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May 2012

7 participants
2 discussions

Invert hand of shelxd res file from cctbx
by Graeme.Winter＠diamond.ac.uk 23 Jul '12

23 Jul '12

Hi Folks, This should be easy but I can't find anything! I have a .res file: [gw56@ws050 fast_ep]$ cat sad_fa.res REM Best SHELXD solution: CC 41.11 CC(weak) 23.51 CFOM 64.62 REM TITL sad_fa.ins SAD in P422 CELL 0.98000 78.17 78.17 37.87 90.00 90.00 90.00 LATT -1 SYMM -Y+1/2,X+1/2,Z+1/4 SYMM -X,-Y,Z+1/2 SYMM Y+1/2,-X+1/2,Z+3/4 SYMM X+1/2,-Y+1/2,-Z+3/4 SYMM Y,X,-Z SYMM -X+1/2,Y+1/2,-Z+1/4 SYMM -Y,-X,-Z+1/2 SFAC SE UNIT 256 SE01 1 0.600227 0.892868 0.042187 1.0000 0.2 SE02 1 0.627518 0.852661 0.427392 0.8667 0.2 SE03 1 0.867409 0.911667 0.394418 0.8420 0.2 SE04 1 0.489761 0.805634 0.391009 0.7279 0.2 SE05 1 0.642792 0.649048 0.369694 0.7172 0.2 SE06 1 0.678879 0.535027 0.477918 0.4571 0.2 SE07 1 0.609207 0.572754 0.421746 0.4212 0.2 SE08 1 0.584526 0.536499 0.322047 0.4154 0.2 SE09 1 0.843063 0.846794 0.480296 0.3831 0.2 SE10 1 0.622429 0.743332 0.157899 0.3604 0.2 SE11 1 0.626114 0.528595 0.644789 0.3590 0.2 HKLF 3 END which I would like to read, invert the hand of and write as a pdb file. I got stuck trying to work through the example / test code. Can someone point me in the right direction? Thanks, Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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controlling types over the C++/Python interface
by David Waterman 16 May '12

16 May '12

Hi, I'm starting to explore the use of boost.python in cctbx. I've written a simple C++ class and exposed its accessor methods as attributes using the .add_property syntax in the wrapper. In the C++ class my member data and accessor return types are, for example, scitbx::vec3<double>. When I access the attribute in Python with the usual dot operator I get a tuple. What I'd really like though is an object of type <class 'scitbx.matrix.col'>, which is what I passed to the constructor of the object in Python. So the conversion from Python to C++ does what I want, but not the other way round. How do I take control of the type of the attribute in Python, without having to explicitly construct a scitbx.matrix.col from the tuple? It's the same case if I use .def and expose the accessor as a method instead of an attribute. I admit I don't fully understand the details of conversions in either direction. I found I had to add from cctbx.array_family import flex to the package __init__.py where my C++ extension is imported, so that I could pass scitbx.matrix.col objects (or scitbx.matrix.rec, or tuples) to the constructor in Python and not get a Boost.Python.ArgumentError. I've not yet figured out what this import is doing though. Apologies for the remedial question. These are still early days for me. Thanks -- David

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