Release Notes: Dynamic filtering of the oligomer data obtained after a polymer sequence cleavage was added. This allows an immediate scrutiny of the obtained oligomers when these are numerous and one experimental mass peak needs to be interpreted.
Release Notes: Intra-molecular cross-links were implemented. For protein chemists, this means that sulfide bonds are now handled in the sequence and that simulation of the fluorescent proteins also (their chromophore is created by internal cross-links involving three monomers). Finding a sequence motif in a polymer sequence was implemented. This is a rather simple implementation but very handy for long polymer sequences. A serious bug with how composite formulas are handled in certain cases was fixed. You should really be upgrading to version 1.7.1 for this reason. Various bugfixes and other small improvements were made.
Release Notes: This release fixes a serious crash when computing the elemental composition of a polymer sequence that bore a formula-defined modification as opposed to selecting a modification from the list. This bugfix triggered a wave of code cleanup and the coding of a new, more robust way of modifying the polymer sequence. The polymer sequence file format changed, but older formats are handled with a versioning scheme that was coded in this release.
Release Notes: This release improves the flexibility of the monomer modification procedure: now it is possible to define a modification in the monomer modification dialog without the modification having to be defined in the polymer chemistry definition. This makes it much faster to test structural hypotheses. The polymer modifications are now easily visualized in the polymer sequence editor, and there they can be easily modified. The documentation has been updated.
Release Notes: The polymer chemistry definition code has been fully rewritten, and the user interface redesigned. There are bugfixes here and there. Coding of the framework for intra-molecular cross-link has begun. There is a new package for Fedora core, and the usual packages for Debian GNU/Linux.
Release Notes: This release fixes a bug with the calculation of polymer net charges given a pH. The bug would not show up at each calculation. pI calculations were also affected. The project has been converted from the qmake build system to the more powerful CMake build system, which is portable and can build the software for all the Qt-supported platforms. Note that the documentation still does not reflect the conversion.
Release Notes: When cleaving or fragmenting a sequence, you may now ask for the generation of cleavage- or fragmentation-based oligomers of any given ionization state. For example, when cleaving a protein using an enzyme, it is possible to ask that the generated peptides be in an ionized state between z=1 and z=5. A bug with the acido-basicity calculations where the user could only enter integer pH values was fixed. Double values (precision 2 decimals) may now be used to allow finer grained calculations. Various minor bugs were fixed.
Release Notes: A feature was added whereby, upon definition of a monomer chemical modification, the user might tell which monomers are targets of that modification. If the user tries to modify a monomer with a modification that cannot be used for that, she is alerted. A mechanism overriding the modification target limitations is available for maximum flexibility. Bugs related to the chemical modification of polymer sequences were fixed. The user manual was updated to document the new features.
Release Notes: The translation framework was set up and the program was fully translated to French. The handling of monomer modifications was definitely improved when no svg file has been defined for these: the program is now crash-proof. A bunch of bugs were fixed regarding the modifications being declared in the polymer chemistry definitions but not available as svg files (which would lead to crashes). The User Manual was fixed.
Release Notes: This release adds the ability to modify a polymer sequence using arbitrary formulas, not necessarily modifications from the polymer chemistry definition. It fixes many bugs with the modifications in the modification_dictionary file and related graphical vignettes. The code has been updated to comply with Qt 4.3.0 on GNU/Linux. Some glitches have been fixed in the sequence editor window. Recorder output in the calculator window has been improved. The documentation has been greatly improved by making it more concise and specific. The problematic MS Windows package creation procedure should hopefully be fixed.