cage_enum.hpp

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//-----------------------------------------------------------------------------------
// d-SEAMS - Deferred Structural Elucidation Analysis for Molecular Simulations
// SPDX-License-Identifier: MIT
//-----------------------------------------------------------------------------------
#ifndef SEAMS_CAGE_ENUM_H_
#define SEAMS_CAGE_ENUM_H_
 
#include <cage.hpp>
 
#include <array>
#include <map>
#include <string>
#include <vector>

namespace cage {

struct FoundCage {
  Signature signature;
  std::vector<int> faces;     
  std::vector<int> vertices;  
  std::string certificate;    
  bool closed = true;         
  int danglingEdges = 0;      
};

bool isClosedPolyhedron(const std::vector<std::vector<int>> &rings,
                        const std::vector<int> &faces);

std::vector<FoundCage>
findBySignature(const std::vector<std::vector<int>> &rings,
                const Signature &signature);

bool speciesCycleMatches(const std::vector<int> &cycle,
                         const std::vector<int> &pattern);

std::vector<FoundCage>
findBySignature(const std::vector<std::vector<int>> &rings,
                const Signature &signature, const std::vector<int> &species,
                const std::vector<std::vector<int>> &patterns);

std::vector<FoundCage>
findBySignature(const std::vector<std::vector<int>> &rings,
                const std::vector<std::vector<int>> &nList,
                const Signature &signature);

std::vector<FoundCage>
findIncompleteBySignature(const std::vector<std::vector<int>> &rings,
                          const Signature &signature, int minFaces);

struct CageShape {
  int nVertices = 0;
  int status = 1;
  double rmsd = -1.0;
  std::string pointGroup;
};

std::vector<std::array<double, 3>>
coordsOfVertices(const std::vector<std::array<double, 3>> &all,
                 const std::vector<int> &vertices);

CageShape shapeOfVertices(const std::vector<std::array<double, 3>> &cageXyz);

CageShape overlayVertices(const std::vector<std::array<double, 3>> &ref,
                          const std::vector<std::array<double, 3>> &cageXyz);

struct FormerRow {
  int index = -1;
  int species = 0;
  int coord = 0;
  int homopolar = 0;
  std::map<int, int> rings;
};

std::vector<FormerRow>
formerRows(const std::vector<std::vector<int>> &nList,
           const std::vector<std::vector<int>> &rings,
           const std::vector<int> &species, int formerSpecies);

bool sameNetwork(const std::vector<FormerRow> &early,
                 const std::vector<FormerRow> &late);
 
} // namespace cage
 
#endif // SEAMS_CAGE_ENUM_H_