applications/engineering

olex2 - Is a visualisation software for small-molecule crystallography

Website: http://sourceforge.net/projects/olex2/
License: BSD
Description:
Olex2 is a program for the determination, visualisation and analysis of
molecular crystal structures. It has a portable, mouse-driven,
workflow-oriented and fully comprehensive graphical user interface (GUI).

It provides the user with a GUI for structure solution, refinement and report
generation as well as novel tools for structure analysis. All this whilse it
seamlessly links all aspects of the structure solution, refinement and
publication process and present them in a single, workflow-driven package –
with the ultimate goal of producing an application which will be useful to both
chemists and crystallographers.

Reference:
J. Appl. Cryst. (2009). 42, 339–341

Packages

olex2-1.0.4-20091010svn.1.fc10.src [33.1 MiB] Changelog by John (2009-10-10):
- SVN version TRUNK 893
- r856 - File menu item is fixed (besides the case of empty recent files list);
	 improvement to the H-add detecting of the coordination to metal;
- r857 SGInfo is exposed to python; structure inversion now takes the space 
	group inversion centre into account; re-factoring - push, inv and 
	transform are moved to the xlib to be accessible from the headless;
- r858 if symbol H or D is provided for mode name, the H and D atoms labels are
	 switched on
- r859 a test for alphanumeric and alphabetic chars is added to the string class;
	 fixHL now takes fragments into account and does not need multiple runs 
	to converge, however if there are Q-peaks connecting fragments the 
	procedure might give wrong labelling scheme
- r860 typo fixed...
- r861 an attempt to fix OwnerDrawCombobox KILL_FOCUS event...
- r862 non-windows compilation is fixed, though there is a very strange 
	behaviour on GTK, then the onleave/onenter events just recurring
- r863 a bug on linux regarding pending object deletion and causing various
	 problems with reloading html from controls is fixed
- r864 the ASelectionOwner is extended to provide a list of TSAtoms; TTextCtrl
	and TComboBox do not implement of focus change anymore - the THtml
	manages it instead (since problems on Windows, then focus events are 
	broken for wxOwnerDrawnCombobox); Tab item traversal is now managed by
	 the THtml; fixhl now might take a selection to specify the order in 
	this fragments should be processed; 
- r865 some Mac features are fixed, but buttons and other controls which do not
	 accept input cannot be focused and traversed on Mac...
- r866 a fix for #151
- r867 right mouse button click is fixed on Mac...
- r868 a fix for #152
- r869 just a typo fixed...
- r871 fix for the #144, uninitialised variable was used...
- r872 typos fixed; the focus change from mouse is handled now in the html;
	weight and proposed weight is now exported to python and oxm;
- r873 hadd for R3B-H is added; the bug with incorrect virtual function name in
	 TXGrid is fixed (#16, internal); hadd for coordinated linear C-N->M is
	 skipped; 
- r874 a fix for the focus being stolen after clicking or a read-only combobox...
- r875 SAME now can take a set of atoms (provided the number of groups as first
	 argument)
- r876 the SetVisible function of the AGDrawObject is made virtual...;
	some modification are made to the HTML processing, an attempt to get 
	current BGCOLOR to use with controls have failed, though the text color 
	can be easily accessed through the GetActualColor o wxHTMLWinParser 
- r877 some modifications done to the casting, so that underlying object can be
	used as a reference or const reference without the need to create a new
	 instance; the next step would be to pre-cache the casting operators
	(this will require a static method to get an operator though)
- r878 and a crash is fixed when trying to deallocated already deallocated memory...
- r879 no comment--
- r880 typo is fixed
- r881 a bug is fixed in the octahedral distortion calculation using best plane
	approach also automatic evaluation of the total distortion is added
- r882 a Alt+drag is added for MAC for zooming; the use of fastsymm is now can 
	be controlled by defining __OLX_USE_FASTSYMM, it is off for now, since 
	there are no many demanding tasks...; more work on the octahedral 
	distortion calculation
- r883 a newly introduced memory leak is fixed...
- r885 a fix for exyz - only a selected atom and set of new types is sued now; 
	a fix for conn - now both number of bonds and radius are used...; a fix
	 for mode grow -r
- r886 an update for the logic behind fvar macro...
- r887 ExtractFileExt and ChangeFileExt functions are fixed for the '.' only in
	 the path, however these till not work for c:\xxx.yyy ... DataDir is 
	now appended with tag
- r888 some re-factoring to leave all HTTP, ZIP and other protocols in
	UpdateAPI and move all other stuff into the PatchAPI; TEFile dealing
	with extensions now checks if the given name is a folder (so does the 
	ExtractFileName); TIns now replaces all tabs with spaces...; a large 
	change to the DataDir, not DataDir is defined by the BaseDir and the 
	repository tag, however if the DataDir does not exist and old Olex2u 
	folder does, the content of that folder will be copied across (only if
	 Olex2 was not run before); installer will update will also rename 
	DataDir when renaming an installation (will be used for new 
	installations only); 
- r889 and mac/linux picularities
- r890 launch now removes OLEX2_DIR and OLEX2_DATADIR when running olex2, 
	I hope it is for good; a static method Copy for folders is added into
	 TFileTree for convenience;
- r891 never ending bugs...
- r892 debug info stripped..., last for today
- and finally this is what released today

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