Re: [IMP-dev] NBL cleanup and other small patches

[Ben Webb <>]

Daniel Russel wrote:
...
> The second patches the init file as above. It also adds an argument 
> extraroot which adds to the include search path and the lib path (and to 
> the runtime link path since it is needed to make the boost tests pass 
> currently).

I can't apply this patch because it would break builds for everything 
except gcc and Python 2.5 on Linux. But I can certainly put in an 
equivalent feature which works everywhere if you can briefly explain the 
use case.

> Also, as a general point, the SConscript files 
> which build things should all be changed to add the local include and 
> lib paths to the front so that local headers mask globally installed 
> headers.

I'm 95% sure the include path search order is compiler-dependent, so 
this probably would only have the desired effect for gcc, but I agree 
that it's a good statement of intent if nothing else.

> The fifth adds set_particles to the the list restraint I added before 
> (this is independent of anything else).

Wouldn't compile for me:
kernel/include/IMP/restraints/SingletonListRestraint.h:41: error: no 
members matching 'using IMP::Restraint::set_particles' in 'class 
IMP::Restraint'

As regards the nonbonded list, we cannot include CGAL in the kernel 
since it restricts the use of IMP to that of the QPL license. I 
certainly agree that CGAL has some useful features which we may want to 
use in IMP - but it cannot go in the kernel. Thus, it should go in an 
extension module. This appears to preclude use of the current patch, 
since Algorithm is an enum - I guess either Algorithm needs to become a 
class, or a CGAL_NBL class (in a module) can derive from a base NBL 
class (in the kernel). At the Python level it is easy to fall back from 
CGAL_NBL to regular NBL at runtime if the extension module is not 
available - just wrap the import in a try block.

	Ben
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle