- IMP-dev - salilab.org

Re: [IMP-dev] [IMP-commits] r2043 - trunk/modules/atom/pyext
by Daniel Russel 19 Mar '09

19 Mar '09

On Mar 19, 2009, at 9:53 PM, Notification of IMP commits <imp-commits(a)salilab.org > wrote: > Author: kerenl(a)SALILAB.ORG > Date: 2009-03-19 21:53:02 -0700 (Thu, 19 Mar 2009) > New Revision: 2043 > > Modified: > trunk/modules/atom/pyext/atom.i > Log: > expose MolecularHierarchyDecorators to python > > Modified: trunk/modules/atom/pyext/atom.i > =================================================================== > --- trunk/modules/atom/pyext/atom.i 2009-03-20 04:03:51 UTC (rev > 2042) > +++ trunk/modules/atom/pyext/atom.i 2009-03-20 04:53:02 UTC (rev > 2043) > @@ -31,6 +31,7 @@ > } > } > > + > /*namespace IMP { > namespace core { > // stupid hack for swig > @@ -72,6 +73,8 @@ > // swig has random, perplexing issues if these are higher in the > file > %template(AtomTypeBase) ::IMP::KeyBase<IMP_ATOM_TYPE_INDEX>; > %template(ResidueTypeBase) ::IMP::KeyBase<IMP_RESIDUE_TYPE_INDEX>; > + > %template( > MolecularHierarhcyDecorators) > ::std::vector<MolecularHierarchyDecorator>; > + > } > } > %include "IMP/atom/AtomDecorator.h" > > _______________________________________________ > IMP-commits mailing list > IMP-commits(a)salilab.org > https://salilab.org/mailman/listinfo/imp-commits

1 0

distance in ConnectivityRestraint
by Friedrich Foerster 19 Mar '09

19 Mar '09

hi all, is there any way to print the distance(s) used in the ConnectivityRestraint? i'd like to print the actual distances of the minimal spanning tree. thanks frido

2 5

exposing MolecularHierarchyDecorators to python
by Keren Lasker 18 Mar '09

18 Mar '09

hi, I am trying to use write_pdb, which gets as input a set of MolecularHierarchyDecorator (MolecularHierarchyDecorators) This type (MolecularHierarchyDecorators) is not exposed in python. I tried to add typedef in the atom.i file, but then the compiler complained that this has already been declared in MolecularHierarchyDecorator.h ( which is true). but still the python interface does not include MolecularHierarchyDecorators. any ideas how to solve it ? thank you, Keren.

2 1

ParticleRefiner->Refiner
by Daniel Russel 18 Mar '09

18 Mar '09

To shorten the names (and since it was trivial) ParticleRefiner has become Refiner. If you use them explicitly anywhere, run this to update your code: sed -i.old "s#ParticleRefiner#Refiner#g" `find * -name \*.py -or -name \*.cpp -or -name \*.h` A better name would be appreciated and any suggestions are welcome.

1 0

Proposal: rename PrincipleComponents to PrincipalComponents
by Ben Webb 17 Mar '09

17 Mar '09

Unless the code is referring to some kind of PCA with which I'm not familiar, this should be Principal not Principle, surely? If no objections, I'll make the change. But obviously the interface will change when I do - just letting you know... Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

2 1

Last week in IMP
by Daniel Russel 16 Mar '09

16 Mar '09

It was a quite week. - The new web site has gone live. Please check it out and pass on any comments/problems. - Several new geometric shapes have been added to the algebra module. - There is now a wiki page <https://salilab.org/imp/wiki/changes> which lists significant changes that have been made to IMP. Please update the page when you make major changes (the standard of what counts as major will emerge as we go on :-)

1 0

Interacting particles and score states
by Daniel Russel 12 Mar '09

12 Mar '09

The graph of interacting particles returned by calling get_interacting_particles() on all the restraints doesn't reflect the true interactions as soon as you involve things like centroids, rigid bodies or covers. One solution would be to allow ScoreStates to produce lists of interacting particles as restraints currently do (and have Domino add these lists to its graph). Other thoughts? Keren?

2 2

is there an easy way to copy a hierarchy ?
by Keren Lasker 12 Mar '09

12 Mar '09

I would like to implement a function copy_molecule ( which requires creating new particles with the appropriate attributes). More generally, I would like to have a functionality of taking a root of some hierarchy and copying all attributes values into a new root. did someone do something similar already ? thanks, Keren.

2 1

math functions in c++
by Daniel Russel 12 Mar '09

12 Mar '09

You need to use the std:: versions of the math functions when writing C ++ code. That is use "std::abs", "std::sin" etc. By using the C++ versions, rather than the C version, you make sure that the correctly overloaded version is used. If you, for example, use just "abs", then the argument is implicitly converted to an int, which is probably not what you want. Likewise, using "sinf" in algebra where we are using doubles for computation truncates the argument, loosing accuracy for no reason.

1 0

set_print_exceptions
by Keren Lasker 11 Mar '09

11 Mar '09

IMP.set_print_excpetions() does not exist anymore, at least in the swig interface - was the function renamed? thanks, keren.

2 3