July 2010 - IMP-dev - salilab.org

[Bug 107] New: TextInput reports mismatched arguments rather than failure to open file
by bugzilla-daemon＠salilab.org 30 Jul '10

30 Jul '10

https://salilab.org/imp/bugs/show_bug.cgi?id=107 Summary: TextInput reports mismatched arguments rather than failure to open file Product: IMP Version: unspecified Platform: All OS/Version: All Status: NEW Severity: minor Priority: P5 Component: kernel AssignedTo: drussel(a)SALILAB.ORG ReportedBy: drussel(a)SALILAB.ORG CC: imp-dev(a)salilab.org Estimated Hours: 0.0 Swig eats the I/O exception and reports it as an argument mismatch. -- Configure bugmail: https://salilab.org/imp/bugs/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

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[Bug 64] Need a comprehensive solution for symmetry in models
by bugzilla-daemon＠salilab.org 30 Jul '10

30 Jul '10

https://salilab.org/imp/bugs/show_bug.cgi?id=64 --- Comment #1 from Daniel <drussel(a)SALILAB.ORG> 2010-07-30 10:32:53 PDT --- *** Bug 110 has been marked as a duplicate of this bug. *** -- Configure bugmail: https://salilab.org/imp/bugs/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

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[Bug 110] New: Add periodic boundary conditions
by bugzilla-daemon＠salilab.org 30 Jul '10

30 Jul '10

https://salilab.org/imp/bugs/show_bug.cgi?id=110 Summary: Add periodic boundary conditions Product: IMP Version: unspecified Platform: All OS/Version: All Status: NEW Severity: enhancement Priority: P5 Component: core AssignedTo: drussel(a)SALILAB.ORG ReportedBy: drussel(a)SALILAB.ORG CC: imp-dev(a)salilab.org Estimated Hours: 0.0 Initially just have a special purpose close pairs restraint and a class to wrap things at the boundary. See if bounding box sweep can work with circular boundary? Seems unlikely. Grid might be best. -- Configure bugmail: https://salilab.org/imp/bugs/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

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[Bug 108] New: NetCDF I/O
by bugzilla-daemon＠salilab.org 30 Jul '10

30 Jul '10

https://salilab.org/imp/bugs/show_bug.cgi?id=108 Summary: NetCDF I/O Product: IMP Version: unspecified Platform: All OS/Version: All Status: NEW Severity: enhancement Priority: P5 Component: kernel AssignedTo: drussel(a)SALILAB.ORG ReportedBy: drussel(a)SALILAB.ORG CC: imp-dev(a)salilab.org Estimated Hours: 0.0 It would be nice to have a write_model_binary/read_model_binary using NetCDF to go along with the current text versions. There is a standard for writing series of molecule structures to a file, but it would be also good, for maximimal compactness to have an option to just write optimized attributes. -- Configure bugmail: https://salilab.org/imp/bugs/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

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Just for fun
by Daniel Russel 28 Jul '10

28 Jul '10

Here are stats extracted from the svn logs <http://www.salilab.org/~drussel/imp_stats/>. It excludes data files and commits made before they were connected to usernames.

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Restraint::get_is_part_of_model() and ScoreState::get_has_model()
by Daniel Russel 22 Jul '10

22 Jul '10

do the same thing. I propose to rename the first to be like the second.

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[Bug 109] New: Add google native client compatibility
by bugzilla-daemon＠salilab.org 20 Jul '10

20 Jul '10

https://salilab.org/imp/bugs/show_bug.cgi?id=109 Summary: Add google native client compatibility Product: IMP Version: unspecified Platform: Other OS/Version: All Status: NEW Severity: enhancement Priority: P5 Component: kernel AssignedTo: drussel(a)SALILAB.ORG ReportedBy: drussel(a)SALILAB.ORG CC: imp-dev(a)salilab.org Estimated Hours: 0.0 And a test platform. -- Configure bugmail: https://salilab.org/imp/bugs/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

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Re: [IMP-dev] problem with current IMP
by Daniel Russel 13 Jul '10

13 Jul '10

Boost got upgraded on the Linux machines recently, and scons doesn't notice, leading to the compiler errors below. The easiest thing to do is to delete all the scons databases and things (rm .scons*). On Jul 13, 2010, at 7:18 PM, Keren Lasker <kerenl(a)salilab.org> wrote: > does not compile ... > not sure who made these recent changes: > > build/include/IMP/base_types.h:105: error: invalid application of 'sizeof' to incomplete type 'boost::STATIC_ASSERTION_FAILURE<false>' > In file included from build/include/IMP/VectorOfRefCounted.h:13, > from build/include/IMP/Object.h:18, > from build/include/IMP/Model.h:13, > from kernel/src/Model_dependencies.cpp:9: > build/include/IMP/base_types.h:105: error: invalid application of 'sizeof' to incomplete type 'boost::STATIC_ASSERTION_FAILURE<false>' > g++ -o modules/algebra/src/vector_search.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC \ > -Wall -Woverloaded-virtual -g -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY=\"/usr/share/imp\" -DIMP_EXAMPLE_DIRECTORY=\"/usr/share/doc/imp/examples\" -DIM\ > PALGEBRA_EXPORTS -DGCC_VISIBILITY -Ibuild/include modules/algebra/src/vector_search.cpp > g++ -o build/src/algebra_link_0.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -Wall -Wo\ > verloaded-virtual -g -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY=\"/usr/share/imp\" -DIMP_EXAMPLE_DIRECTORY=\"/usr/share/doc/imp/examples\" -DIMPALGEBRA_\ > EXPORTS -DGCC_VISIBILITY -Ibuild/include build/src/algebra_link_0.cpp > g++ -o build/src/algebra_link_1.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -Wall -Wo\ > verloaded-virtual -g -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY=\"/usr/share/imp\" -DIMP_EXAMPLE_DIRECTORY=\"/usr/share/doc/imp/examples\" -DIMPALGEBRA_\ > EXPORTS -DGCC_VISIBILITY -Ibuild/include build/src/algebra_link_1.cpp > > can you please help? > > thanks, keren.

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automatic force field restraint setup
by Dave Barkan 12 Jul '10

12 Jul '10

Hi all, I was wondering if there is a quick way to set up force field restraints on a hierarchy of atoms generated by read_pdb()? Right now I have to explicitly set up three or four types of restraints myself (following the protocol in the charm_forcefield.py example in the atom module). This is likely to be re-implemented often and it would be nice if IMP provided an easy way to do this. Maybe less useful to others, but potentially to me, would be if you could specify a region of the protein to which to add the forcefield restraints (instead of the whole PDB you just read in). thanks, db

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