> First off, I strongly suggest trying the development "master" from Git, which > has a number of improvements to CIF support. > > > The following three points would need to be addressed: > > 1. Instead of Cartesian coordinates, fractional coordinates must be used in > the .cif file. > > 2. The space-group symmetry must be added to the .cif file. > > 3. Ideally, only the asymmetric unit must be retained in the .cif file, > > ideally > with the same atoms and in the same order as the original cif file (before > energy-minimisation), but that information is probably lost. > > I'm fairly confident that #1 and #2 are addressed. I'm about 80% confident #3 > is already addressed, but if not it's fairly easy to address the code. > > > I have ample experience with scientific software development (C++ and > FORTRAN) within the crystallographic field so I would be able to provide > e.g. algorithms, but I have never used OpenBabel before and I have never > seen the source code, so I would need help. > > We can *definitely* help you. First off, get the Git repository: > https://github.com/openbabel/openbabel > > Try compiling that. I don't see the space group support in > src/formats/casstepformat.cpp but with an example file and a few minutes > with C++ that can be solved.
Thank you to those who responded. It turned out that we already had three OpenBabel versions installed, so it took a while to get the paths to the correct development libraries sorted out, hence the late reply. Indeed, the atomic coordinates are fractional coordinates in the development version (2.3.90) and the cif is very close to being useful. However, the following manual changes are still necessary: 1. The space group is not added to the cif file. This is sort of understandable, as it is not in the .castep file. It can be added to the output in the .castep file by switching on more verbose output, it is present in the accompanying .cell file (the input file of the CASTEP calculation) and it is present in the .castep file in an implicit way in the sense that the space-group symmetry can be derived from the atomic coordinates of the symmetry-related molecules, but that does not change the fact that the space-group symmetry is lost when the .castep file is written out with the default settings. 2. Related to 1., all atoms are kept in the .cif file, including the symmetry-related ones. So the .cif output from .castep files in OpenBabel is very close to useful, but some more changes are needed. I can provide examples, but the first decision that needs to be taken is where the space-group information is coming from: is it taken from the .cell file (i.e. a different file than that indicated by the user), is it derived from the .castep file (that would require a symmetry perception algorithm) or is the user responsible for switching on the option that the space-group symmetry is written to the .castep file (this can only be done by increasing the verbosity, so it would lead to lots of other debug output being written out as well). Using a symmetry perception would be the most general way, but would require quite a bit of coding if this is not already available somewhere. Best wishes, -- Dr Jacco van de Streek Department of Pharmacy University of Copenhagen ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
