molecule_parsing.h

// -*-c++-*-
#ifndef STORMM_MOLECULE_PARSING_H
#define STORMM_MOLECULE_PARSING_H
 
#include <string>
#include <vector>
#include "copyright.h"
#include "Chemistry/atommask.h"
#include "Chemistry/chemical_features.h"
#include "MoleculeFormat/mdlmol.h"
#include "Parsing/polynumeric.h"
#include "Topology/atomgraph.h"
#include "Trajectory/coordinateframe.h"
 
namespace stormm {
namespace structure {
 
using chemistry::AtomMask;
using chemistry::ChemicalFeatures;
using parse::NumberFormat;
using parse::PolyNumeric;
using structure::MdlMol;
using topology::AtomGraph;
using trajectory::CoordinateFrame;

std::string condenseSdfItemDataLines(const std::string &item_name, const MdlMol &molecule);
  
AtomMask maskFromSdfDataItem(const std::string &item_name, const MdlMol &molecule,
                             const AtomGraph *ag, const ChemicalFeatures &chemfe,
                             const CoordinateFrame &cf,
                             ExceptionResponse policy = ExceptionResponse::DIE);
 
AtomMask maskFromSdfDataItem(const std::string &item_name, const MdlMol &molecule,
                             const AtomGraph *ag,
                             ExceptionResponse policy = ExceptionResponse::DIE);

std::vector<PolyNumeric> valuesFromSdfDataItem(const std::string &item_name,
                                               const MdlMol &molecule, const NumberFormat fmt,
                                               ExceptionResponse policy = ExceptionResponse::DIE);

std::vector<double> realFromSdfDataItem(const std::string &item_name, const MdlMol &molecule,
                                        ExceptionResponse policy = ExceptionResponse::DIE);

std::vector<int> intFromSdfDataItem(const std::string &item_name, const MdlMol &molecule,
                                    ExceptionResponse policy = ExceptionResponse::DIE);

std::vector<char4> char4FromSdfDataItem(const std::string &item_name, const MdlMol &molecule,
                                        ExceptionResponse policy = ExceptionResponse::DIE);
 
} // namespace structure
} // namespace stormm
 
#endif