AmberTools

This is to help document the process to get AmberTools, a set of tools for Assisted Model Building with Energy Refinement (AMBER) into Fedora.

Bundled packages already in Fedora

Fedora package	location in AmberTools	bundled version
arpack	src/arpack	2.1
blas	src/blas	3.0?
boost	src/boost	1.64.0
eigen3	src/mtkpp/src/eigen3b2	3.0b2
fftw	src/fftw-3.3	3.3
lapack	src/lapack	3.2
libXmu	src/leap/src/Xmu	20001128
libXpm	src/leap/src/Xpm	3.4
mpi4py	src/mpi4py-3.1.4	3.1.4
netcdf	src/netcdf	3.6.2b6
perl-Math-VectorReal	src/PerlMol-0.3500/inc/BUNDLES/Math-VectorReal-1.02	1.02
ucpp	src/ucpp-1.3	1.3
xblas	src/xblas	1.0 (2005)

Bundled packages which should be fine to put in Fedora

Fedora package	Upstream	Version in AmberTools	Review Request/Status	Notes
boost-numeric-bindings	http://beta.boost.org/community/sandbox.html			(not necessary for build)
cifparse	http://sw-tools.pdb.org/apps/CIFPARSE/source.html
libpdb	http://www.cgl.ucsf.edu/Overview/software.html			bundled in ptraj
libpdb++	http://www.cgl.ucsf.edu/Overview/software.html			bundled in reduce
perl-Chemistry-3DBuilder	https://metacpan.org/pod/Chemistry::3DBuilder	0.10		bundled in PerlMol
perl-Chemistry-Bond-Find	https://metacpan.org/pod/Chemistry::Bond::Find	0.21	#2417767	bundled in PerlMol
perl-Chemistry-File-SMILES	https://metacpan.org/pod/Chemistry::File::SMILES	0.44	#2417812	bundled in PerlMol
perl-Chemistry-Mol	https://metacpan.org/pod/Chemistry::Mol	0.35	#2417375	bundled in PerlMol
perl-Chemistry-Canonicalize	https://metacpan.org/pod/Chemistry::Canonicalize	0.10	#2417811	bundled in PerlMol
perl-Chemistry-Pattern	https://metacpan.org/pod/Chemistry::Patterns	0.26	#2417373	bundled in PerlMol
perl-Statistics-Regression	https://metacpan.org/pod/Statistics::Regression	0.15	#2417808	bundled in PerlMol
Wcl	http://search.cpan.org/~jhpb/Wcl-2.7.3/		Old review request

Bundled packages which may be problematic to put in Fedora

Name	Upstream	Version in AmberTools	Status
chamber	AmberTools		non-free license?
libXraw	http://canonical.org/~kragen/Xraw/index.html		non-commercial clause in license
leap	AmberTools		non-free license?
reduce	http://kinemage.biochem.duke.edu/software/reduce.php	3.14.080821	sale restriction?