May 2012 - IMP-dev - salilab.org

Re: [IMP-dev] hierarchy
by Daniel Russel 21 May '12

21 May '12

The quick answer is "nope" :-) Part of the reason is that we don't want to embed the assumption that the hierarchy has the same depth everywhere in code, and methods like that are hard to use without that assumption. The original idea had been that one would extract layers from the hierarchy by various criteria, such as radius. That is, ask for - give me the finest level representation - give me a representation where the particles all have radius close to 15A etc The atom::Selection class gives that sort of capability (by setting the radius for the selection). On Mon, May 21, 2012 at 1:43 PM, Charles Greenberg <cgreen(a)salilab.org>wrote: > Hey Daniel. Question for you. Kale is doing some very cool domino > experiments, using multiple levels of beads (coarse to fine) with a set of > distance restraints at each level. Currently he's using a simple dictionary > to establish connections between the levels, but he suggested it would be > cool to use the IMP hierarchy format. It's pretty clear how to make a > general hierarchy of particles, and to get children and parents, but is > there code to do simple queries like "How many levels are there?" and "Get > me all particles at level X"? Thanks! > > --Charles

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Re: [IMP-dev] runtime question
by Daniel Russel 21 May '12

21 May '12

Each module has a get_data_path(file_name) function that returns the path to a file named "file_name" located in the data directory (whether you are running it our of the build dir or have installed IMP). For some reason the methods are currently excluded from the docs. I'll fix that. Similarly, there is a get_example_path(file_name) that returns the path to a file in the example directory (to be used in writing examples that load data). On May 20, 2012, at 9:43 PM, Keren Lasker wrote: > daniel - > i have scripts that copy from module/data folder. how can i access that in runtime from python without using $IMP/module/data? > keren.

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Re: [IMP-dev] ISD module compile error on Mac?
by Daniel Russel 20 May '12

20 May '12

I doubt things have ever been looked into for doing static compilation of isd with cholmod. One needs to figure out which libraries cholmod depends on and add them to the add_dependency call (when doing dynamic linking they are brought in automatically). To help us get started, you can do ldd on the cholmod dynamic lib (somehting like /usr/lib/libcholmod.so) and send the results (if you are in a mac, you need to run "otool -L " on the .dylib instead). That shows what libraries the dynamic lib brings in on your platform. If you don't need isd, just disbable it as I'm not sure we want to get this working unless really needed as it could be painful. On May 19, 2012, at 7:41 PM, Seung Joong Kim wrote: > Hi Yannick, > > Suddenly I have a problem in compiling the ISD module as follows. Do you have any idea what happens? I recently upgraded to OSX 10.7 Lion, hopefully that is not an issue.. Thanks a lot! > > Compiling shared build/src/imp_isd_config.cpp > Compiling modules/isd/bin/benchmark_gaussianprocess.cpp > Install file: "build/swig/IMP_isd.i" as "build/data/swig/IMP_isd.i" > Running swig on file build/swig/IMP_isd.i > /opt/local/bin/swig -castmode -interface _IMP_isd -DPySwigIterator=IMP_ISD_PySwigIterator -DSwigPyIterator=IMP_ISD_SwigPyIterator -python -c++ -naturalvar -fvirtual -Wextra -o /Users/sjkim/imp/trunk/build/src/IMP_isd_wrap.cpp-in -oh /Users/sjkim/imp/trunk/build/src/IMP_isd_wrap.h-in -Ibuild/swig -I/opt/local/include -I/usr/include -I/usr/local/include -I/Users/sjkim/imp/trunk/build/include -I/Users/sjkim/imp/trunk -DIMP_SWIG /Users/sjkim/imp/trunk/build/swig/IMP_isd.i > /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' > /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' > /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' > /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' > /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' > /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' > /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' > /Users/sjkim/imp/trunk/build/include/IMP/isd/bivariate_functions.h:129: Warning 314: 'lambda' is a python keyword, renaming to '_lambda' > Install file: "build/src/IMP.isd.py" as "build/lib/IMP/isd/__init__.py" > Patching swig file build/src/IMP_isd_wrap.h > Patching swig file build/src/IMP_isd_wrap.cpp > Compiling shared build/src/IMP_isd_wrap.cpp > Linking Shared Library build/lib/libimp_isd.dylib > Undefined symbols for architecture x86_64: > "_dpotrf_", referenced from: > _r_cholmod_super_numeric in libcholmod.a(cholmod_super_numeric.o) > "_zpotrf_", referenced from: > _c_cholmod_super_numeric in libcholmod.a(cholmod_super_numeric.o) > _z_cholmod_super_numeric in libcholmod.a(cholmod_super_numeric.o) > ld: symbol(s) not found for architecture x86_64 > collect2: ld returned 1 exit status > scons: *** [build/lib/libimp_isd.dylib] Error 1 > scons: building terminated because of errors. > > - SJ > > -- > Seung Joong Kim, Ph.D. > > Postdoctoral Scholar, Andrej Sali group > Department of Bioengineering and Therapeutic Sciences > University of California at San Francisco (UCSF) > 1-217-649-2147 >

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sampler vs. optimizer
by Dina Schneidman 19 May '12

19 May '12

Hi, I am trying to figure out the difference between sampler and optimizer. When each one should be used/developed? What is the relationship between them? How each one works with restraints and scoring functions? Dina

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add_attribute vs. add_cache_attribute
by Dina Schneidman 18 May '12

18 May '12

Hi, What is the difference between the two functions for adding Particle attributes? Dina

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git and svn
by Daniel Russel 11 May '12

11 May '12

Since there have been a couple of questions about using git with imp svn recently, I finished a cheat sheet I had started. See < http://salilab.org/imp/wiki/git> and please add more helpful commands.

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