- cctbxbb - phenix-online.org

Python documentation
by David Waterman 10 Oct '12

10 Oct '12

Hi, I've got a few questions about the automatically generated Python documentation. 1. Is this done by doxygen like the C++ documentation? 2. What are the rules that determine whether text in source files is included as documentation or not? Clearly docstrings are, but also some comments do (only those at module scope?) 3. Similarly, what determines which packages are documented or not? For example, from http://cctbx.sourceforge.net/current/python/rstbx.html, cftbx is documented but bpcx is not. Is there at some point a manual decision about what should be documented? Cheers -- David

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Going from a pdb file to an x_ray_structure object
by Claudia Millán Nebot 09 Oct '12

09 Oct '12

Hi everyone, i'm trying to get an xray.structure object from a pdb file, as i'm interested on using both this and a Miller array coming from a reflection file to calculate correlation coefficients between Fobs and Fcalc. For this purpose, i was searching for something that will do the same as the iotbx.pdb.xray_structure.as_pdb_file but the other way around. Is there such a tool? I've look for a while but as i'm new to all that maybe i missed something. Thanks in advance and my excuses if is a too evident question, Claudia Millán (cmncri(a)ibmb.csic.es) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain

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Re: [cctbxbb] RE : cctbx debian package: new commit
by Radostan Riedel 04 Oct '12

04 Oct '12

On Wed, 03. Oct 11:11, Baptiste Carvello wrote: > 2) there are a few C++ applications which depend on cctbx, the one I > know is FOX ( http://vincefn.net/Fox/ , objcryst-fox in Debian). For > those use cases, should we still build a libcctbx-dev package with the > headers and static libs (for those we don't need to care about ABI > stability)? I think this is a very important point here. Let's assume I want to extent the cctbx by adding a module, for let's say absorbtion correction and I want to implement a method called "multiscan" and I want to make a fast python boost extension to integrate with my python code. I need some symbols from any of the shared libs in cctbx. How could this be done in Debian or in any other distribution? About the check for version: In my patch I did this with SCons[1]. What this does is to compile and link a test program and check for success. I saw in your code that you are doing similar things and we could write some simple c++ program that for example includes boost/version and check some "BOOST_VERSION"? This way it checks globally for the availability of a shared library. [1] http://www.scons.org/doc/2.0.1/HTML/scons-user/x4146.html

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Explicit import for iotbx.pdb.amino_acid_codes
by Claudia Millán Nebot 01 Oct '12

01 Oct '12

Hello everyone :) I've just started to look into the cctbx facilities, and as i'm a newbie in both object oriented programming and in general to the system, i'm tryng to play around and find by myself how things are working. Using the cctbx.python, i realised that it is necessary to import explicitly the module amino_acid_codes, while for others like atom_name_interpretation this is done straigthforward if you do an import from a lower level (like from iotbx.pdb import *). Is there some good reason because this has to be like that? Thanks in advance for the answer, and excuse me if is it is a question too simple! Claudia Millán (cmncri(a)ibmb.csic.es) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain

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Build failing
by Graeme.Winter＠diamond.ac.uk 01 Oct '12

01 Oct '12

Hi Folks, Following an svn update and several attempts to build, I am still getting this compile error /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/detail/bessel_jy.hpp:346:11: error: 'bessel_y_small_z_series' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/detail/bessel_jn.hpp:17:0, from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/bessel.hpp:18, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/bessel.h:9, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/boost_python/math_ext.cpp:3: /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/detail/bessel_jy_series.hpp:139:10: note: 'template<class T, class Policy> T boost::math::detail::bessel_y_small_z_series(T, T, T*, const Policy&)' declared here, later in the translation unit In file included from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/bessel.hpp:17:0, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/bessel.h:9, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/boost_python/math_ext.cpp:3: /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/detail/bessel_jy.hpp:356:11: error: 'bessel_j_small_z_series' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/detail/bessel_jn.hpp:17:0, from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/bessel.hpp:18, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/bessel.h:9, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/boost_python/math_ext.cpp:3: /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/detail/bessel_jy_series.hpp:47:10: note: 'template<class T, class Policy> T boost::math::detail::bessel_j_small_z_series(T, T, const Policy&)' declared here, later in the translation unit In file included from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/bessel.hpp:17:0, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/bessel.h:9, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/boost_python/math_ext.cpp:3: /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/detail/bessel_jy.hpp:363:11: error: 'bessel_yn_small_z' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/detail/bessel_jn.hpp:17:0, from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/bessel.hpp:18, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/bessel.h:9, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/boost_python/math_ext.cpp:3: /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/detail/bessel_jy_series.hpp:213:3: note: 'template<class T, class Policy> T boost::math::detail::bessel_yn_small_z(int, T, T*, const Policy&)' declared here, later in the translation unit scons: *** [scitbx/math/boost_python/math_ext.o] Error 1 scons: building terminated because of errors. usr+sys time: 26.64 seconds, ticks: 51849408, micro-seconds/tick: 0.514 wall clock time: 8 minutes 5.55 seconds (485.55 seconds total) make: *** [default] Error 2 OS X Lion machine Graemes-MacBook-Pro:build graeme$ uname -a Darwin Graemes-MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 Graemes-MacBook-Pro:build graeme$ gcc --version gcc (GCC) 4.7.0 20120314 (prerelease) Copyright (C) 2012 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Have I missed something? Nightly builds seem to be OK. Commands ../../cctbx_plus/base/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python ../sources/cctbx_project/libtbx/configure.py --compiler=gcc labelit cctbx bpcx_regression rstbx . setpaths.sh make 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. 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dropping Python 2.4 support?
by Nathaniel Echols 27 Sep '12

27 Sep '12

Hi all-- Will it ruin anyone's work if we make Python 2.5 the minimum platform for using CCTBX? 2.4 is now almost eight years old and the lack of certain newer features (decorators, 'with') is starting to hold us back. thanks, Nat

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Enabling OpenMP for phaser on OS X
by William G. Scott 17 Sep '12

17 Sep '12

Hi folks: I found if I created a symbolic link from a g++4.7 compiler to /usr/bin/g++, I could "trick" phaser into compiling with OpenMP enabled. This is kind of an ugly hack. How do I force it to use /sw/bin/g++-4 ? Is there some place in the source code for cctbx (or phaser) that I can make such a change? Thanks. Bil William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA

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Quick start info?
by esserlo＠helix.nih.gov 11 Sep '12

11 Sep '12

Hi all, this is a question about how to get started quickly. I have looked at the sourceforge site for cctbx and read diverse documents but so far I have not found documentation that would help me get started fast. I have a crystallographic problem which I can probably program from scratch but then again why bother if there is a crystallographic tool box around. But well despite all the power in it getting it to work seems a bit daunting. Are there really good examples? I did get the "sand box quartz model" script to work but this is still far off of what I want to do. Thanks for all advice and sorry if I missed the 'obvious' one. Lothar

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Question about sigma(I) calculation in merge_equivalents
by Keitaro Yamashita 07 Sep '12

07 Sep '12

Dear CCTBX developers, I have a question about the method in CCTBX to calculate sigma(averaged I) when merging. In cctbx/miller/merge_equivalents.h (line 594 in phenix-dev-1148), sigma(averaged I)^2 will be calculated by max(mv.gsl_stats_wvariance()/values.size(), 1/mv.sum_weights()). It takes maximum value of the two options. I know the latter equation - this is just sigma(averaged I)^2 = 1/sum(w), where w = 1/sigma(I)^2. And I believe this equation is widely used in other crystallographic programs e.g. XDS. The former is, according to the comment in the code, the emulation of gsl_stats_wvariance, and we can find the information from gsl website: http://www.gnu.org/software/gsl/manual/html_node/Weighted-Samples.html I don't know how this "wvariance" is derived. Is it a better estimate of sigma(averaged I)? Why does it take the maximum from the two options? I would like to know the theory of this sigma calculation in CCTBX. Best regards, Keitaro

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Debian Package
by Radostan Riedel 05 Sep '12

05 Sep '12

Dear CCTBX Maintainers, Maybe some of you remember me last year asking on this mailing list[1]. I was asked by the Debian Science Team[2] to contribute my former work to get cctbx finally packaged in Debian. The last month I was working with Baptiste Carvello and Picca Frédéric-Emmanuel to get this done. Our packaging efforts + patches can be found in our git[3]. We organize our packaging efforts in a wiki[4]. But we don't want to overlook you and give some of our work back into the main project. We have a few patches to give back upstream that would really help us and hopefully help to increase the cctbx user community. To explain a little bit what we've done. First of all we tried respectfully not to change too much about your build system. We integrated a few options in libtbx/env_config which shouldn't break anything. The primary changes are: * Option to check and use system libraries (in case any library is already installed no need to compile the bundled shlib) * Install targets for headers and shlibs and binaries: calling "scons install" * Shlib versioning: This is achieved by utilizing libtool (the GNU standard) * --install-prefix, --install-destdir and --libdir option * support for LD_FLAGS in --use_environment_flags option * Fallback to avoid using "LIBTBX_BUILD" env variable after install * Full integration of your scons build system in distutils: setup.py and sconsutils.py. You can just call 'python setup.py install' * Adaption of your test system to be called by distutils * Autogenerate pkg-config files for shlibs What we now need to know is if our changes are appreciated or if we need to spend more work on this. Keep in mind that our work is still work in progress! One big concern is always the ABI/API stability. But if we can count on the shlib versioning as mentioned here[5] it would help us and other developers a lot. Libtool should be available on most systems, works with common compilers and it provides the quasi standard for versioning shlibs. We have other issues too but I guess I won't overkill this mail to much for now. I hope we can discuss and work on this together. Please tell us your honest opinion and critics. kind regards Radostan Riedel P.S: This work is intended to work on other distributions too. We also hope that Fedora, openSUSE, Gentoo etc. can benefit from it too. [1] http://phenix-online.org/pipermail/cctbxbb/2011-June/000192.html [2] http://wiki.debian.org/DebianScience [3] http://anonscm.debian.org/gitweb/?p=debian-science/packages/cctbx.git;a=sum… [4] http://wiki.debian.org/DebianScience/cctbx [5] http://www.gnu.org/software/libtool/manual/html_node/Updating-version-info.…

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