bulkTUM.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_BULKTUM_H_
#define SEAMS_BULKTUM_H_
 
#include <algorithm>
#include <array>
#include <fstream>
#include <iostream>
#include <iterator>
#include <cmath>
#include <memory>
#include <sstream>
#include <string>
#include <vector>
 
#include <franzblau.hpp>
#include <neighbours.hpp>
#include <pntCorrespondence.hpp>
#include <topo_bulk.hpp>


 
namespace tum3 {

[[nodiscard]] int topoUnitMatchingBulk(
    std::string path, const std::vector<std::vector<int>> &rings,
    const std::vector<std::vector<int>> &nList,
    molSys::PointCloud<molSys::Point<double>, double> &yCloud, int firstFrame,
    bool printClusters, bool onlyTetrahedral,
    std::string templatePath = "templates");

Eigen::MatrixXd buildRefHC(const std::string &fileName);

Eigen::MatrixXd buildRefDDC(const std::string &fileName);

[[nodiscard]] int shapeMatchHC(molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                 const Eigen::MatrixXd &refPoints, cage::Cage cageUnit,
                 const std::vector<std::vector<int>> &rings,
                 const std::vector<std::vector<int>> &nList, std::vector<double> &quat,
                 double &rmsd);

[[nodiscard]] int shapeMatchDDC(molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                  const Eigen::MatrixXd &refPoints,
                  const std::vector<cage::Cage> &cageList, int cageIndex,
                  const std::vector<std::vector<int>> &rings,
                  std::vector<double> &quat, double &rmsd);

[[nodiscard]] int updateRMSDatom(const std::vector<std::vector<int>> &rings, cage::Cage cageUnit,
                   double rmsd, std::vector<double> &rmsdPerAtom,
                   std::vector<int> &noOfCommonAtoms,
                   const std::vector<cage::iceType> &atomTypes);

[[nodiscard]] int averageRMSDatom(std::vector<double> &rmsdPerAtom,
                    std::vector<int> &noOfCommonAtoms);

std::vector<cage::Cage>
topoBulkCriteria(std::string path, const std::vector<std::vector<int>> &rings,
                 const std::vector<std::vector<int>> &nList,
                 molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                 int firstFrame, int &numHC, int &numDDC,
                 std::vector<ring::strucType> &ringType);

[[nodiscard]] int clusterCages(molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                 std::string path, const std::vector<std::vector<int>> &rings,
                 const std::vector<cage::Cage> &cageList, int numHC, int numDDC);

std::vector<int> atomsFromCages(const std::vector<std::vector<int>> &rings,
                                const std::vector<cage::Cage> &cageList,
                                const std::vector<int> &clusterCages);
 
} // namespace tum3
 
#endif // SEAMS_BULKTUM_H_