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 SEAMS_BONDING_H_
#define SEAMS_BONDING_H_
 
#include <algorithm>
#include <array>
#include <cmath>
#include <fstream>
#include <iostream>
#include <iterator>
#include <memory>
#include <sstream>
#include <string>
#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,
               const std::vector<std::vector<int>> &nList, int targetFrame,
               int Htype, double distCutoff = 2.42, double angleCutoff = 30.0);

// ! 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,
    const std::vector<std::vector<int>> &nList, double distCutoff = 2.42,
    double angleCutoff = 30.0);

bool donatedHydrogenBond(
    const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    const molSys::PointCloud<molSys::Point<double>, double> &hCloud,
    int acceptorIndex, int donorIndex, const std::vector<int> &donorHs,
    double distCutoff = 2.42, double angleCutoff = 30.0);

std::vector<std::vector<int>> populateHbondsFromDonors(
    molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    molSys::PointCloud<molSys::Point<double>, double> &hCloud,
    const std::vector<std::vector<int>> &nList,
    const std::vector<int> &donorHs, double distCutoff = 2.42,
    double angleCutoff = 30.0);

double getHbondDistanceOH(
    const molSys::PointCloud<molSys::Point<double>, double> &oCloud,
    const molSys::PointCloud<molSys::Point<double>, double> &hCloud,
    int oAtomIndex, int hAtomIndex);

std::vector<std::vector<int>>
populateBonds(const std::vector<std::vector<int>> &nList,
              const molSys::PointCloud<molSys::Point<double>, double> &yCloud);

std::vector<std::vector<int>>
populateBonds(const std::vector<std::vector<int>> &nList,
              const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
              const std::vector<cage::iceType> &atomTypes);

std::vector<std::vector<int>>
createBondsFromCages(const 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 // SEAMS_BONDING_H_