Summary: A set of tools for Assisted Model Building with Energy Refinement (AMBER)
Name: AmberTools
Version: 14
Release: 1
URL: http://ambermd.org/#AmberTools
Group: Applications/Engineering
# http://ambermd.org/AmberTools14-get.html
Source0: %{name}%{version}.tar.bz2
Patch0: AmberTools-rpm.patch
License: BSD and GPLv2+ and GPLv3 and MIT
# bundled, ok to put in Fedora:
# cifparse: http://sw-tools.pdb.org/apps/CIFPARSE/source.html
# libpdb (ptraj)
# libpdb++ (reduce)
# problematic:
# chamber: non-free license?
# leap: non-free license?
# reduce: sale restriction? http://kinemage.biochem.duke.edu/software/reduce.php
# src/FEW/additional_libs/perlMol
BuildRequires: arpack-devel
BuildRequires: atlas-devel
BuildRequires: bzip2-devel
BuildRequires: byacc
BuildRequires: fftw-devel
BuildRequires: flex
BuildRequires: gcc-gfortran
BuildRequires: libpdb-devel
BuildRequires: libWcl-devel
BuildRequires: libXdmcp-devel
BuildRequires: libXmu-devel
BuildRequires: libXpm-devel
BuildRequires: libXraw-devel
BuildRequires: mtkpp-devel
BuildRequires: netcdf-fortran-devel
BuildRequires: tcsh
BuildRequires: ucpp
BuildRequires: xblas-devel

#BuildRequires: mpi4py-mpich2/openmpi
#Requires: mpi4py-mpich2/openmpi

%description
AmberTools consists of several independently developed packages that work
well by themselves, and with Amber itself. The suite can also be used to
carry out complete (non-periodic) molecular dynamics simulations (using
NAB), with generalized Born solvent models.

AmberTools consists of:

* NAB - builds molecules; runs MD or distance geometry, using generalized Born,
        Poisson-Boltzmann or 3D-RISM implicit solvent models
* antechamber - creates force fields for general organic molecules
* ptraj - analyzes trajectories from Amber or CHARMM
* tleap and xleap - basic preparation program for Amber simulations
* sleap - replaces and expands tleap
* sqm - semiempirical and DFTB quantum chemistry program
* pbsa - performs numerical solutions to Poisson-Boltzmann models

%prep
%setup -q -n amber%{version}
# delete bundled libraries to make sure they're not used for build
pushd AmberTools/src
rm -r \
 arpack \
 blas \
 boost-* \
 byacc \
 fftw-* \
 lapack \
 leap/src/{Wc,Xmu,Xpm,Xraw} \
 mmpbsa_py/mpi4py-1.2.2.tar.gz \
 mtkpp \
 netcdf-4.3.0 \
 netcdf-fortran-4.2 \
 ptraj/pdb \
 xblas/{config,doc,m4,src,testing,LICENSE,Makefile*,README*,configure.*,make.*} \
 ucpp-1.3 \

popd
%patch0 -p1 -b .r

%build
export AMBERHOME="$(pwd)" AMBERBUILDFLAGS="%{optflags}" CUSTOMBUILDFLAGS="%{optflags}"
pushd AmberTools/src
./configure2 --with-netcdf %{_prefix} gnu
make
popd

%install
rm -rf %{buildroot}
pushd AmberTools/src
#mkdir -p %{buildroot}/etc
make DESTDIR=%{buildroot} install
popd

%files
%doc AmberTools/README AmberTools/LICENSE

%changelog
* Sun Jul 14 2013 Dominik Mierzejewski <rpm@greysector.net> 12-1
- initial build