April 2012 - cctbxbb - phenix-online.org

Niggli-reduced cell C++ implementation
by Martin Uhrin 24 Apr '12

24 Apr '12

Dear Cctbx community, Firstly I'd like to say thank you to Rolf, Nicholas and Paul for their expertly thought through implementation of the reduced cell algorithm. I've found it to be extremely useful for my work. My code is all in C++ and I'd like to be able to use the Krivy-Gruber algorithm. My understanding is that only the reduced (Buerger) unit cell algorithm is implemented in C++ [1] which guarantees shortest lengths but not unique angles. From my understanding the Krivy-Gruber would also guarantee me uniqueness of unit cell angles, however this is only implemented in Python [2]. Sorry to be so verbose, I just wanted to check that I was on the right page. Would it be possible for me to implement the Krivy-Gruber in C++ by adding in the epsilon_relative to the parameter and following the procedure found in the python version? Many thanks, -Martin [1] http://cctbx.sourceforge.net/current/c_plus_plus/classcctbx_1_1uctbx_1_1fas… [2] http://cctbx.sourceforge.net/current/python/cctbx.uctbx.krivy_gruber_1976.h… -- Martin Uhrin Tel: +44 207 679 3466 Department of Physics & Astronomy Fax:+44 207 679 0595 University College London martin.uhrin.10(a)ucl.ac.uk Gower St, London, WC1E 6BT, U.K. http://www.cmmp.ucl.ac.uk

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Handling unmerged reflections from MTZ
by Graeme.Winter＠Diamond.ac.uk 24 Apr '12

24 Apr '12

Hi Folks, I have been writing very bad Python code to handle unmerged MTZ files using CCTBX - in essence copying all of the measurements to lists for each Miller index. Inefficient. Has anyone looked a neater way of handling these files perhaps with doing the "hard work" from C++? Reading the file is very easy, but managing the data is harder. Essentially I would like to be able to read in a scaled-summed-but-unmerged MTZ file (equivalent to unmerged scale pack no-merge-original-index) and get back all observations of a given HKL, which I can then subsequently analyse… I could crack on and write something but it strikes me as a good idea to ask first. 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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Branches
by Graeme.Winter＠Diamond.ac.uk 22 Apr '12

22 Apr '12

Hi Folks, Quick question - does anyone ever use branches with the CCTBX repository? Just at the moment I'm up to a few things which I would like to be able to commit, but I don't want to break the existing code... however as a project it does not seem CCTBX uses branches much... 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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Type checking in Phil...
by Graeme.Winter＠Diamond.ac.uk 11 Apr '12

11 Apr '12

… is there any? This does not give an error: from libtbx.phil import parse working_phil = parse(""" parameter { toy = 10 .type = int } """) if __name__ == '__main__': working_phil.show() # this should crash right? working_phil = working_phil.fetch(parse('parameter.toy=foo')) working_phil.show() Output: cctbx.python toy_phil.py parameter { toy = 10 } parameter { toy = foo } 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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