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kfile_chemical 0.12
kfile_chemical is a set of kfile plugins for chemistry documents. more>>
kfile_chemical is a set of kfile plugins for chemistry documents. It has support for XYZ, PDB, MDL mol/sd, Mol2, CML, ShelX, SMILES and CIF files.
kfile_chemical is currently in alpha stage: 1.0 will be alpha too; it will be feature complete, i.e. proving plugins kfile plugins for all files mentioned at the official chemical mime page (and a few more).
Version 2.0 will be beta, and feature a more organized set of extracted pieces of information.
Version 3.0 will be beta too, and mime magic, which is a method to detect the mime type not from the file extension, but from the content.
Verion 4.0 will be the first stable release and is aimed to be ready with Kubuntu 6.04 and KDE 4.0.
Enhancements:
- This release adds support for chemical-mime-data, thus synchronizing with the main MIME type library for chemical data.
- It also fixes QChar / QString conversion, the FSF address, and the contact email address.
<<lesskfile_chemical is currently in alpha stage: 1.0 will be alpha too; it will be feature complete, i.e. proving plugins kfile plugins for all files mentioned at the official chemical mime page (and a few more).
Version 2.0 will be beta, and feature a more organized set of extracted pieces of information.
Version 3.0 will be beta too, and mime magic, which is a method to detect the mime type not from the file extension, but from the content.
Verion 4.0 will be the first stable release and is aimed to be ready with Kubuntu 6.04 and KDE 4.0.
Enhancements:
- This release adds support for chemical-mime-data, thus synchronizing with the main MIME type library for chemical data.
- It also fixes QChar / QString conversion, the FSF address, and the contact email address.
Download (0.10MB)
Added: 2006-07-10 License: GPL (GNU General Public License) Price:
1201 downloads
chemicalInventory 20070120
chemicalInventory is an intelligent tool for managing chemical inventories. more>>
Chemicalinventory is a web application that manage the chemical stock in a laboratory-, production- or other facilities, where chemicals must be safely stored, easily found and tracked. chemicalInventory solution is currently productive at The Danish University of Pharmaceutical Sciences
Main features:
- Search facility, with textual, structure and substructure search.
- Check in and out of containers.
- Multi-level location management.
- Label print with container information.
- Administration module for all data.
- History tracking of essential data.
- Report generation - on screen and paper.
- Sample Module - track analytical data.
- Share data cross organisation.
- Batch module. Link samples in batches/projects.
- Link to external ressources, msds
- ... and lots more..
Chemicalinventory is an open source project. The application is free*. Specific components of this application is licenced by third parties, and may require separate licence.
<<lessMain features:
- Search facility, with textual, structure and substructure search.
- Check in and out of containers.
- Multi-level location management.
- Label print with container information.
- Administration module for all data.
- History tracking of essential data.
- Report generation - on screen and paper.
- Sample Module - track analytical data.
- Share data cross organisation.
- Batch module. Link samples in batches/projects.
- Link to external ressources, msds
- ... and lots more..
Chemicalinventory is an open source project. The application is free*. Specific components of this application is licenced by third parties, and may require separate licence.
Download (30.7MB)
Added: 2007-02-17 License: GPL (GNU General Public License) Price:
979 downloads
Chemsuite 0.0.7
Chemsuite is a set of programs to process chemical information. more>>
Chemsuite is a set of programs designed for the processing of chemical information on Linux/X11. It is free software and released under GPL.
It requires the QT GUI library version 2.3.1 from Trolltech Inc. . It intends to run primary on Linux, but we think it can compile and run on othe Unices.
Chemsuite is composed by several program:
- Chem2D: A 2D molecular drawer.
- Molcalc: A molecular weight calculator
- ChemModel3D: Molecular 3D modeler
- ChemIR: An infrared spectra processor. It can read, process, export and print Perkin Elmer spectra.
- ChemNMR: 1D NMR Processor
- ChemMC: Monte carlo Simulator and Integrator
Enhancements:
- chem2d new engine
- chemIR print spectra bug corrected
- Supports GNU configure utility
<<lessIt requires the QT GUI library version 2.3.1 from Trolltech Inc. . It intends to run primary on Linux, but we think it can compile and run on othe Unices.
Chemsuite is composed by several program:
- Chem2D: A 2D molecular drawer.
- Molcalc: A molecular weight calculator
- ChemModel3D: Molecular 3D modeler
- ChemIR: An infrared spectra processor. It can read, process, export and print Perkin Elmer spectra.
- ChemNMR: 1D NMR Processor
- ChemMC: Monte carlo Simulator and Integrator
Enhancements:
- chem2d new engine
- chemIR print spectra bug corrected
- Supports GNU configure utility
Download (0.69MB)
Added: 2005-04-01 License: GPL (GNU General Public License) Price:
1673 downloads
XDrawChem 1.9.9
XDrawChem is a chemical drawing program. more>>
XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. XDrawChem is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft).
It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS. XDrawChem has been tested on Linux, SGI IRIX 6.5, Sun Solaris, Mac OS X, and Windows.
Main features:
- 100% compatible Windows 95/98/NT version
- Fixed length, fixed angle drawing.
- Automatic alignment of figures. Detects structures, text, and arrows and places them automatically.
- Can automatically draw rings and other structures - has all standard amino acids and nucleic acids in built-in library.
- Can retrieve structures from a network database based on CAS number, formula, or name.
- Can draw symbols such as partial charge, radicals, etc.
- Can read MDL Molfiles, CML [Chemical Markup Language, defined in J. Chem. Inf. Comput. Sci.39(1999), 928-942], ChemDraw(TM) binary format, ChemDraw(TM) XML text format.
- Can write MDL Molfiles, CML, ChemDraw(TM) XML text format.
- Can also read and write any format supported by the current release of OpenBabel.
- Can export pictures in PNG, Windows bitmap (*.bmp), Encapsulated PostScript (EPS), and Scalable Vector Graphics (SVG).
- Can generate 3-D structures with the help of the external program BUILD3D.
- Online help, including tool tips.
- 13C-NMR prediction, based on Bremser W, Mag. Res. Chem.23(4):271-275
- 1H-NMR prediction, based on additive rules and functional group lookup methods, described in Pretsch, Clerc, Seibl, Simon, "Tables of Spectral Data for Structure Determination of Organic Compounds", 2ed., 1989, Springer-Verlag
- Simple IR prediction.
- Simple pKa estimation.
- Octanol-water partition coefficient estimation.
- Reaction analysis: gas-phase enthalpy change estimate, 1H NMR and 13C NMR comparison.
- Integration with OpenBabel, allowing XDrawChem to read and write over 20 different chemical file formats.
<<lessIt can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS. XDrawChem has been tested on Linux, SGI IRIX 6.5, Sun Solaris, Mac OS X, and Windows.
Main features:
- 100% compatible Windows 95/98/NT version
- Fixed length, fixed angle drawing.
- Automatic alignment of figures. Detects structures, text, and arrows and places them automatically.
- Can automatically draw rings and other structures - has all standard amino acids and nucleic acids in built-in library.
- Can retrieve structures from a network database based on CAS number, formula, or name.
- Can draw symbols such as partial charge, radicals, etc.
- Can read MDL Molfiles, CML [Chemical Markup Language, defined in J. Chem. Inf. Comput. Sci.39(1999), 928-942], ChemDraw(TM) binary format, ChemDraw(TM) XML text format.
- Can write MDL Molfiles, CML, ChemDraw(TM) XML text format.
- Can also read and write any format supported by the current release of OpenBabel.
- Can export pictures in PNG, Windows bitmap (*.bmp), Encapsulated PostScript (EPS), and Scalable Vector Graphics (SVG).
- Can generate 3-D structures with the help of the external program BUILD3D.
- Online help, including tool tips.
- 13C-NMR prediction, based on Bremser W, Mag. Res. Chem.23(4):271-275
- 1H-NMR prediction, based on additive rules and functional group lookup methods, described in Pretsch, Clerc, Seibl, Simon, "Tables of Spectral Data for Structure Determination of Organic Compounds", 2ed., 1989, Springer-Verlag
- Simple IR prediction.
- Simple pKa estimation.
- Octanol-water partition coefficient estimation.
- Reaction analysis: gas-phase enthalpy change estimate, 1H NMR and 13C NMR comparison.
- Integration with OpenBabel, allowing XDrawChem to read and write over 20 different chemical file formats.
Download (0.85MB)
Added: 2005-12-01 License: GPL (GNU General Public License) Price:
1436 downloads
Chemtool 1.6.10
Chemtool is a X11/GTK-based chemical formula drawing program. more>>
Chemtool project is a small program for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
Chemtool relies on transfig by Brian Smith for postscript printing and exporting files in PicTeX and EPS formats. Its companion program, XFig, is recommended for enhancing the output of chemtool, and for creation of 2D diagrams and schematics in general.
Both are included with most distributions of Linux, and are available through a number of websites including www.xfig.org. If you want to import chemtool drawings into word processing programs other than LaTeX, you will probably want to add a preview bitmap to them, as neither StarOffice/OpenOffice nor that software from Redmond seem to be able to display postscript inserts on screen without them.
For this purpose, using either ps2epsi, which comes with ghostscript, or epstool, a part of gsview is recommended. Since chemtool-1.6, this option is supported directly (through the equivalent function offered by recent versions of transfig).
Chemtool was originally written by Thomas Volk, then a student of chemistry and biology at the university of Ulm, Germany. His version, which was described in an article in the german periodical LinuxMagazin, was using plain X11.
The bond types available in chemtool are:
- a single bond
- a double bond (with one line shorter than the other)
- a double bond (having the shorter line on the opposite side)
- a centered double bond
- a triple bond (with the flanking lines shorter than the center)
- a wedge-shaped bond
- a dashed wedge-shaped bond
- a wavy line
- a dashed wide line
- a half arrow
- an arrow
- a wide bond
- a circle
- a dotted line
- a single bond that cuts out a segment from any bond it crosses
- a triple bond (with equal line lengths)
- a quadruple bond
Enhancements:
- PNG export, kprinter support, and a few new template structures were added.
- Screen rendering of complex labels was improved.
- Several problems with text input in UTF8-enabled locales were fixed.
- Arrowhead size in EPS output and the appearance of arrowheads, superscripts, and national characters in SVG output were fixed.
<<lessChemtool relies on transfig by Brian Smith for postscript printing and exporting files in PicTeX and EPS formats. Its companion program, XFig, is recommended for enhancing the output of chemtool, and for creation of 2D diagrams and schematics in general.
Both are included with most distributions of Linux, and are available through a number of websites including www.xfig.org. If you want to import chemtool drawings into word processing programs other than LaTeX, you will probably want to add a preview bitmap to them, as neither StarOffice/OpenOffice nor that software from Redmond seem to be able to display postscript inserts on screen without them.
For this purpose, using either ps2epsi, which comes with ghostscript, or epstool, a part of gsview is recommended. Since chemtool-1.6, this option is supported directly (through the equivalent function offered by recent versions of transfig).
Chemtool was originally written by Thomas Volk, then a student of chemistry and biology at the university of Ulm, Germany. His version, which was described in an article in the german periodical LinuxMagazin, was using plain X11.
The bond types available in chemtool are:
- a single bond
- a double bond (with one line shorter than the other)
- a double bond (having the shorter line on the opposite side)
- a centered double bond
- a triple bond (with the flanking lines shorter than the center)
- a wedge-shaped bond
- a dashed wedge-shaped bond
- a wavy line
- a dashed wide line
- a half arrow
- an arrow
- a wide bond
- a circle
- a dotted line
- a single bond that cuts out a segment from any bond it crosses
- a triple bond (with equal line lengths)
- a quadruple bond
Enhancements:
- PNG export, kprinter support, and a few new template structures were added.
- Screen rendering of complex labels was improved.
- Several problems with text input in UTF8-enabled locales were fixed.
- Arrowhead size in EPS output and the appearance of arrowheads, superscripts, and national characters in SVG output were fixed.
Download (0.41MB)
Added: 2007-04-24 License: GPL (GNU General Public License) Price:
914 downloads
GChemPaint 0.8.2
GChemPaint is a 2D chemical structures editor for the Gnome desktop. more>>
GChemPaint is a 2D chemical structures editor for the Gnome desktop.
GChemPaint should enable embedding some chemistry in files from other programs using Bonobo.
<<lessGChemPaint should enable embedding some chemistry in files from other programs using Bonobo.
Download (1.5MB)
Added: 2007-07-28 License: GPL (GNU General Public License) Price:
822 downloads
The Romalizer 0.61
The Romalizer project is a Tcl script to analyze your MAME roms and report errors. more>>
The Romalizer project is a Tcl script to analyze your MAME roms and report errors.
The ROMalizer is a Tcl script that examines your .zip files for MAME ROMs and lets you know if you have any extra data in them. It can also report incorrect filenames, CRCs, etc.
Enhancements:
- romalizer will no longer move the zipfiles it has fixed into your roms directory unless you specify the -M option. This will allow you to run romalizer as a normal user on a roms filesystem that is only writable by root or some other games administrator. If you use the -M option, romalzier will back up your old roms into the working directory as usual, if the -M option is not used, the new (fixed) roms will be located in the working directory.
- romalizer now fully supports two new styles of merging your roms. You may now use the -g or -G options to tell romalizer to use one of these new merging formats. When -g is used, romalizer will merge all clones into a single zip file. When -G is used, romalizer will create clone zip files that are capable of being run independantly of the parent romset. I have tested these new merging features on my pacman romset and it works beautifully, however more testing probably needs to be done on a complete romset for these options.
- neogeo games are now supported, romalizer will just ignore any CRC that matches 354029fc (ng-sfix.rom), 9036d879 (neo-geo.rom), and 97cf998b (ng-sm1.rom). Thus neogeo roms are now fully supported except for these 3 which should be placed in a file called neogeo.zip.
- romalizer requires usage of UnZip version 5.41 or higher due to a Y2K bug in UnZip. This patch will now check your unzip version and abort if you do not have a recent version of UnZip.
<<lessThe ROMalizer is a Tcl script that examines your .zip files for MAME ROMs and lets you know if you have any extra data in them. It can also report incorrect filenames, CRCs, etc.
Enhancements:
- romalizer will no longer move the zipfiles it has fixed into your roms directory unless you specify the -M option. This will allow you to run romalizer as a normal user on a roms filesystem that is only writable by root or some other games administrator. If you use the -M option, romalzier will back up your old roms into the working directory as usual, if the -M option is not used, the new (fixed) roms will be located in the working directory.
- romalizer now fully supports two new styles of merging your roms. You may now use the -g or -G options to tell romalizer to use one of these new merging formats. When -g is used, romalizer will merge all clones into a single zip file. When -G is used, romalizer will create clone zip files that are capable of being run independantly of the parent romset. I have tested these new merging features on my pacman romset and it works beautifully, however more testing probably needs to be done on a complete romset for these options.
- neogeo games are now supported, romalizer will just ignore any CRC that matches 354029fc (ng-sfix.rom), 9036d879 (neo-geo.rom), and 97cf998b (ng-sm1.rom). Thus neogeo roms are now fully supported except for these 3 which should be placed in a file called neogeo.zip.
- romalizer requires usage of UnZip version 5.41 or higher due to a Y2K bug in UnZip. This patch will now check your unzip version and abort if you do not have a recent version of UnZip.
Download (0.008MB)
Added: 2006-11-20 License: Freeware Price:
624 downloads
EasyChem 0.5
EasyChem is a software to draw chemical molecules easily and with high quality. more>>
EasyChem is a program designed to draw chemical molecules, written under Linux and using Gtk+ 2.
Main features:
- Drawing very easily ornaments (non-bonding electron pairs, ...)
- EPS exporting with LaTeX fonts (Computer Modern)
<<lessMain features:
- Drawing very easily ornaments (non-bonding electron pairs, ...)
- EPS exporting with LaTeX fonts (Computer Modern)
Download (0.24MB)
Added: 2005-04-01 License: GPL (GNU General Public License) Price:
1669 downloads
Kemistry 0.7
Kemistry is a collection of chemistry applications for the K Desktop Environment. more>>
Kemistry is a collection of chemical applications for the K Desktop Environment (release 3.x).
Originally the applications were distributed in a single source package, but currently every application is distributed in a standalone package. The available applications are
* KMolCalc - molecular weight and elemental composition calculator
* KemBabel - a file conversion program based on Open Babel
<<lessOriginally the applications were distributed in a single source package, but currently every application is distributed in a standalone package. The available applications are
* KMolCalc - molecular weight and elemental composition calculator
* KemBabel - a file conversion program based on Open Babel
Download (1.15MB)
Added: 2005-04-01 License: GPL (GNU General Public License) Price:
1666 downloads
gElemental 1.0.0
gElemental is a periodic table viewer that provides detailed information on the chemical elements. more>>
gElemental is a periodic table viewer that provides detailed information on the chemical elements. It uses the GTK+ toolkit and is available for Linux and other GTK+ platforms. It is free software released under the GNU General Public License.
The project was developed and is currently maintained by Kevin Daughtridge. It is derived from GPeriodic, developed by Jonas Frantz and originally by Kyle R. Burton.
Main features:
- The table view allows the elements to be coloured thematically. Colouring by chemical series and by phase is currently supported.
- The list view displays key information about the elements, and can be sorted by number, symbol, and name, among others.
- The element properties dialog displays a variety of information, including historical, thermodynamic, electrochemical, and crystallographic properties. (A full list of properties is available.)
- gElemental supports multiple languages. (See translation status for a list.)
- Additional improvements over GPeriodic include:
- Improved interface with better theme compatibility.
- Updated and corrected data set.
- Element and table data in separate data library, libgelemental.
- C++ code base with appropriate typing of element information.
<<lessThe project was developed and is currently maintained by Kevin Daughtridge. It is derived from GPeriodic, developed by Jonas Frantz and originally by Kyle R. Burton.
Main features:
- The table view allows the elements to be coloured thematically. Colouring by chemical series and by phase is currently supported.
- The list view displays key information about the elements, and can be sorted by number, symbol, and name, among others.
- The element properties dialog displays a variety of information, including historical, thermodynamic, electrochemical, and crystallographic properties. (A full list of properties is available.)
- gElemental supports multiple languages. (See translation status for a list.)
- Additional improvements over GPeriodic include:
- Improved interface with better theme compatibility.
- Updated and corrected data set.
- Element and table data in separate data library, libgelemental.
- C++ code base with appropriate typing of element information.
Download (0.42MB)
Added: 2007-05-16 License: GPL (GNU General Public License) Price:
896 downloads
AdvanceSCAN 1.13
AdvanceSCAN project is a commandline ROM manager for emulators. more>>
AdvanceSCAN project is a commandline ROM manager for emulators.
AdvanceSCAN is a command line ROM manager for MAME, MESS, AdvanceMAME, AdvanceMESS, and Raine for Unix, DOS, and Windows.
Main features:
- Directly read, write zip archives without decompressing and recompressing them for the best performance.
- Add, copy, move and rename files in the zip archives. Any rom that you have is placed automatically in the correct zip.
- Recognize the text files added by rom sites and delete them.
- Recognize the text files added by the rom dumpers and keep or delete them.
- Its safe. On all the zip operations any file removed or overwritten is saved in the `rom_unknown `sample_unknown directories and kept for future uses. This will prevent any unwanted remove operation.
- Generate differential rom sets.
Enhancements:
- New rom zips are now created only if at least one unique rom is found. Roms shared with other games dont trigger the zip creation. For example, galaga88
- and pacmania share the rom ns1-mcu.bin. This functionality prevents the creation of the galaga88 zip from a correct copy of pacmania using only the
- ns1-mcu.bin file.
- Relaxed a consistency check for the local header in zip files. The crc and size entries are allowed to contain the real value also if a data descriptor is present.
<<lessAdvanceSCAN is a command line ROM manager for MAME, MESS, AdvanceMAME, AdvanceMESS, and Raine for Unix, DOS, and Windows.
Main features:
- Directly read, write zip archives without decompressing and recompressing them for the best performance.
- Add, copy, move and rename files in the zip archives. Any rom that you have is placed automatically in the correct zip.
- Recognize the text files added by rom sites and delete them.
- Recognize the text files added by the rom dumpers and keep or delete them.
- Its safe. On all the zip operations any file removed or overwritten is saved in the `rom_unknown `sample_unknown directories and kept for future uses. This will prevent any unwanted remove operation.
- Generate differential rom sets.
Enhancements:
- New rom zips are now created only if at least one unique rom is found. Roms shared with other games dont trigger the zip creation. For example, galaga88
- and pacmania share the rom ns1-mcu.bin. This functionality prevents the creation of the galaga88 zip from a correct copy of pacmania using only the
- ns1-mcu.bin file.
- Relaxed a consistency check for the local header in zip files. The crc and size entries are allowed to contain the real value also if a data descriptor is present.
Download (0.29MB)
Added: 2006-12-05 License: GPL (GNU General Public License) Price:
1055 downloads
BKchem 0.12.0_02
BKchem is a chemical drawing program. more>>
BKchem is a free chemical drawing program. BKchem was concieved and written by Beda Kosata.
BKchem is written in Python, an interpreted and very nice programming language.
Main features:
Drawing
- bond-by-bond drawing
- bond lenght and angle restrictions to assist with the drawing
- ready to use templates of common rings
- ability to expand common groups from abbreviated to structural form
- radicals, charges...
- arrows
- rich text
- color support
- simple vector graphics (rectangles, circles, polygons etc.)
Editing
- unlimited undo and redo capabilities
- aligning
- scaling
- rotation (2D, 3D)
- aligning of molecules so that particular bond is horizontal/vertical
- rotation of molecular fragments around bonds (conformation changes)
- definition of personal preferred drawing style (bond lenghts, widths, colors...)
Export
- full export to SVG (native data are transparently embedded into SVG file)
- full export to OpenOffice Draw format
- full export to Encapsulated PostScript
- basic support for both CML1 and CML2
- Molfiles
- generation of SMILES
Import
- basic support for both CML1 and CML2
- Molfiles
- SMILES (subset)
- INChI (subset)
Other features
- localization support (currently English, French, Czech and Polish translations are available)
- native format is XML based
- validity checking of drawn structures
Whats New in 0.11.6 Stable Release:
- In this release, two major bugs were fixed: one in the German translation (causing a crash when a file was saved) and one in the OpenOffice export plugin.
- A few other minor bugs were also fixed.
Whats New in 0.12.0_02 Development Release:
- This release fixes several bugs, most importantly incompatibility with Python 2.5.
<<lessBKchem is written in Python, an interpreted and very nice programming language.
Main features:
Drawing
- bond-by-bond drawing
- bond lenght and angle restrictions to assist with the drawing
- ready to use templates of common rings
- ability to expand common groups from abbreviated to structural form
- radicals, charges...
- arrows
- rich text
- color support
- simple vector graphics (rectangles, circles, polygons etc.)
Editing
- unlimited undo and redo capabilities
- aligning
- scaling
- rotation (2D, 3D)
- aligning of molecules so that particular bond is horizontal/vertical
- rotation of molecular fragments around bonds (conformation changes)
- definition of personal preferred drawing style (bond lenghts, widths, colors...)
Export
- full export to SVG (native data are transparently embedded into SVG file)
- full export to OpenOffice Draw format
- full export to Encapsulated PostScript
- basic support for both CML1 and CML2
- Molfiles
- generation of SMILES
Import
- basic support for both CML1 and CML2
- Molfiles
- SMILES (subset)
- INChI (subset)
Other features
- localization support (currently English, French, Czech and Polish translations are available)
- native format is XML based
- validity checking of drawn structures
Whats New in 0.11.6 Stable Release:
- In this release, two major bugs were fixed: one in the German translation (causing a crash when a file was saved) and one in the OpenOffice export plugin.
- A few other minor bugs were also fixed.
Whats New in 0.12.0_02 Development Release:
- This release fixes several bugs, most importantly incompatibility with Python 2.5.
Download (0.69MB)
Added: 2007-04-04 License: GPL (GNU General Public License) Price:
934 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
Chemistry Development Kit 1.0.1
Chemistry Development Kit is a Java classes for chemo- and bioinformatics. more>>
Chemistry Development Kit classes are Java utitility classes for ChemoInformatics and Computational chemistry, written in Java. They are developed constantly developed parallel to other projects that make use of them.
They are a complete re-write of the CompChem classes that were the basis of JChemPaint, a Java Editor for 2D chemical structures, and of JMDraw, a Java package for the graphical layout of 2D chemical structures.
The CDK project was started in September 2000 to replace the CompChem libraries used by JChemPaint, Jmol and SENECA. It no longer is in its initial stage, but is slowly getting a solid state.
The people involved in setting up the project are Christoph Steinbeck then at the Chemoinformatics Group at the Max Planck Institute of Chemical Ecology in Jena, as well as Egon Willighagen from the University of Nijmegen, The Netherlands, who is also involved with JChemPaint and many other Java Chemoinformatics programs, and Dan Gezelter from Notre Dame University, South Bend, USA, the initiator of Jmol, a 3D viewer and analyzer for molecules .
Now, the rewrite of these CompChem/CDK library classes do somehow effect all of our projects. All of our code relies to some extend on the so-called CompChem classes for computational chemistry.
Christoph Steinbeck started this chemistry library when he started programming SENECA, a system for Computer Assisted Structure Elucidation. It turned out that some of the code had design flaws that prevented others, like the authors of (Jmol) to use it.
Enhancements:
- This release consists of mostly some bugfixes, but also solves a few Java 1.4.2 compile problems and adds more functionality to the SMARTS parser.
<<lessThey are a complete re-write of the CompChem classes that were the basis of JChemPaint, a Java Editor for 2D chemical structures, and of JMDraw, a Java package for the graphical layout of 2D chemical structures.
The CDK project was started in September 2000 to replace the CompChem libraries used by JChemPaint, Jmol and SENECA. It no longer is in its initial stage, but is slowly getting a solid state.
The people involved in setting up the project are Christoph Steinbeck then at the Chemoinformatics Group at the Max Planck Institute of Chemical Ecology in Jena, as well as Egon Willighagen from the University of Nijmegen, The Netherlands, who is also involved with JChemPaint and many other Java Chemoinformatics programs, and Dan Gezelter from Notre Dame University, South Bend, USA, the initiator of Jmol, a 3D viewer and analyzer for molecules .
Now, the rewrite of these CompChem/CDK library classes do somehow effect all of our projects. All of our code relies to some extend on the so-called CompChem classes for computational chemistry.
Christoph Steinbeck started this chemistry library when he started programming SENECA, a system for Computer Assisted Structure Elucidation. It turned out that some of the code had design flaws that prevented others, like the authors of (Jmol) to use it.
Enhancements:
- This release consists of mostly some bugfixes, but also solves a few Java 1.4.2 compile problems and adds more functionality to the SMARTS parser.
Download (13.1MB)
Added: 2007-06-26 License: LGPL (GNU Lesser General Public License) Price:
851 downloads
3D Spatialization of Sound
3D Spatialization of Sound is a Linux/X11 port of the 3D spatializer library from the CRC. more>>
3D Spatialization of Sound is a Linux/X11 port of the 3D spatializer library from the CRC.
This program creates "directional" stereo sound from mono source. CRC folks told me I shouldnt have raised the sampling frequency without adjusting other stuff.
Oh well. This was a proof-of-concept type project anyway. I think to get correct 3D effect, you need to drop sampling rate back to 11025.
To Build the X11 implementation:
1. make
2. cp audio-filter /usr/local/bin
3. mpg123 -m -s some_music.mp3 | audio-filter | aplay -S -s 44100 -f s16l -
audio-filter is implemented as a filter, it reads signed 16 bit mono input at 44100 khz from stdin, and outputs signed 16 bit stereo, 44100 khz output to stdout. You can replace mpg123 with any sound source generating signed 16 bit 44100 khz mono signal. "aplay" is a sound player utility which comes with ALSA linux sound driver. You can use "play" from the sox package, or "ampctl", or any other sound player that would read 44100 khz, signed 16 bit stereo raw data from stdin. For "sox" play script, you would replace "aplay" command line with "play -c 2 -f s -r 44100 -s w -t raw -"
If everything is good, a 640x480 window will come up, with some cryptic writing on the top, a filled circle with an arrow pointing right, and a empty circle slightly to the right of the circle with arrow.
NOTE, that just like in the original Windows implementation, the axiss are reversed. The arrow on the "head" is pointing "forward". So, in the default startup configuration, the sound is located in front of the listener. Moving the sound source "up" moves it to the left of the listener, and "down", to the right. You can visualize this well if you turn your monitor 90 degrees counter
clock wise.
The filled circle with an arrow is your "head"
The empty circle is the "sound source"
You can move the "sound source" around by clicking the mouse at any position in the window, or by clicking on the "sound source" circle, and dragging it to the desired position. Soundfield will be dynamically updated as you do this.
You can move the "head" by moving the mouse to desired position, and right-clicking. The "head" icon will move to the new position and soundfield will be updated.
<<lessThis program creates "directional" stereo sound from mono source. CRC folks told me I shouldnt have raised the sampling frequency without adjusting other stuff.
Oh well. This was a proof-of-concept type project anyway. I think to get correct 3D effect, you need to drop sampling rate back to 11025.
To Build the X11 implementation:
1. make
2. cp audio-filter /usr/local/bin
3. mpg123 -m -s some_music.mp3 | audio-filter | aplay -S -s 44100 -f s16l -
audio-filter is implemented as a filter, it reads signed 16 bit mono input at 44100 khz from stdin, and outputs signed 16 bit stereo, 44100 khz output to stdout. You can replace mpg123 with any sound source generating signed 16 bit 44100 khz mono signal. "aplay" is a sound player utility which comes with ALSA linux sound driver. You can use "play" from the sox package, or "ampctl", or any other sound player that would read 44100 khz, signed 16 bit stereo raw data from stdin. For "sox" play script, you would replace "aplay" command line with "play -c 2 -f s -r 44100 -s w -t raw -"
If everything is good, a 640x480 window will come up, with some cryptic writing on the top, a filled circle with an arrow pointing right, and a empty circle slightly to the right of the circle with arrow.
NOTE, that just like in the original Windows implementation, the axiss are reversed. The arrow on the "head" is pointing "forward". So, in the default startup configuration, the sound is located in front of the listener. Moving the sound source "up" moves it to the left of the listener, and "down", to the right. You can visualize this well if you turn your monitor 90 degrees counter
clock wise.
The filled circle with an arrow is your "head"
The empty circle is the "sound source"
You can move the "sound source" around by clicking the mouse at any position in the window, or by clicking on the "sound source" circle, and dragging it to the desired position. Soundfield will be dynamically updated as you do this.
You can move the "head" by moving the mouse to desired position, and right-clicking. The "head" icon will move to the new position and soundfield will be updated.
Download (0.046MB)
Added: 2006-10-19 License: GPL (GNU General Public License) Price:
1114 downloads
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