XyzParser.hpp

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#ifndef _XYZ_PARSER_
#define _XYZ_PARSER_
 
#include <string>
#include <vector>
#include <algorithm>
#include <fstream>
#include <map>
#include <util/Parsing.hpp>
#include <regex>
 
struct Atom {
  const std::string symbol;
  const struct {
    double x, y, z;
  } position;
};
 
namespace pars {
 
struct XyzParser {
 
  const Regex sep = blank + oneOrMore // any number > 1 of spaces or tabs
      ,
              atom = upper + lower + optional // atom is Upper + lower?
      ,
              xyz_line = bof + blank + anyOf     // spaces at the start allowed
                       + capture(atom.s) + sep.s // capture atom symbol
                       + capture(realNumber) + sep.s + capture(realNumber)
                       + sep.s + capture(realNumber) + blank + anyOf + eof;
 
  Atom parseLine(const std::string &line) {
    std::smatch m;
    std::regex_match(line, m, xyz_line.r);
    if (m.size() == 0) { throw "Line " + line + " is malformed"; }
    return {std::string(m[1]),
            {std::atof(std::string(m[2]).c_str()),
             std::atof(std::string(m[3]).c_str()),
             std::atof(std::string(m[4]).c_str())}};
  }
 
  std::vector<Atom> parseFile(const std::string &fileName) {
    std::fstream f(fileName);
    std::string line;
    std::vector<Atom> atoms;
    if (!f.good()) throw "File " + fileName + " not found";
    if (!f.is_open()) throw "File IO error: " + fileName;
 
    std::getline(f, line); // Number of atoms
    const int natoms = std::atoi(line.c_str());
 
    std::getline(f, line); // Title of xyz file
 
    // parse lines
    for (int i(0); i < natoms; i++) {
      std::getline(f, line);
      atoms.push_back(parseLine(line));
    }
 
    return atoms;
  }
};
 
} // namespace pars
 
#endif