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 __BULKTUM_H_
#define __BULKTUM_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>
 
#include <franzblau.hpp>
#include <neighbours.hpp>
#include <pntCorrespondence.hpp>
#include <topo_bulk.hpp>
 
namespace tum3 {
 
int topoUnitMatchingBulk(
    std::string path, std::vector<std::vector<int>> rings,
    std::vector<std::vector<int>> nList,
    molSys::PointCloud<molSys::Point<double>, double> *yCloud, int firstFrame,
    bool printClusters, bool onlyTetrahedral);
 
Eigen::MatrixXd buildRefHC(std::string fileName);
 
Eigen::MatrixXd buildRefDDC(std::string fileName);
 
int shapeMatchHC(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                 const Eigen::MatrixXd &refPoints, cage::Cage cageUnit,
                 std::vector<std::vector<int>> rings,
                 std::vector<std::vector<int>> nList, std::vector<double> *quat,
                 double *rmsd);
 
int shapeMatchDDC(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                  const Eigen::MatrixXd &refPoints,
                  std::vector<cage::Cage> cageList, int cageIndex,
                  std::vector<std::vector<int>> rings,
                  std::vector<double> *quat, double *rmsd);
 
int updateRMSDatom(std::vector<std::vector<int>> rings, cage::Cage cageUnit,
                   double rmsd, std::vector<double> *rmsdPerAtom,
                   std::vector<int> *noOfCommonAtoms,
                   std::vector<cage::iceType> atomTypes);
 
int averageRMSDatom(std::vector<double> *rmsdPerAtom,
                    std::vector<int> *noOfCommonAtoms);
 
std::vector<cage::Cage>
topoBulkCriteria(std::string path, std::vector<std::vector<int>> rings,
                 std::vector<std::vector<int>> nList,
                 molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                 int firstFrame, int *numHC, int *numDDC,
                 std::vector<ring::strucType> *ringType);
 
int clusterCages(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                 std::string path, std::vector<std::vector<int>> rings,
                 std::vector<cage::Cage> cageList, int numHC, int numDDC);
 
std::vector<int> atomsFromCages(std::vector<std::vector<int>> rings,
                                std::vector<cage::Cage> cageList,
                                std::vector<int> clusterCages);
 
} // namespace tum3
namespace tum3 {…}
 
#endif // __BULKTUM_H_