ensembles.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(LOOS_ENSEMBLES_HPP)
#define LOOS_ENSEMBLES_HPP
 
#include <vector>
#include <boost/tuple/tuple.hpp>
 
#include <loos_defs.hpp>
#include <MatrixImpl.hpp>
#include <MatrixOps.hpp>
 
#include <ProgressCounters.hpp>
#include <ProgressTriggers.hpp>
 
#include <AtomicGroup.hpp>
#include <Trajectory.hpp>
 
namespace loos {
  class XForm;
 
  AtomicGroup averageStructure(const std::vector<AtomicGroup>& ensemble);
 
 
  AtomicGroup averageStructure(const std::vector<AtomicGroup>& ensemble, const std::vector<XForm>& xforms);
 
 
  AtomicGroup averageStructure(const AtomicGroup&, const std::vector<XForm>&, pTraj& traj, const std::vector<uint>& indices);
 
 
  AtomicGroup averageStructure(const AtomicGroup&, const std::vector<XForm>&, pTraj& traj);
 
 
  void applyTransforms(std::vector<AtomicGroup>& ensemble, std::vector<XForm>& xforms);
 
  void readTrajectory(std::vector<AtomicGroup>& ensemble, const AtomicGroup& model, pTraj trajectory);
  void readTrajectory(std::vector<AtomicGroup>& ensemble, const AtomicGroup& model, pTraj trajectory, std::vector<uint>& frames);
 
 
 
 
  
#if !defined(SWIG)
  RealMatrix extractCoords(const std::vector<AtomicGroup>& ensemble);
  RealMatrix extractCoords(const std::vector<AtomicGroup>& ensemble, const std::vector<XForm>& xforms);
 
  void subtractAverage(RealMatrix& M);
 
 
  boost::tuple<RealMatrix, RealMatrix, RealMatrix> svd(std::vector<AtomicGroup>& ensemble, const bool align = true);
 
 
 
#endif   // !defined(SWIG)
 
 
  void appendCoords(std::vector< std::vector<double> >& ensemble,
                    AtomicGroup& model,
                    pTraj& traj,
                    const std::vector<uint>& indices,
                    const bool updates);
 
 
  std::vector< std::vector<double> > readCoords(AtomicGroup& model,
                                                pTraj& traj,
                                                const std::vector<uint>& indices,
                                                const bool updates);
};
 
 
 
#endif