amber_ascii.h

// -*-c++-*-
#ifndef STORMM_AMBER_ASCII_H
#define STORMM_AMBER_ASCII_H
 
#include "copyright.h"
#include "Constants/behavior.h"
#include "Accelerator/hybrid.h"
#include "Parsing/polynumeric.h"
#include "Parsing/textfile.h"
#include "coordinateframe.h"
 
namespace stormm {
namespace trajectory {
 
using constants::ExceptionResponse;
using card::Hybrid;
using parse::PolyNumeric;
using parse::TextFile;

int getAmberRestartAtomCount(const TextFile &tf);

void getAmberRestartAtomCountAndTime(const TextFile &tf, int *atom_count, double *start_time,
                                     ExceptionResponse policy = ExceptionResponse::WARN);

void splitInterlacedCoordinates(const std::vector<PolyNumeric> &allcrd, double* x, double* y,
                                double* z, int natom);

void getAmberInputCoordinates(const TextFile &tf, double* x_coordinates, double* y_coordinates,
                              double* z_coordinates, int natom, double* box_space_transform,
                              double* inverse_transform, double* box_dimensions);
  
void getAmberInputCoordinates(const TextFile &tf, Hybrid<double> *x_coordinates,
                              Hybrid<double> *y_coordinates,  Hybrid<double> *z_coordinates,
                              Hybrid<double> *box_space_transform,
                              Hybrid<double> *inverse_transform, Hybrid<double> *box_dimensions);
  
void getAmberRestartVelocities(const TextFile &tf, Hybrid<double> *x_velocities,
                               Hybrid<double> *y_velocities,  Hybrid<double> *z_velocities);

int countAmberCrdFormatFrames(const TextFile &tf, int natom, UnitCellType unit_cell);

void readAmberCrdFormat(const TextFile &tf, double *x_coordinates, double *y_coordinates,
                        double *z_coordinates, int natom, UnitCellType unit_cell,
                        double *box_space_transform, double *inverse_transform,
                        double* box_dimensions, int frame_number = 0);
 
void readAmberCrdFormat(const TextFile &tf, Hybrid<double> *x_coordinates,
                        Hybrid<double> *y_coordinates,  Hybrid<double> *z_coordinates,
                        UnitCellType unit_cell, Hybrid<double> *box_space_transform,
                        Hybrid<double> *inverse_transform, Hybrid<double> *box_dimensions,
                        int frame_number = 0);
 
void readAmberCrdFormat(const TextFile &tf, CoordinateFrameWriter *cfw, int frame_number = 0);
 
} // namespace trajectory
} // namespace stormm
 
#endif