fid-lib.hpp

/*
  Fiducial library
*/
 
 
/*
 
  This file is part of LOOS.
 
  LOOS (Lightweight Object-Oriented Structure library)
  Copyright (c) 2010, Tod D. Romo
  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/>.
*/
 
// @cond PACKAGES_INTERNAL
 
#if !defined(LOOS_FIDLIB_HPP)
#define LOOS_FIDLIB_HPP
 
 
 
#include <loos.hpp>
 
 
typedef std::vector<int>                   vecInt;
typedef std::vector<uint>                 vecUint;
typedef std::vector<loos::AtomicGroup>   vecGroup;
typedef std::vector<double>             vecDouble;
 
 
 
 
// Return indices of non-zero entries in the vector (i.e. frames that are not assigned)
vecUint findFreeFrames(const vecInt& map);
 
// Given a set of reference structures and a trajectory, classify the trajectory
// based on which reference structure is closest to each trajectory frame
vecUint assignStructures(loos::AtomicGroup& model, loos::pTraj& traj, const vecUint& frames, const vecGroup& refs);
 
// Given a vector that contains indices into a trajectory, will trim off the
// end so the # of frames is an even multiple of the requested bin size (via frac)
vecUint trimFrames(const vecUint& frames, const double frac);
 
// Randomly partition trajectory space
// f = the fractional bin size (i.e. probability)
boost::tuple<vecGroup, vecUint> pickFiducials(loos::AtomicGroup& model, loos::pTraj& traj, const vecUint& frames, const double f);
 
// Find the max value in the vector
int findMaxBin(const vecInt& assignments);
 
// Simple histogram of bin assignments
vecUint histogramBins(const vecInt& assignments);
 
#endif
 
 
// @endcond TOOLS_INTERNAL