bond.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 __BONDING_H_
#define __BONDING_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>
 
// Internal
#include <cage.hpp>
#include <mol_sys.hpp>
#include <seams_input.hpp>
 
namespace bond {
 
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);
 
// ! The H atom PointCloud should be for the entire system 
std::vector<std::vector<int>>
populateHbondsWithInputClouds(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
               molSys::PointCloud<molSys::Point<double>, double> *hCloud,
               std::vector<std::vector<int>> nList);
 
double
getHbondDistanceOH(molSys::PointCloud<molSys::Point<double>, double> *oCloud,
                   molSys::PointCloud<molSys::Point<double>, double> *hCloud,
                   int oAtomIndex, int hAtomIndex);
 
std::vector<std::vector<int>>
populateBonds(std::vector<std::vector<int>> nList,
              molSys::PointCloud<molSys::Point<double>, double> *yCloud);
 
std::vector<std::vector<int>>
populateBonds(std::vector<std::vector<int>> nList,
              molSys::PointCloud<molSys::Point<double>, double> *yCloud,
              std::vector<cage::iceType> atomTypes);
 
std::vector<std::vector<int>>
createBondsFromCages(std::vector<std::vector<int>> rings,
                     std::vector<cage::Cage> *cageList, cage::cageType type,
                     int *nRings);
 
std::vector<std::vector<int>> trimBonds(std::vector<std::vector<int>> bonds);
 
} // namespace bond
 
#endif // __BONDING_H_