topo_one_dim.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_TOPO_ONE_DIM_H_
#define SEAMS_TOPO_ONE_DIM_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>
#include <shapeMatch.hpp>


 
namespace ring {

std::vector<int> findPrisms(
    const std::vector<std::vector<int>> &rings, std::vector<strucType> &ringType,
    int &nPerfectPrisms, int &nImperfectPrisms,
    const std::vector<std::vector<int>> &nList,
    molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    std::vector<double> &rmsdPerAtom, bool doShapeMatching = false);

bool basalPrismConditions(const std::vector<std::vector<int>> &nList,
                          std::vector<int> &basal1, std::vector<int> &basal2);

bool relaxedPrismConditions(const std::vector<std::vector<int>> &nList,
                            std::vector<int> &basal1, std::vector<int> &basal2);

bool discardExtraTetragonBlocks(
    std::vector<int> &basal1, std::vector<int> &basal2,
    molSys::PointCloud<molSys::Point<double>, double> &yCloud);

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

[[nodiscard]] int prismAnalysis(std::string path, const std::vector<std::vector<int>> &rings,
                  const std::vector<std::vector<int>> &nList,
                  molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                  int maxDepth, int &atomID, int firstFrame, int currentFrame,
                  bool doShapeMatching = false);

[[nodiscard]] int assignPrismType(const std::vector<std::vector<int>> &rings,
                    const std::vector<int> &listPrism, int ringSize,
                    const std::vector<ring::strucType> &ringType,
                    std::vector<int> &atomTypes,
                    std::vector<ring::strucType> &atomState);

[[nodiscard]] int deformedPrismTypes(const std::vector<ring::strucType> &atomState,
                       std::vector<int> &atomTypes, int maxDepth);

[[nodiscard]] int rmAxialTranslations(
    molSys::PointCloud<molSys::Point<double>, double> &yCloud, int &atomID,
    int firstFrame, int currentFrame);
 
}  // namespace ring
 
#endif  // __TOPOCONFINED_H_