bond.hpp
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10 
11 #ifndef __BONDING_H_
12 #define __BONDING_H_
13 
14 #include <algorithm>
15 #include <array>
16 #include <fstream>
17 #include <iostream>
18 #include <iterator>
19 #include <math.h>
20 #include <memory>
21 #include <sstream>
22 #include <string>
23 #include <sys/stat.h>
24 #include <vector>
25 
26 // Internal
27 #include <cage.hpp>
28 #include <mol_sys.hpp>
29 #include <seams_input.hpp>
30 
65 namespace bond {
66 
74  std::vector<std::vector<int>> nList, int targetFrame, int Htype);
75 
78 double
81  int oAtomIndex, int hAtomIndex);
82 
88  molSys::PointCloud<molSys::Point<double>, double> *yCloud);
89 
97  std::vector<cage::iceType> atomTypes);
98 
103  std::vector<cage::Cage> *cageList, cage::cageType type,
104  int *nRings);
105 
108 
109 } // namespace bond
110 
111 #endif // __BONDING_H_
File for cage types for topological network criteria.
std::vector< std::vector< int > > populateHbonds(std::string filename, molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, int targetFrame, int Htype)
Definition: bond.cpp:170
std::vector< std::vector< int > > trimBonds(std::vector< std::vector< int >> bonds)
Remove duplicate bonds.
Definition: bond.cpp:436
std::vector< std::vector< int > > populateBonds(std::vector< std::vector< int >> nList, molSys::PointCloud< molSys::Point< double >, double > *yCloud)
Definition: bond.cpp:22
double getHbondDistanceOH(molSys::PointCloud< molSys::Point< double >, double > *oCloud, molSys::PointCloud< molSys::Point< double >, double > *hCloud, int oAtomIndex, int hAtomIndex)
Definition: bond.cpp:334
std::vector< std::vector< int > > createBondsFromCages(std::vector< std::vector< int >> rings, std::vector< cage::Cage > *cageList, cage::cageType type, int *nRings)
Definition: bond.cpp:365
cageType
Definition: cage.hpp:50
The main molecular system handler.
Functions for bond-related analyses.
Definition: bond.hpp:65
File for functions that read in files).
This contains a collection of points; contains information for a particular frame.
Definition: mol_sys.hpp:166
This contains per-particle information.
Definition: mol_sys.hpp:145