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 __TOPO_ONE_DIM_H_
#define __TOPO_ONE_DIM_H_
 
#include <math.h>
#include <sys/stat.h>
#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(
    std::vector<std::vector<int>> rings, std::vector<strucType> *ringType,
    int *nPerfectPrisms, int *nImperfectPrisms,
    std::vector<std::vector<int>> nList,
    molSys::PointCloud<molSys::Point<double>, double> *yCloud,
    std::vector<double> *rmsdPerAtom, bool doShapeMatching = false);
 
bool basalPrismConditions(std::vector<std::vector<int>> nList,
                          std::vector<int> *basal1, std::vector<int> *basal2);
 
bool relaxedPrismConditions(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(
    std::vector<std::vector<int>> rings,
    molSys::PointCloud<molSys::Point<double>, double> *yCloud);
 
int prismAnalysis(std::string path, std::vector<std::vector<int>> rings,
                  std::vector<std::vector<int>> nList,
                  molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                  int maxDepth, int *atomID, int firstFrame, int currentFrame,
                  bool doShapeMatching = false);
 
int assignPrismType(std::vector<std::vector<int>> rings,
                    std::vector<int> listPrism, int ringSize,
                    std::vector<ring::strucType> ringType,
                    std::vector<int> *atomTypes,
                    std::vector<ring::strucType> *atomState);
 
int deformedPrismTypes(std::vector<ring::strucType> atomState,
                       std::vector<int> *atomTypes, int maxDepth);
 
int rmAxialTranslations(
    molSys::PointCloud<molSys::Point<double>, double> *yCloud, int *atomID,
    int firstFrame, int currentFrame);
 
}  // namespace ring
 
#endif  // __TOPOCONFINED_H_