topo_fingerprint.hpp

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//-----------------------------------------------------------------------------------
// d-SEAMS - Deferred Structural Elucidation Analysis for Molecular Simulations
// SPDX-License-Identifier: MIT
//-----------------------------------------------------------------------------------
#ifndef SEAMS_TOPO_FINGERPRINT_H_
#define SEAMS_TOPO_FINGERPRINT_H_
 
#include <cstdint>
#include <map>
#include <string>
#include <utility>
#include <vector>

namespace topo {

using Rows = std::vector<std::vector<int>>;
 
struct LocalKey {
  std::string key;     
  std::string method;  
  int vertices = 0;    
  int edges = 0;       
};
 
struct FrameFingerprint {
  std::string key;                    
  std::string method;                 
  std::vector<std::string> atomKeys;  
  std::map<std::string, int> classes; 
  std::vector<int> ringCensus;        
  std::vector<std::uint64_t> wlAtom;  
  int hops = 0;
  bool coloured = false;              
};

std::vector<int> hopNeighbourhood(const Rows &rows, int atom, int hops);

std::uint64_t wlHash(const std::vector<std::vector<int>> &adjacency, int root,
                     int rounds, const std::vector<int> &colours = {});

LocalKey localKey(const Rows &rows, int atom, int hops,
                  const std::vector<int> &colours = {});

FrameFingerprint fingerprint(const Rows &rows, int hops = 2, int maxRingSize = 7,
                             const std::vector<int> &colours = {});

FrameFingerprint incrementalFingerprint(const FrameFingerprint &prev,
                                        const Rows &rows,
                                        const std::vector<int> &dirtyAtoms,
                                        int hops, int maxRingSize = 7,
                                        const std::vector<int> &colours = {});

std::string hex(std::uint64_t value);

struct KeyLibrary {
  std::string method;  
  int hops = 0;
  bool coloured = false;  
  std::map<std::string, std::string> labelOf;  
};

void addToLibrary(KeyLibrary &lib, const FrameFingerprint &fp, const std::string &label);

std::string writeLibrary(const KeyLibrary &lib);
KeyLibrary readLibrary(const std::string &text);
 
struct LibraryMatch {
  std::vector<std::string> labels;      
  std::map<std::string, int> counts;    
  std::vector<int> depth;               
  int matched = 0;
};

LibraryMatch matchLibrary(const FrameFingerprint &fp, const KeyLibrary &lib);

LibraryMatch matchLibraries(const Rows &rows, const std::vector<KeyLibrary> &libs,
                            int maxRingSize = 7, const std::vector<int> &colours = {});
 
} // namespace topo
 
#endif // SEAMS_TOPO_FINGERPRINT_H_