loos_defs.hpp

/*
  This file is part of LOOS.
 
  LOOS (Lightweight Object-Oriented Structure library)
  Copyright (c) 2008, Tod D. Romo, Alan Grossfield
  Department of Biochemistry and Biophysics
  School of Medicine & Dentistry, University of Rochester
 
  This package (LOOS) is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation under version 3 of the License.
 
  This package is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.
 
  You should have received a copy of the GNU General Public License
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/
 
 
 
 
 
 
#if !defined(LOOSDEFS_HPP)
#define LOOSDEFS_HPP
 
 
// Requirements check
#if __GNUC__ < 4
#error LOOS Requires GCC-4.0.1 or higher
#endif
 
 
 
#if !defined(BOOST_VERSION)
#include <boost/version.hpp>
#endif
 
#if (((BOOST_VERSION / 100) % 1000) < 36)
#error LOOS require Boost 1.36 or higher
#endif
 
#include <sys/types.h>
 
 
 
#if defined(REQUIRES_UINT)
typedef unsigned int     uint;
#endif
 
#if defined(REQUIRES_ULONG)
typedef unsigned long    ulong;
#endif
 
#if defined(__linux__) || defined(__CYGWIN__) || defined(__FreeBSD__)
 
extern "C" {
 
  void dsyev_(char*, char*, int*, double*, int*, double*, double*, int*, int*);
  void dgesvd_(char*, char*, int*, int*, double*, int*, double*, double*, int*, double*, int*, double*, int*, int*);
  void dgesvj_(char*, char*, char*, int*, int*, double*, int*, double*, int*, double*, int*, double*, int*, int*);
  void dgemm_(const char* const, const char* const, const int* const, const int* const, const int* const,
              const double* const, const double* const, const int* const, const double* const,
              const int* const, const double* const, double* consnt, const int* const);
  void dggev_(char*, char*, int*, double*, int*, double*, int*, double*, double*, double*, double*, int*, double*, int*, double*, int*, int*);
 
  void sgesvd_(char*, char*, int*, int*, float*, int*, float*, float*, int*, float*, int*, float*, int*, int*);
  void sgemm_(char*, char*, int*, int*, int*, float*, float*, int*, float*, int*, float*, float*, int*);
  void sggev_(char*, char*, int*, float*, int*, float*, int*, float*, float*, float*, float*, int*, float*, int*, float*, int*, int*);
  void ssyev_(char*, char*, int*, float*, int*, float*, float*, int*, int*);
  void dsyev_(char*, char*, int*, double*, int*, double*, double*, int*, int*);
  void ssygv_(int*, char*, char*, int*, float*, int*, float*, int*, float*, float*, int*, int*);
  void ssygvx_(int*, char*, char*, char*, int*, float*, int*, float*, int*, float*, float*, int*, int*, float*, int*, float*, float*, int*, float*, int*, int*, int*, int*);
  void dgels_(char*, int*, int*, int*, double*, int*, double*, int*, double*, int*, int*);
  double dlamch_(const char*);
}
 
 
typedef int f77int;
 
#elif defined(__APPLE__)
 
 
// MacOS 10.9 requires this to appear before Accelerate
#include <boost/random.hpp>
 
#include <Accelerate/Accelerate.h>
 
 
typedef __CLPK_integer f77int;
 
#else
 
#error You are building in an unsupported environment.  You will need to specify how to access ATLAS.
 
#endif
 
 
 
 
 
#include <boost/shared_ptr.hpp>
#include <boost/tuple/tuple.hpp>
 
 
 
 
namespace loos {
 
  typedef double greal;
  typedef long gint;
 
  typedef float dcd_real;
  typedef double dcd_double;
 
  template<typename T> class Coord;
 
 
  typedef Coord<double> GCoord;
  typedef boost::shared_ptr<GCoord> pGCoord;
 
  // Writers
  class TrajectoryWriter;
  class DCDWriter;
  class XTCWriter;
 
  // Trajectory and subclasses...
  class Atom;
  class Trajectory;
  class DCD;
  class AmberTraj;
  class AmberNetcdf;
  class CCPDB;
  class TinkerArc;
  class PDBTraj;
  class XTC;
  class TRR;
 
 
  typedef boost::shared_ptr<Atom> pAtom;
  typedef boost::shared_ptr<Trajectory> pTraj;
  typedef boost::shared_ptr<DCD> pDCD;
  typedef boost::shared_ptr<AmberTraj> pAmberTraj;
  typedef boost::shared_ptr<AmberNetcdf> pAmberNetcdf;
  typedef boost::shared_ptr<CCPDB> pCCPDB;
  typedef boost::shared_ptr<TinkerArc> pTinkerArc;
  typedef boost::shared_ptr<PDBTraj> pPDBTraj;
  typedef boost::shared_ptr<XTC> pXTC;
  typedef boost::shared_ptr<TRR> pTRR;
  typedef boost::shared_ptr<TrajectoryWriter> pTrajectoryWriter;
 
  // AtomicGroup and subclasses (i.e. systems formats)
  class AtomicGroup;
  class PDB;
  class PSF;
  class Amber;
  class AmberRst;
  class TinkerXYZ;
  class Gromacs;
  class CHARMM;
  class MDTraj;
  class MMCIF;
 
  typedef boost::shared_ptr<AtomicGroup> pAtomicGroup;
  typedef boost::shared_ptr<PDB> pPDB;
  typedef boost::shared_ptr<PSF> pPSF;
  typedef boost::shared_ptr<Amber> pAmber;
  typedef boost::shared_ptr<AmberRst> pAmberRst;
  typedef boost::shared_ptr<TinkerXYZ> pTinkerXYZ;
  typedef boost::shared_ptr<Gromacs> pGromacs;
  typedef boost::shared_ptr<CHARMM> pCHARMM;
  typedef boost::shared_ptr<MMCIF> pMMCIF;
 
 
  // Misc
  class Remarks;
 
  const uint kilobytes = 1024;
  const uint megabytes = 1024 * kilobytes;
  const uint gigabytes = 1024 * megabytes;
 
}
 
#endif