franzblau.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 __FRANZBLAU_H_
#define __FRANZBLAU_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 <cage.hpp>
#include <mol_sys.hpp>
#include <seams_input.hpp>
#include <seams_output.hpp>
 
namespace primitive {
 
struct Vertex {
  int atomIndex;                   
  std::vector<int> neighListIndex; 
  bool inGraph =
      true; 
};
 
struct Graph {
  std::vector<Vertex> pts; 
  std::vector<std::vector<int>>
      rings; 
};
 
std::vector<std::vector<int>> ringNetwork(std::vector<std::vector<int>> nList,
                                          int maxDepth);
 
Graph populateGraphFromNListID(
    molSys::PointCloud<molSys::Point<double>, double> *yCloud,
    std::vector<std::vector<int>> neighHbondList);
 
Graph populateGraphFromIndices(std::vector<std::vector<int>> nList);
 
Graph restoreEdgesFromIndices(Graph *fullGraph,
                              std::vector<std::vector<int>> nList);
 
Graph countAllRingsFromIndex(std::vector<std::vector<int>> neighHbondList,
                             int maxDepth);
 
Graph removeNonSPrings(Graph *fullGraph);
 
int findRings(Graph *fullGraph, int v, std::vector<int> *visited, int maxDepth,
              int depth, int root = -1);
 
int shortestPath(Graph *fullGraph, int v, int goal, std::vector<int> *path,
                 std::vector<int> *visited, int maxDepth, int depth = 1);
 
Graph clearGraph(Graph *currentGraph);
 
} // namespace primitive
 
#endif // __FRANZBLAU_H_