molecule_file_io.h

// -*-c++-*-
#ifndef STORMM_MOLECULE_FILE_IO
#define STORMM_MOLECULE_FILE_IO
 
#include "copyright.h"
#include "Constants/behavior.h"
#include "DataTypes/stormm_vector_types.h"
#include "Parsing/textfile.h"
#include "molecule_format_enumerators.h"
 
namespace stormm {
namespace structure {
 
using constants::ExceptionResponse;
using parse::TextFile;
using parse::TextFileReader;
  
int getMdlMolSectionEnd(const TextFileReader &tfr, int line_start, int line_end_in = -1);
 
int getMdlMolSectionEnd(const TextFile &tf, int line_start, int line_end_in = -1);

int getCompoundSectionEnd(const TextFileReader &tfr, int line_start, int line_end_in = -1);
 
int getCompoundSectionEnd(const TextFile &tf, int line_start, int line_end_in = -1);
  
MdlMolVersion findMolObjVersion(const char* text, const int nchar);
  
MdlMolVersion findMolObjVersion(const TextFile &tf, const int line_number);

std::vector<int2> findEntryLimits(const TextFile &tf, const std::string &marker);

std::vector<double3> extractSdfCoordinates(const TextFile &tf, int line_start, int line_end_in,
                                           ExceptionResponse policy = ExceptionResponse::WARN);
 
std::vector<double3> extractSdfCoordinates(const TextFile &tf, int frame_number = 0,
                                           ExceptionResponse policy = ExceptionResponse::WARN);

std::vector<double3> extractPdbCoordinates(const TextFile &tf, int line_start, int line_end_in,
                                           ExceptionResponse policy = ExceptionResponse::WARN);
 
std::vector<double3> extractPdbCoordinates(const TextFile &tf, int frame_number = 0,
                                           ExceptionResponse policy = ExceptionResponse::WARN);
  
} // namespace structure
} // namespace stormm
 
#endif