pntCorrespondence.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_PNTCORRESPONDENCE_H_
#define SEAMS_PNTCORRESPONDENCE_H_
 
#include <algorithm>
#include <array>
#include <fstream>
#include <iostream>
#include <iterator>
#include <cmath>
#include <memory>
#include <sstream>
#include <string>
#include <vector>
 
// External
#include <Eigen/Core>
 
#include <cage.hpp>
#include <mol_sys.hpp>
#include <seams_input.hpp>
#include <seams_output.hpp>
 
namespace pntToPnt {

Eigen::MatrixXd getPointSetRefRing(int n, int axialDim);

Eigen::MatrixXd
createPrismBlock(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                 const Eigen::MatrixXd &refPoints, int ringSize,
                 const std::vector<int> &basal1, const std::vector<int> &basal2);

double
getRadiusFromRings(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                   const std::vector<int> &basal1, const std::vector<int> &basal2);

double getAvgHeightPrismBlock(
    const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    const std::vector<int> &basal1, const std::vector<int> &basal2);

[[nodiscard]] int relOrderPrismBlock(
    const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    const std::vector<int> &basal1, const std::vector<int> &basal2,
    const std::vector<std::vector<int>> &nList, std::vector<int> &outBasal1,
    std::vector<int> &outBasal2);

[[nodiscard]] int relOrderPrismBlock(
    const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    const std::vector<int> &basal1, const std::vector<int> &basal2,
    std::vector<int> &outBasal1, std::vector<int> &outBasal2);

Eigen::MatrixXd
fillPointSetPrismRing(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                      const std::vector<int> &basalRing, int startingIndex);

Eigen::MatrixXd fillPointSetPrismBlock(
    const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    const std::vector<int> &basal1, const std::vector<int> &basal2, int startingIndex);

Eigen::MatrixXd getPointSetCage(ring::strucType type);

[[nodiscard]] int relOrderHC(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
               const std::vector<int> &basal1, const std::vector<int> &basal2,
               const std::vector<std::vector<int>> &nList,
               std::vector<int> &matchedBasal1,
               std::vector<int> &matchedBasal2);

std::vector<int> relOrderDDC(int index, const std::vector<std::vector<int>> &rings,
                             const std::vector<cage::Cage> &cageList);

std::vector<int> relOrderDDC(const std::vector<int> &equatorial, int index,
                             const std::vector<std::vector<int>> &rings,
                             const std::vector<cage::Cage> &cageList);

Eigen::MatrixXd
changeHexCageOrder(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                   const std::vector<int> &basal1, const std::vector<int> &basal2,
                   int startingIndex = 0);

Eigen::MatrixXd
changeDiaCageOrder(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                   const std::vector<int> &ddcOrder, int startingIndex = 0);
 
} // namespace pntToPnt
 
#endif // SEAMS_PNTCORRESPONDENCE_H_