February 2009 - IMP-dev

Moving algebra to doubles
by Daniel Russel 13 Feb '09

13 Feb '09

As was mentioned before, it is probably a good idea to move all the storage and computations in the algebra module to use "doubles" in order to improve numerical robustness. IMP::Float would stay as "float" for now. Probably the cleanest way to do this is to replace all "Float" with "double" in the existing code. This appears to work without problems. If no one objects, I'll submit the patch soon.

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Minor changes
by Daniel Russel 13 Feb '09

13 Feb '09

the version info headers now don't have the redundant module name prefix: IMP/core/internal/core_version_info.h -> IMP/core/internal/version_info.h Same for the class defined inside. There is now one big swig macro to wrap the constructor (IMP_OWN_CONSTRUCTOR) instead of different macros depending on the number of arguments. Everything in SVN has been fixed.

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Moved PI
by Daniel Russel 12 Feb '09

12 Feb '09

PI is no longer internal as is used all over the place and was kind of hard to find. More centrally, the constants have been refactored to separate the unitless ones (PI, NA), which are now public, from the ones with units which will remain internal until something nice happens to units (that will probably wait a year or so until we adopt Boost 1.36 or whichever version first introduced the Boost.Units library).

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proposal to rename DecoratorBase -> Decorator
by Daniel Russel 10 Feb '09

10 Feb '09

Just to make the docs prettier: i.e. you can see all restraints by going to the Restraint page, so it would make sense to go to the Decorator page to see all decorators (even if the Decorator class is not used in the same way as the Restraint class).

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imp / python version
by Keren Lasker 06 Feb '09

06 Feb '09

hi, how can I make the imp build to use not the default python version ( for example on the cluster - I would like to compile to python2.5 and the default is 2.4) ? thanks, Keren.

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intermediate models while optimizing
by Keren Lasker 05 Feb '09

05 Feb '09

hi, How do you write out intermediate models while optimizing ? thanks, Keren.

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Removing deprecated classes
by Daniel Russel 05 Feb '09

05 Feb '09

Since we now have a recent Ben Blessed Branch (aka stable branch), I'd like to remove the deprecated classes from core. Last chance to squawk. --Daniel

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Switching to the new website
by Daniel Russel 05 Feb '09

05 Feb '09

Now that I have Marc's prettier IMP website up and running on guitar, I propose we switch the public face of IMP over to it. Any important things that should be changed before unveiling (not that anyone is really looking at the IMP site :-)? <http://www.salilab.org/~drussel/hidden/IMPc> Obviously we are going to want to tweak and modify things a lot as we move forward but we need to start with something.

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more than one molecular hierarchy
by Keren Lasker 03 Feb '09

03 Feb '09

hi, So , I have a molecular with proper hierarchy, and would like to add rigid bodies. To define the rigid bodies I am using molecular hierarhcy, so a particle may have more than one parent ( one for the molecule, for example an atom belongs to a molecule, and one for his rigid body). Currently a particle can have at most one parent in molecular hierarchy. I think the solution should be adding RigidBodyHierarchyDecorator - thoughts? thanks, Keren.

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scons arguments names
by Daniel Russel 03 Feb '09

03 Feb '09

We (mostly I) haven't been very consistent about naming the arguments to scons in terms of whether they have path in the name or not. I propose: lib->libpath include->includepath

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