selection.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_SELECTION_H_
#define SEAMS_SELECTION_H_
 
#include <cmath>
#include <algorithm>
#include <array>
#include <fstream>
#include <iostream>
#include <iterator>
#include <memory>
#include <sstream>
#include <string>
#include <vector>
 
#include <mol_sys.hpp>
#include <order_parameter.hpp>
#include <ring.hpp>
#include <seams_input.hpp>
#include <seams_output.hpp>


 
namespace gen {

molSys::PointCloud<molSys::Point<double>, double>
getPointCloudOneAtomType(
    molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    molSys::PointCloud<molSys::Point<double>, double> &outCloud,
    int atomTypeI, bool isSlice = false,
    std::array<double, 3> coordLow = std::array<double, 3>{0, 0, 0},
    std::array<double, 3> coordHigh = std::array<double, 3>{0, 0, 0});

void moleculesInSingleSlice(
    molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    bool clearPreviousSliceSelection=true,
    std::array<double, 3> coordLow = std::array<double, 3>{0, 0, 0},
    std::array<double, 3> coordHigh = std::array<double, 3>{0, 0, 0});

void atomsInSingleSlice(
    molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    bool clearPreviousSliceSelection=true,
    std::array<double, 3> coordLow = std::array<double, 3>{0, 0, 0},
    std::array<double, 3> coordHigh = std::array<double, 3>{0, 0, 0});

void setAtomsWithSameMolID(
    molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    const std::unordered_multimap<int,int> &molIDAtomIDmap,
    int molID, bool inSliceValue=true);
 
}  // namespace gen

 
namespace ring {

void getEdgeMoleculesInRings(
    const std::vector<std::vector<int>> &rings, molSys::PointCloud<molSys::Point<double>, double> &oCloud,
    molSys::PointCloud<molSys::Point<double>, double> &yCloud, 
    std::array<double, 3> coordLow, std::array<double, 3> coordHigh,
    bool identicalCloud=false);

void printSliceGetEdgeMoleculesInRings(
    std::string path, const std::vector<std::vector<int>> &rings,
    molSys::PointCloud<molSys::Point<double>, double> &oCloud,
    molSys::PointCloud<molSys::Point<double>, double> &yCloud, 
    std::array<double, 3> coordLow, std::array<double, 3> coordHigh,
    bool identicalCloud=false);
 
}  // namespace ring
 
#endif  // SEAMS_SELECTION_H_