08-15 License: GPL (GNU General Public License) Price:
1531 downloads
goblinhack 1.11
goblinhackis a rogue-like game with ASCII graphics, OpenGL, and smooth scrolling. more>>
goblinhackis a rogue-like game with ASCII graphics, OpenGL, and smooth scrolling.
Goblins hoard in their foul, dark hole, Plotting and digging and hating all things, Theyll gnash on your bones and eat you whole, And deliver your soul to the Goblin King.
Enhancements:
- This release adds animated black, white, and amethyst dragons, jelly molds, evil blobs, knee gnashers, fractal lakes, fate points, acid weapons, fire/cold/acid proof armour, and many bugfixes.
<<lessGoblins hoard in their foul, dark hole, Plotting and digging and hating all things, Theyll gnash on your bones and eat you whole, And deliver your soul to the Goblin King.
Enhancements:
- This release adds animated black, white, and amethyst dragons, jelly molds, evil blobs, knee gnashers, fractal lakes, fate points, acid weapons, fire/cold/acid proof armour, and many bugfixes.
Download (0.72MB)
Added: 2007-08-12 License: Free for non-commercial use Price:
804 downloads
Knoppix STD 0.1
STD is a Linux-based Security Tool. Actually, it is a collection of hundreds if not thousands of open source security tools. more>>
STD is a Linux-based Security Tool. Actually, it is a collection of hundreds if not thousands of open source security tools. Its a Live Linux Distro, which means it runs from a bootable CD in memory without changing the native operating system of the host computer. Its sole purpose in life is to put as many security tools at your disposal with as slick an interface as it can.
STD is meant to be used by both novice and professional security personnel but is not ideal for the Linux uninitiated. STD assumes you know the basics of Linux as most of your work will be done from the command line. If you are completely new to Linux, its best you start with another live Distro like Knoppix to practice the basics.
STD tools are divided into the following categories:
- authentication
- encryption
- forensics
- firewall
- honeypot
- ids
- network utilities
- password tools
- servers
- packet sniffers
- tcp tools
- tunnels
- vulnerability assessment
- wireless tools
Enhancements:
- Eliminated all windows managers except fluxbox
- built kernel from kernel.org 2.4.21 src. added ntfs/rw, superfreeswan and openmosix patches.
- ntfs rw is very limited. You can basically only modify existing files and only if you dont change the size. Good for making basic registry changes.
- Superfreeswan adds IPSEC support for VPNs.
- OpenMosix adds clustering support with automatic discovery of other nodes.
- Added /usr/bin/tunnels category
- Eliminated /usr/bin/pen-test category and moved tools to /usr/bin/vuln-test
- Moved some tools in /usr/bin/sniff to /usr/bin/tcp-tools
- Eliminated /usr/bin/pen-test category and moved tools to /usr/bin/vuln-test
- ACID/MySQL/Snort configured to work automatically
- update nessus plugins, clamAV signatures, and snort signatures
- If you have 640MB of RAM or more you run boot: knoppix toram and free up the CD drive
- patched orinoco driver is the default. no more patch-orinoco
- Kismet updated to 3.0.1 and is pre-configured for orinoco on eth0
- all init scripts now check the knoppix home dir before copying from the CD.This means that if youre using a persistant home dir the init scripts act as restore scripts
- blockall now allows connections from localhost so you can block all external traffic but still run nessus or ntop or kismet or.....
- added many new tools and updated all existing tools
<<lessSTD is meant to be used by both novice and professional security personnel but is not ideal for the Linux uninitiated. STD assumes you know the basics of Linux as most of your work will be done from the command line. If you are completely new to Linux, its best you start with another live Distro like Knoppix to practice the basics.
STD tools are divided into the following categories:
- authentication
- encryption
- forensics
- firewall
- honeypot
- ids
- network utilities
- password tools
- servers
- packet sniffers
- tcp tools
- tunnels
- vulnerability assessment
- wireless tools
Enhancements:
- Eliminated all windows managers except fluxbox
- built kernel from kernel.org 2.4.21 src. added ntfs/rw, superfreeswan and openmosix patches.
- ntfs rw is very limited. You can basically only modify existing files and only if you dont change the size. Good for making basic registry changes.
- Superfreeswan adds IPSEC support for VPNs.
- OpenMosix adds clustering support with automatic discovery of other nodes.
- Added /usr/bin/tunnels category
- Eliminated /usr/bin/pen-test category and moved tools to /usr/bin/vuln-test
- Moved some tools in /usr/bin/sniff to /usr/bin/tcp-tools
- Eliminated /usr/bin/pen-test category and moved tools to /usr/bin/vuln-test
- ACID/MySQL/Snort configured to work automatically
- update nessus plugins, clamAV signatures, and snort signatures
- If you have 640MB of RAM or more you run boot: knoppix toram and free up the CD drive
- patched orinoco driver is the default. no more patch-orinoco
- Kismet updated to 3.0.1 and is pre-configured for orinoco on eth0
- all init scripts now check the knoppix home dir before copying from the CD.This means that if youre using a persistant home dir the init scripts act as restore scripts
- blockall now allows connections from localhost so you can block all external traffic but still run nessus or ntop or kismet or.....
- added many new tools and updated all existing tools
Download (497MB)
Added: 2005-05-13 License: GPL (GNU General Public License) Price:
1629 downloads
Trackballs 1.1.4
Trackballs is a simple game similar to the classic game Marble Madness. more>>
Trackballs is a FREE and simple game similar to the classic game Marble Madness.
By steering a marble through a track filled with vicious hammers, pools of acid, and other obstacles the player collects points.
When the ball reaches the destination, the player continue to the next, more difficult track - unless, of course, time runs out first.
Enhancements:
- This update includes new user contributed material (new songs and maps) as well as a number of new API functions and cleanups to make it easier and more flexible to design new levels.
- The built in map editor has some improvements (a few missing features have been added).
- Event callbacks on arbitrary animated objects and customizable score/time bonuses when killing arbitrary animated objects have been implemented.
- The documentation for the built-in scripting language has been rewritten.
<<lessBy steering a marble through a track filled with vicious hammers, pools of acid, and other obstacles the player collects points.
When the ball reaches the destination, the player continue to the next, more difficult track - unless, of course, time runs out first.
Enhancements:
- This update includes new user contributed material (new songs and maps) as well as a number of new API functions and cleanups to make it easier and more flexible to design new levels.
- The built in map editor has some improvements (a few missing features have been added).
- Event callbacks on arbitrary animated objects and customizable score/time bonuses when killing arbitrary animated objects have been implemented.
- The documentation for the built-in scripting language has been rewritten.
Download (5.8MB)
Added: 2007-05-25 License: GPL (GNU General Public License) Price:
534 downloads
tektracker 0.7.0
ttrk (tektracker) is a console MIDI sequencer with a tracker-style step editor. more>>
ttrk (tektracker) is a console MIDI sequencer with a tracker-style step editor.I was annoyed by the bad step editors found on pretty much all MIDI sequencers I could find, and since I was big fan of the tracker interface, I used the user interface ideas behind a tracker in my design.
There are five main goals for creating ttrk:
1. Tracker-style step editor, think ScreamTracker3.
2. Pattern based sequencer per track, more like Sonic Foundrys ACID.
3. Big, accessable track mute buttons, think Alesis MMT8.
4. Realtime editing, never need to push stop.
5. All functions directly accessable from the keyboard for rapid editing.
Main features:
- Tracker-style step editor.
- 256 channels, each with 256 patterns.
- Songs up to 4096 patterns long.
- Pattern copy and paste.
- Sync to external MIDI.
- Sends MIDI sync.
- Convenient channel mute buttons for live play.
<<lessThere are five main goals for creating ttrk:
1. Tracker-style step editor, think ScreamTracker3.
2. Pattern based sequencer per track, more like Sonic Foundrys ACID.
3. Big, accessable track mute buttons, think Alesis MMT8.
4. Realtime editing, never need to push stop.
5. All functions directly accessable from the keyboard for rapid editing.
Main features:
- Tracker-style step editor.
- 256 channels, each with 256 patterns.
- Songs up to 4096 patterns long.
- Pattern copy and paste.
- Sync to external MIDI.
- Sends MIDI sync.
- Convenient channel mute buttons for live play.
Download (0.29MB)
Added: 2006-07-25 License: GPL (GNU General Public License) Price:
1186 downloads
Python Macromolecular Library 1.0.0
Python Macromolecular Library is a software toolkit and library of routines for the analysis of macromolecular structural models more>>
Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.
Python Macromolecular Library is accessed via a layered, object-oriented application programming interface, and provides a range of useful software components for parsing mmCIF, and PDB files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer.
The mmLib data model is designed to provide easy access to the various levels of detail needed to implement high-level application programs for macromolecular crystallography, NMR, modeling, and visualization.
This includes specialized classes for proteins, DNA, amino acids, and nucleic acids. Also included is a extensive monomer library, element library, and specialized classes for performing unit cell calculations combined with a full space group library.
<<lessPython Macromolecular Library is accessed via a layered, object-oriented application programming interface, and provides a range of useful software components for parsing mmCIF, and PDB files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer.
The mmLib data model is designed to provide easy access to the various levels of detail needed to implement high-level application programs for macromolecular crystallography, NMR, modeling, and visualization.
This includes specialized classes for proteins, DNA, amino acids, and nucleic acids. Also included is a extensive monomer library, element library, and specialized classes for performing unit cell calculations combined with a full space group library.
Download (7.9MB)
Added: 2007-05-22 License: Artistic License Price:
888 downloads
MassSpec::ViewSpectrum::RealVsHypPeptide 0.02
MassSpec::ViewSpectrum::RealVsHypPeptide is a Perl module to view a real mass spectrum on the same graph. more>>
MassSpec::ViewSpectrum::RealVsHypPeptide is a Perl module to view a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico.
SYNOPSIS
use MassSpec::ViewSpectrum::RealVsHypPeptide;
open GRAPHIC, ">mygraphic.png" or die "Unable to open output filen";
binmode GRAPHIC;
my @masses = (78.1,81.1,81.7,85.4,86.8,88.8,89.4,97.6,99.0,99.4,108.7,112.1,129.1,
130.1,132.1,147.7,157.1,158.1,159.1,169.1,171.1,175.1,187.1,229.1,246.2,258.1,
266.0,327.2,328.2,345.2,415.2,426.2,432.2,531.2,559.3,623.4,639.3,643.3,644.4,
645.0,647.5,686.4,687.4,689.4);
my @intensities = (8.7,7.7,7.3,10.5,7.7,7.3,8.4,8.0,9.1,9.1,7.3,29.0,12.6,7.3,8.0,
7.7,11.9,9.8,10.1,7.3,10.5,131.0,9.4,50.3,22.7,44.7,16.8,30.4,18.2,53.1,25.5,
15.7,7.7,14.0,46.8,38.4,7.3,11.5,8.7,7.3,8.7,7.3,24.8,194.2);
my $peptide = "RTSVAR";
my $vs = MassSpec::ViewSpectrum::RealVsHypPeptide->new($peptide, @masses,@intensities);
$vs->set(yaxismultiplier => 1.8); # a sample tweak to adjust the output
$vs->set(title => "BSA-689 -- " . $peptide);
my $output = $vs->plot();
print GRAPHIC $output;
close GRAPHIC;
MassSpec::ViewSpectrum::RealVsHypPeptide - View a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico. The in silico fragmention is performed by generating all of the possible peptides which contain either the amino-terminal or carboxyl-terminal amino acids.
Negative peak intensity values are permitted; this permits the drawing of "pseudospectra" which, for example, illustrate peaks present in one spectrum but missing in another. Note that these negative peaks have no true intensities, but in some cases we assign different heights to illustrate the differences among different hypothetical peaks. In addition, pseudocoloring of both positive and negative peaks is performed to illustrate what type of ion that peak represents. In some cases these ions are labelled explicitly, although in practice it is best to minimize this labelling to avoid excessive clutter.
<<lessSYNOPSIS
use MassSpec::ViewSpectrum::RealVsHypPeptide;
open GRAPHIC, ">mygraphic.png" or die "Unable to open output filen";
binmode GRAPHIC;
my @masses = (78.1,81.1,81.7,85.4,86.8,88.8,89.4,97.6,99.0,99.4,108.7,112.1,129.1,
130.1,132.1,147.7,157.1,158.1,159.1,169.1,171.1,175.1,187.1,229.1,246.2,258.1,
266.0,327.2,328.2,345.2,415.2,426.2,432.2,531.2,559.3,623.4,639.3,643.3,644.4,
645.0,647.5,686.4,687.4,689.4);
my @intensities = (8.7,7.7,7.3,10.5,7.7,7.3,8.4,8.0,9.1,9.1,7.3,29.0,12.6,7.3,8.0,
7.7,11.9,9.8,10.1,7.3,10.5,131.0,9.4,50.3,22.7,44.7,16.8,30.4,18.2,53.1,25.5,
15.7,7.7,14.0,46.8,38.4,7.3,11.5,8.7,7.3,8.7,7.3,24.8,194.2);
my $peptide = "RTSVAR";
my $vs = MassSpec::ViewSpectrum::RealVsHypPeptide->new($peptide, @masses,@intensities);
$vs->set(yaxismultiplier => 1.8); # a sample tweak to adjust the output
$vs->set(title => "BSA-689 -- " . $peptide);
my $output = $vs->plot();
print GRAPHIC $output;
close GRAPHIC;
MassSpec::ViewSpectrum::RealVsHypPeptide - View a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico. The in silico fragmention is performed by generating all of the possible peptides which contain either the amino-terminal or carboxyl-terminal amino acids.
Negative peak intensity values are permitted; this permits the drawing of "pseudospectra" which, for example, illustrate peaks present in one spectrum but missing in another. Note that these negative peaks have no true intensities, but in some cases we assign different heights to illustrate the differences among different hypothetical peaks. In addition, pseudocoloring of both positive and negative peaks is performed to illustrate what type of ion that peak represents. In some cases these ions are labelled explicitly, although in practice it is best to minimize this labelling to avoid excessive clutter.
Download (0.008MB)
Added: 2007-02-23 License: Perl Artistic License Price:
974 downloads
Iter Vehemens ad Necem 0.50
Iter Vehemens ad Necem project is a graphical roguelike game. more>>
Iter Vehemens ad Necem project is a graphical roguelike game.
Iter Vehemens ad Necem (IVAN) is a graphical roguelike game which currently runs in Windows, DOS, and Linux. It features advanced bodypart and material handling, multi-colored lighting and, above all, deep gameplay.
Fellow adventurer, turn back while you can! For here begins the roguelike Iter Vehemens ad Necem, a Violent Road to Death. If you choose to travel along it, you will dive into countless exciting adventures to gain items of great magic, attain powerful equipment made of mysterious materials, bathe in the blessings of mighty gods and recruit loyal allies of various shapes and sizes.
Unfortunately, along the way you will also often be dangerously injured, poisoned, catch numerous diseases, lose several limbs and transform into manifold different kinds of pitiful creatures in the darkest depths of hostile dungeons. And, at the end of the road, you are bound to perish in a most gruesome and painful way. Dont say we didnt warn you.
Enhancements:
- fluids can now cover items and characters and interact with them
- items made of iron alloys can now rust
- added directional light and day and night which use it
- added some cosmetical weather effects
- New Attnam has now many new NPCs, for instance a sumo wrestler who can be challenged
- polymorph control is now more interesting; you need to see a monster once before you can polymorph into it, and more powerful ones require more intelligence
- added wands of acid rain, mirroring and necromancy
- added scrolls of detect material, harden material and golem creation
- added several new monsters, eg. powerful named archangels for each god and necromancers who raise skeletons and zombies to do their bidding
- one can now give pets tactical commands, change their equipment and use them to carry extra stuff (these are accessed using Chat and Issue commands keys)
- the player can now panic if he gets hit too much, like the monsters have done in previous versions
- the player can now become exhausted if he fights for too long and/or uses the new run command too much
- spiders are now able to make webs
- you can now get stuck to slime
- badly hurt/trapped bodyparts now become unusable until they regain some HP/become untrapped
- it is now possible to browse detailed death reasons of individual monsters in the postgame massacre lists
- added many new informative graphical details, for instance recently altered attributes are shown with a different color for some time
- gloomy cave is now longer and has more special levels and rooms
- all the endgame battles are more complex
- added leprosy, a nasty disease which causes your limbs to drop off randomly
<<lessIter Vehemens ad Necem (IVAN) is a graphical roguelike game which currently runs in Windows, DOS, and Linux. It features advanced bodypart and material handling, multi-colored lighting and, above all, deep gameplay.
Fellow adventurer, turn back while you can! For here begins the roguelike Iter Vehemens ad Necem, a Violent Road to Death. If you choose to travel along it, you will dive into countless exciting adventures to gain items of great magic, attain powerful equipment made of mysterious materials, bathe in the blessings of mighty gods and recruit loyal allies of various shapes and sizes.
Unfortunately, along the way you will also often be dangerously injured, poisoned, catch numerous diseases, lose several limbs and transform into manifold different kinds of pitiful creatures in the darkest depths of hostile dungeons. And, at the end of the road, you are bound to perish in a most gruesome and painful way. Dont say we didnt warn you.
Enhancements:
- fluids can now cover items and characters and interact with them
- items made of iron alloys can now rust
- added directional light and day and night which use it
- added some cosmetical weather effects
- New Attnam has now many new NPCs, for instance a sumo wrestler who can be challenged
- polymorph control is now more interesting; you need to see a monster once before you can polymorph into it, and more powerful ones require more intelligence
- added wands of acid rain, mirroring and necromancy
- added scrolls of detect material, harden material and golem creation
- added several new monsters, eg. powerful named archangels for each god and necromancers who raise skeletons and zombies to do their bidding
- one can now give pets tactical commands, change their equipment and use them to carry extra stuff (these are accessed using Chat and Issue commands keys)
- the player can now panic if he gets hit too much, like the monsters have done in previous versions
- the player can now become exhausted if he fights for too long and/or uses the new run command too much
- spiders are now able to make webs
- you can now get stuck to slime
- badly hurt/trapped bodyparts now become unusable until they regain some HP/become untrapped
- it is now possible to browse detailed death reasons of individual monsters in the postgame massacre lists
- added many new informative graphical details, for instance recently altered attributes are shown with a different color for some time
- gloomy cave is now longer and has more special levels and rooms
- all the endgame battles are more complex
- added leprosy, a nasty disease which causes your limbs to drop off randomly
Download (MB)
Added: 2007-01-03 License: GPL (GNU General Public License) Price:
1029 downloads
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