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 __PNTCORRESPONDENCE_H_
#define __PNTCORRESPONDENCE_H_
 
#include <algorithm>
#include <array>
#include <fstream>
#include <iostream>
#include <iterator>
#include <math.h>
#include <memory>
#include <sstream>
#include <string>
#include <sys/stat.h>
#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(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                 const Eigen::MatrixXd &refPoints, int ringSize,
                 std::vector<int> basal1, std::vector<int> basal2);
 
double
getRadiusFromRings(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                   std::vector<int> basal1, std::vector<int> basal2);
 
double getAvgHeightPrismBlock(
    molSys::PointCloud<molSys::Point<double>, double> *yCloud,
    std::vector<int> basal1, std::vector<int> basal2);
 
int relOrderPrismBlock(
    molSys::PointCloud<molSys::Point<double>, double> *yCloud,
    std::vector<int> basal1, std::vector<int> basal2,
    std::vector<std::vector<int>> nList, std::vector<int> *outBasal1,
    std::vector<int> *outBasal2);
 
int relOrderPrismBlock(
    molSys::PointCloud<molSys::Point<double>, double> *yCloud,
    std::vector<int> basal1, std::vector<int> basal2,
    std::vector<int> *outBasal1, std::vector<int> *outBasal2);
 
Eigen::MatrixXd
fillPointSetPrismRing(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                      std::vector<int> basalRing, int startingIndex);
 
Eigen::MatrixXd fillPointSetPrismBlock(
    molSys::PointCloud<molSys::Point<double>, double> *yCloud,
    std::vector<int> basal1, std::vector<int> basal2, int startingIndex);
 
Eigen::MatrixXd getPointSetCage(ring::strucType type);
 
int relOrderHC(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
               std::vector<int> basal1, std::vector<int> basal2,
               std::vector<std::vector<int>> nList,
               std::vector<int> *matchedBasal1,
               std::vector<int> *matchedBasal2);
 
std::vector<int> relOrderDDC(int index, std::vector<std::vector<int>> rings,
                             std::vector<cage::Cage> cageList);
 
Eigen::MatrixXd
changeHexCageOrder(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                   std::vector<int> basal1, std::vector<int> basal2,
                   int startingIndex = 0);
 
Eigen::MatrixXd
changeDiaCageOrder(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                   std::vector<int> ddcOrder, int startingIndex = 0);
 
} // namespace pntToPnt
 
#endif // __PNTCORRESPONDENCE_H_