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869 discussions

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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Re: [IMP-dev] IMP-dev Digest, Vol 16, Issue 5
by Javier Ángel Velázquez Muriel 03 Feb '09

03 Feb '09

I would suggest something similar to what I have in em/include/EulerOperations.h, if you find it useful. > Given we already have rotation from_fixed_xyz which is a form of euler > angles, this function should probably have a more descriptive name > describing which Euler angles it uses. > > > On Feb 2, 2009, at 10:10 PM, Notification of IMP commits wrote: > > > Author: kerenl(a)SALILAB.ORG > > Date: 2009-02-02 22:10:39 -0800 (Mon, 02 Feb 2009) > > New Revision: 1414 > > > > Modified: > > trunk/modules/algebra/include/Rotation3D.h > > Log: > > add rotation_from_euler > > > > Modified: trunk/modules/algebra/include/Rotation3D.h > > =================================================================== > > --- trunk/modules/algebra/include/Rotation3D.h 2009-02-03 03:11:05 > > UTC (rev 1413) > > +++ trunk/modules/algebra/include/Rotation3D.h 2009-02-03 06:10:39 > > UTC (rev 1414) > > @@ -114,6 +114,24 @@ > > return Rotation3D(a,b,c,d); > > } > > > > +//! Initialize a rotation from euler angles > > +/** > > + \note http://en.wikipedia.org/wiki/ > > + Conversion_between_quaternions_and_Euler_angles > > + \relates Rotation3D > > +*/ > > +inline Rotation3D rotation_from_euler(Float phi, Float theta, Float > > psi) > > +{ > > + Float a,b,c,d; > > + Float c1,c2,c3,s1,s2,s3; > > + c2=cos(theta/2);c1=cos(phi/2);c3=cos(psi/2); > > + s2=sin(theta/2);s1=sin(phi/2);s3=sin(psi/2); > > + a = c1*c2*c3+s1*s2*s3; > > + b = s1*c2*c3-c1*s2*s3; > > + c = c1*s2*c3+s1*c2*s3; > > + d = c1*c2*s3-s1*s2*c3; > > + return Rotation3D(a,b,c,d); > > +} > > //! Generate a Rotation3D object from a rotation matrix > > /** > > \throw ValueException if the rotation is not a rotation matrix. > > > > _______________________________________________ > > IMP-commits mailing list > > IMP-commits(a)salilab.org > > https://salilab.org/mailman/listinfo/imp-commits > >

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lost my paths
by Keren Lasker 03 Feb '09

03 Feb '09

hi, A recent change in r1369 (imppy.sh no longer propagates external LD_LIBRARY_FLAGS and PYTHONPATH) breaks Frido and my assembler code since our pythonpath contains more than just IMP. Can someone please take a look? thanks, Keren.

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