absOrientation.hpp

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//-----------------------------------------------------------------------------------
// d-SEAMS - Deferred Structural Elucidation Analysis for Molecular Simulations
//
// Copyright (c) 2018--present d-SEAMS core team
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the MIT License as published by
// the Open Source Initiative.
//
// A copy of the MIT License is included in the LICENSE file of this repository.
// You should have received a copy of the MIT License along with this program.
// If not, see <https://opensource.org/licenses/MIT>.
//-----------------------------------------------------------------------------------
 
#ifndef SEAMS_ABSORIENTATION_H_
#define SEAMS_ABSORIENTATION_H_
 
#include <algorithm>
#include <array>
#include <fstream>
#include <iostream>
#include <iterator>
#include <cmath>
#include <memory>
#include <sstream>
#include <string>
#include <vector>
 
// Eigen (SelfAdjointEigenSolver replaces Spectra for 4x4 symmetric matrices)
#include <Eigen/Core>
#include <Eigen/Dense>
#include <Eigen/Eigenvalues>
 
#include <mol_sys.hpp>
#include <ring.hpp>
#include <seams_input.hpp>
#include <seams_output.hpp>
 
// Inspired by AStar_Dual_Tree_HandPose by jsupancic
 
namespace absor {

[[nodiscard]] int hornAbsOrientation(const Eigen::MatrixXd &refPoints,
                       const Eigen::MatrixXd &targetPoints,
                       std::vector<double> &quat, double &rmsd,
                       std::vector<double> &rmsdList, double &scale);

Eigen::MatrixXd calcMatrixS(const Eigen::MatrixXd &centeredRefPnts,
                            const Eigen::MatrixXd &centeredTargetPnts, int nop,
                            int dim);

Eigen::MatrixXd calcMatrixN(const Eigen::MatrixXd &S);

Eigen::MatrixXd centerWRTcentroid(const Eigen::MatrixXd &pointSet);

double calcScaleFactor(const Eigen::MatrixXd &rightSys,
                       const Eigen::MatrixXd &leftSys, int n);

Eigen::MatrixXd quat2RotMatrix(const Eigen::VectorXd &quat);

double getRMSD(const Eigen::MatrixXd &centeredRefPnts,
               const Eigen::MatrixXd &centeredTargetPnts,
               const Eigen::VectorXd &quat, std::vector<double> &rmsdList,
               int nop, double scale);
 
} // namespace absor
 
#endif // SEAMS_ABSORIENTATION_H_