Subject: Re: [IMP-dev] Comments on transformation stuff
From: Keren Lasker <>
Date: Tue, 11 Nov 2008 16:12:03 -0500
Reply-to: List for IMP development <>
Daniel - thanks for your good review!
I'll make the suggested changes.
I agree with everything on Rotation3D and Matrix3D.
Regarding ParticleFunction - see discussion below.
On Nov 11, 2008, at 8:58 AM, Daniel Russel wrote:
Rotation3D:
- the protected methods should probably be private as nothing is
likely to inherit from Rotation3D and doxygen skips documenting
private methods and the methods are not general purpose
- it would be nice to be able to initialize from a vector and an angle
- the current constructor should probably say Euler angle somewhere in
its docs.
Matrix3D:
- why are there the rotation methods there? A cleaner interface would
probably be to have a method is_rotation() and another get_rotation()
so you can check is is close to a rotation and then get the rotation3D
object out directly. Having to go through intermediates of some sort
is messy.
- it needs an operator[] which returns a vector3D (with appropriate
bounds checking and all that).
- I would suggest using \brief to define multi-line brief comments
ParticleFunction:
- Why does ParticleFunction take Particles? If you want that it should
be ParticlesFunction, but it seems to me what we really want is for it
to only take one particle and then use apply methods if we want to
apply it to more than one. Otherwise we will be creating Particles
with one Particle everywhere.
yes ... , but then I'll have to do a loop each time I want to rotate a
molecule.
maybe it would be better to have MolecularHierarchyDecoratorFunction ?
So I could just give as input the root of the molecule?
- apply should be pure virtual so that you can tell if you got the
name or signature wrong when overriding it.
sure.
- at least one of the methods needs to be defined in a .cpp to get
linking and casting right when using multiple libraries
For some reason python can not find the function implementation if it
is in the cpp file. It happened to Joerg as well - is there anything
else other than updating the include/Sconscript, ,src/Sconscript and
pyext/misc.i ?