path: root/include/tng_io.hpp

/* This code is part of the tng binary trajectory format.
 *
 *                      VERSION 1.4
 *
 * Written by Anders Gärdenäs
 * Copyright (c) 2012-2013, The GROMACS development team.
 * Check out http://www.gromacs.org for more information.
 *
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the Revised BSD License.
 */

#ifndef TNG_IO_HPP
#define TNG_IO_HPP

#include "tng_io.h"

namespace Tng
{
class Trajectory;
class Atom;
class Residue;
class Chain;
class Molecule;
typedef class Molecule * Molecule_t;


class Trajectory {
private:
    tng_trajectory_t traj;
    tng_function_status status;
public:
    /**
    * @brief Add a molecule to the trajectory.
    * @param name is a pointer to the string containing the name of the new molecule.
    * @param molecule is a pointer to the newly created molecule.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */

    tng_function_status addMolecule(const char *, Molecule_t);
    tng_function_status addMoleculeWithId(const char *, int64_t id, Molecule_t);
    tng_function_status findMolecule(const char *name, int64_t id, Molecule_t molecule);
    friend class Atom;
    friend class Residue;
    friend class Chain;
    friend class Molecule;

    //! Normal constructor
    Trajectory()
    { status = tng_trajectory_init(&traj); }

    //! Copy constructor
    Trajectory(Trajectory * src)
    { status = tng_trajectory_init_from_src(traj,&src->traj); }

    //! Detructor
    ~Trajectory()
    { status = tng_trajectory_destroy(&traj); }

    //! Status
    tng_function_status getStatus()
    { return status; }


    /**
    * @brief Get the name of the input file.
    * @param file_name the string to fill with the name of the input file,
    * memory must be allocated before.
    * @param max_len maximum char length of the string, i.e. how much memory has
    * been reserved for file_name. This includes \0 terminating character.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred (source string longer than destination string).
    */
    tng_function_status getInputFile (char *file_name, const int max_len)
    {
        return status = tng_input_file_get(traj, file_name,   max_len);
    }

    /**
    * @brief Set the name of the input file.
    * @param file_name the name of the input file.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setInputFile(const char *file_name)
    {
        return status = tng_input_file_set(traj, file_name);
    }


    /**
    * @brief Get the name of the output file.
    * @param file_name the string to fill with the name of the output file,
    * memory must be allocated before.
    * @param max_len maximum char length of the string, i.e. how much memory has
    * been reserved for file_name. This includes \0 terminating character.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred (source string longer than destination string).
    */
    tng_function_status getOutputFile(char *file_name, const int max_len)
    {
        return status = tng_output_file_get(traj, file_name, max_len);
    }


    /**
    * @brief Set the name of the output file.
    * @param file_name the name of the output file.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setOutputFile(const char *file_name)
    {
        return status = tng_output_file_set(traj, file_name);
    }

    /**
    * @brief Get the endianness of the output file.
    * current output file.
    * @param endianness will contain the enumeration of the endianness.
    * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (1) if the endianness
    * could not be retrieved.
    */
    tng_function_status getOutputFileEndianness
                    (tng_file_endianness *endianness)
    {
        return status = tng_output_file_endianness_get(traj, endianness);
    }

    /**
    * @brief Set the endianness of the output file.
    * @param endianness the enumeration of the endianness, can be either
    * TNG_BIG_ENDIAN (0) or TNG_LITTLE_ENDIAN (1).
    * @details The endianness cannot be changed after file output has started.
    * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (1) if the endianness
    * could not be set.
    */
    tng_function_status setOutputFileEndianness
                    (const tng_file_endianness endianness)
    {
        return status = tng_output_file_endianness_set(traj, endianness);
    }

    /**
    * @brief Get the name of the program used when creating the trajectory.
    * @param name the string to fill with the name of the program,
    * memory must be allocated before.
    * @param max_len maximum char length of the string, i.e. how much memory has
    * been reserved for name. This includes \0 terminating character.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred (source string longer than destination string).
    */
    tng_function_status getFirstProgramName(char *name, const int max_len)
    {
        return status = tng_first_program_name_get(traj,name,max_len);
    }


    /**
    * @brief Set the name of the program used when creating the trajectory..
    * @param new_name is a string containing the wanted name.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setFirstProgramName(const char *new_name)
    {
        return status = tng_first_program_name_set(traj, new_name);
    }


    /**
    * @brief Get the name of the program used when last modifying the trajectory.
    * @param name the string to fill with the name of the program,
    * memory must be allocated before.
    * @param max_len maximum char length of the string, i.e. how much memory has
    * been reserved for name. This includes \0 terminating character.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred (source string longer than destination string).
    */
    tng_function_status getLastProgramName(char *name, const int max_len)
    {
        return status = tng_last_program_name_get(traj, name, max_len);
    }


    /**
    * @brief Set the name of the program used when last modifying the trajectory.
    * @param new_name is a string containing the wanted name.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setLastProgramName(const char *new_name)
    {
        return status = tng_last_program_name_set(traj, new_name);
    }


    /**
    * @brief Get the name of the user who created the trajectory.
    * @param name the string to fill with the name of the user,
    * memory must be allocated before.
    * @param max_len maximum char length of the string, i.e. how much memory has
    * been reserved for name. This includes \0 terminating character.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred (source string longer than destination string).
    */
    tng_function_status getFirstUserName(char *name, const int max_len)
    {
        return status = tng_first_user_name_get(traj,name, max_len);
    }


    /**
    * @brief Set the name of the user who created the trajectory.
    * @param new_name is a string containing the wanted name.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setFirstUserName(const char *new_name)
    {
        return status = tng_first_user_name_set(traj, new_name);
    }


    /**
    * @brief Get the name of the user who last modified the trajectory.
    * @param name the string to fill with the name of the user,
    * memory must be allocated before.
    * @param max_len maximum char length of the string, i.e. how much memory has
    * been reserved for name. This includes \0 terminating character.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred (source string longer than destination string).
    */
    tng_function_status getLastUserName(char *name, const int max_len)
    {
        return status = tng_last_user_name_get(traj,name,max_len);
    }


    /**
    * @brief Set the name of the user who last modified the trajectory.
    * @param new_name is a string containing the wanted name.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setLastUserName(const char *new_name)
    {
        return status = tng_last_user_name_set(traj,new_name);
    }



    /**
    * @brief Get the name of the computer used when creating the trajectory.
    * @param name the string to fill with the name of the computer,
    * memory must be allocated before.
    * @param max_len maximum char length of the string, i.e. how much memory has
    * been reserved for name. This includes \0 terminating character.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred (source string longer than destination string).
    */
    tng_function_status getFirstComputerName(char *name, const int max_len)
    {
        return status = tng_first_computer_name_get(traj, name, max_len);
    }


    /**
    * @brief Set the name of the computer used when creating the trajectory.
    * @param new_name is a string containing the wanted name.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setFirstComputerName(const char *new_name)
    {
        return status = tng_first_computer_name_set(traj, new_name);
    }


    /**
    * @brief Get the name of the computer used when last modifying the trajectory.
    * @param name the string to fill with the name of the computer,
    * memory must be allocated before.
    * @param max_len maximum char length of the string, i.e. how much memory has
    * been reserved for name. This includes \0 terminating character.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred (source string longer than destination string).
    */
    tng_function_status getLastComputerName(char *name, const int max_len)
    {
        return status = tng_last_computer_name_get(traj,name,max_len);
    }


    /**
    * @brief Set the name of the computer used when last modifying the trajectory.
    * @param new_name is a string containing the wanted name.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setLastComputerName(const char *new_name)
    {
        return status = tng_last_computer_name_set(traj,new_name);
    }


    /**
    * @brief Get the pgp_signature of the user creating the trajectory.
    * @param signature the string to fill with the signature,
    * memory must be allocated before.
    * @param max_len maximum char length of the string, i.e. how much memory has
    * been reserved for name. This includes \0 terminating character.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred (source string longer than destination string).
    */
    tng_function_status getFirstSignature(char *signature, const int max_len)
    {
        return status = tng_last_computer_name_get(traj, signature,max_len);
    }


    /**
    * @brief Set the pgp_signature of the user creating the trajectory.
    * @param signature is a string containing the pgp_signature.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setFirstSignature(const char *signature)
    {
        return status = tng_first_signature_set(traj, signature);
    }


    /**
    * @brief Get the pgp_signature of the user last modifying the trajectory.
    * @param signature the string to fill with the signature,
    * memory must be allocated before.
    * @param max_len maximum char length of the string, i.e. how much memory has
    * been reserved for name. This includes \0 terminating character.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred (source string longer than destination string).
    */
    tng_function_status getLastSignature(char *signature, const int max_len)
    {
        return status = tng_first_signature_get(traj, signature, max_len);
    }


    /**
    * @brief Set the pgp_signature of the user last modifying the trajectory.
    * @param signature is a string containing the pgp_signature.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setLastSignature(const char *signature)
    {
        return status = tng_last_signature_set(traj, signature);
    }


    /**
    * @brief Get the name of the forcefield used in the trajectory.
    * @param name the string to fill with the name of the forcefield,
    * memory must be allocated before.
    * @param max_len maximum char length of the string, i.e. how much memory has
    * been reserved for name. This includes \0 terminating character.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred (source string longer than destination string).
    */
    tng_function_status getForcefieldName(char *name, const int max_len)
    {
        return status = tng_last_signature_get(traj,name,max_len);
    }


    /**
    * @brief Set the name of the forcefield used in the trajectory.
    * @param new_name is a string containing the wanted name.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setForcefieldName(const char *new_name)
    {
        return status = tng_forcefield_name_set(traj, new_name);
    }


    /**
    * @brief Get the medium stride length of the trajectory.
    * @param len is pointing to a value set to the stride length.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getMediumStrideLength(int64_t *len)
    {
        return status = tng_medium_stride_length_get(traj,len);
    }


    /**
    * @brief Set the medium stride length of the trajectory.
    * @param len is the wanted medium stride length.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred.
    */
    tng_function_status setMediumStrideLength(const int64_t len)
    {
        return status = tng_medium_stride_length_set(traj,len);
    }


    /**
    * @brief Get the long stride length of the trajectory.
    * @param len is pointing to a value set to the stride length.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getLongStrideLength(int64_t *len)
    {
        return status = tng_long_stride_length_get(traj, len);
    }


    /**
    * @brief Set the long stride length of the trajectory.
    * @param len is the wanted long stride length.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred.
    */
    tng_function_status setLongStrideLength(const int64_t len)
    {
        return status = tng_long_stride_length_set(traj,len);
    }


    /**
    * @brief Get the current time per frame of the trajectory.
    * @param len is pointing to a value set to the time per frame.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getTimePerFrame(double *time)
    {
        return status = tng_time_per_frame_get(traj, time);
    }


    /**
    * @brief Set the time per frame of the trajectory.
    * @param len is the new time per frame.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred.
    */
    tng_function_status setTimePerFrame(const double time)
    {
        return status = tng_time_per_frame_set(traj, time);
    }


    /**
    * @brief Get the length of the input file.
    * @param len is pointing to a value set to the file length.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getInputFileLen(int64_t *len)
    {
        return status = tng_input_file_len_get(traj, len);
    }


    /**
    * @brief Get the number of frames in the trajectory
    * @param n is pointing to a value set to the number of frames.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred (could not find last frame set).
    */
    tng_function_status getNumFrames(int64_t *n)
    {
        return status = tng_num_frames_get(traj, n);
    }

    /**
    * @brief Get the current number of particles.
    * @param n is pointing to a value set to the number of particles.
    * @details If variable number of particles are used this function will return
    * the number of particles in the current frame set.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getNumParticles(int64_t *n)
    {
        return status = tng_num_particles_get(traj, n);
    }




    /**
    * @brief Get the current total number of molecules.
    * @param n is pointing to a value set to the number of molecules.
    * @details If variable number of particles are used this function will return
    * the total number of molecules in the current frame set.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getNumMolecules(int64_t *n)
    {
        return status = tng_num_molecules_get(traj,n);
    }

    /**
    * @brief Get the exponential used for distances in the trajectory.
    * @param exp is pointing to a value set to the distance unit exponential.
    * @details Example: If the distances are specified in nm (default) exp is -9.
    * If the distances are specified in Å exp is -10.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getDistanceUnitExponential
                    (int64_t *exp)
    {
        return status = tng_distance_unit_exponential_get(traj, exp);
    }

    /**
    * @brief Set the exponential used for distances in the trajectory.
    * @param exp is the distance unit exponential to use.
    * @details Example: If the distances are specified in nm (default) exp is -9.
    * If the distances are specified in Å exp is -10.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status setDistanceUnitExponential
                    (int64_t exp)
    {
        return status = tng_distance_unit_exponential_set(traj, exp);
    }


    /**
    * @brief Get the number of frames per frame set.
    * per frame set.
    * @param n is pointing to a value set to the number of frames per frame set.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getNumFramesPerFrameSet(int64_t *n)
    {
        return status = tng_num_frames_per_frame_set_get(traj,n);
    }

    /**
    * @brief Set the number of frames per frame set.
    * @param n is the number of frames per frame set.
    * @details This does not affect already existing frame sets. For
    * consistency the number of frames per frame set should be set
    * betfore creating any frame sets.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status setNumFramesPerFrameSet(const int64_t n)
    {
        return status = tng_num_frames_per_frame_set_set(traj,n);
    }

    /**
    * @brief Get the number of frame sets.
    * @param n is pointing to a value set to the number of frame sets.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status getNumFrameSets(int64_t *n)
    {
        return status = tng_num_frame_sets_get(traj, n);
    }


    /**
    * @brief Get the current trajectory frame set.
    * @param frame_set_p will be set to point at the memory position of
    * the found frame set.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getCurrentFrameSet(tng_trajectory_frame_set_t *frame_set_p)
    {
        return status = tng_current_frame_set_get(traj, frame_set_p);
    }


    /**
    * @brief Find the requested frame set number.
    * @param nr is the frame set number to search for.
    * @details tng_data->current_trajectory_frame_set will contain the
    * found trajectory if successful.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status findFrameSetNr(const int64_t nr)
    {
        return status = tng_frame_set_nr_find(traj,nr);
    }


    /**
    * @brief Find the frame set containing a specific frame.
    * @param frame is the frame number to search for.
    * @details tng_data->current_trajectory_frame_set will contain the
    * found trajectory if successful.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status findFrameSetOfFrame(const int64_t frame)
    {
        return status = tng_frame_set_of_frame_find(traj, frame);
    }


    /**
    * @brief Get the file position of the next frame set in the input file.
    * @param frame_set is the frame set of which to get the position of the
    * following frame set.
    * @param pos is pointing to a value set to the file position.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getNextFrameSetFilePos
        (const tng_trajectory_frame_set_t frame_set,int64_t *pos)
    {
        return status = tng_frame_set_next_frame_set_file_pos_get(traj,frame_set,pos );
    }

    /**
    * @brief Get the file position of the previous frame set in the input file.
    * @param frame_set is the frame set of which to get the position of the
    * previous frame set.
    * @param pos is pointing to a value set to the file position.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getPrevFrameSetFilePos
        (const tng_trajectory_frame_set_t frame_set,int64_t *pos)
    {
        return status = tng_frame_set_prev_frame_set_file_pos_get(traj, frame_set, pos);
    }


    /**
    * @brief Get the first and last frames of the frame set.
    * @param frame_set is the frame set of which to get the frame range.
    * @param first_frame is set to the first frame of the frame set.
    * @param last_frame is set to the last frame of the frame set.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getFrameSetFrameRange
        (const tng_trajectory_frame_set_t frame_set,
        int64_t *first_frame,
        int64_t *last_frame)
    {
        return status = tng_frame_set_frame_range_get(traj,frame_set, first_frame, last_frame);
    }


    /**
    * @brief Get the molecume name of real particle number (number in mol system).
    * @param nr is the real number of the particle in the molecular system.
    * @param name is a string, which is set to the name of the molecule. Memory
    * must be reserved beforehand.
    * @param max_len is the maximum length of name.
    * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error
    * has occured.
    */
    tng_function_status getMoleculeNameOfParticleNr
        (const int64_t nr,char *name,int max_len)
    {
        return status = tng_molecule_name_of_particle_nr_get(traj,nr,name,max_len);
    }


    /**
    * @brief Get the chain name of real particle number (number in mol system).
    * @param nr is the real number of the particle in the molecular system.
    * @param name is a string, which is set to the name of the chain. Memory
    * must be reserved beforehand.
    * @param max_len is the maximum length of name.
    * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error
    * has occured.
    */
    tng_function_status getChainNameOfParticleNr
        (const int64_t nr,char *name,int max_len)
    {
        return status = tng_chain_name_of_particle_nr_get(traj, nr, name, max_len);
    }


    /**
    * @brief Get the residue name of real particle number (number in mol system).
    * @param nr is the real number of the particle in the molecular system.
    * @param name is a string, which is set to the name of the residue. Memory
    * must be reserved beforehand.
    * @param max_len is the maximum length of name.
    * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error
    * has occured.
    */
    tng_function_status getResidueNameOfParticleNr
        (const int64_t nr,char *name,int max_len)
    {
        return status = tng_residue_name_of_particle_nr_get(traj,nr,name,max_len);
    }


    /**
    * @brief Get the atom name of real particle number (number in mol system).
    * @param nr is the real number of the particle in the molecular system.
    * @param name is a string, which is set to the name of the atom. Memory
    * must be reserved beforehand.
    * @param max_len is the maximum length of name.
    * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error
    * has occured.
    */
    tng_function_status getAtomNameOfParticleNr
        (const int64_t nr,char *name,int max_len)
    {
        return status = tng_atom_name_of_particle_nr_get(traj, nr,name,max_len);
    }


    /**
    * @brief Add a particle mapping table.
    * @details Each particle mapping table will be written as a separate block,
    * followed by the data blocks for the corresponding particles. In most cases
    * there is one particle mapping block for each thread writing the trajectory.
    * @details The mapping information is added to the currently active frame set
    * of tng_data
    * @param first_particle_number is the first particle number of this mapping
    * block.
    * @param n_particles is the number of particles in this mapping block.
    * @param mapping_table is a list of the real particle numbers (i.e. the numbers
    * used in the molecular system). The list is n_particles long.
    * @details mapping_table[0] is the real particle number of the first particle
    * in the following data blocks.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status addParticleMapping
        (const int64_t first_particle_number,
        const int64_t n_particles,
        const int64_t *mapping_table)
    {
        return status = tng_particle_mapping_add(traj,first_particle_number,n_particles,mapping_table );
    }


    /**
    * @brief Read the header blocks from the input_file of tng_data.
    * @details The trajectory blocks must be read separately and iteratively in chunks
    * to fit in memory.
    * @details tng_data->input_file_path specifies
    * which file to read from. If the file (input_file) is not open it will be
    * opened.
    * @param hash_mode is an option to decide whether to use the md5 hash or not.
    * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be
    * compared to the md5 hash of the read contents to ensure valid data.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status readFileHeaders(const tng_hash_mode hash_mode)
    {
        return status = tng_file_headers_read(traj, hash_mode);
    }


    /**
    * @brief Write the header blocks to the output_file of tng_data.
    * @details The trajectory blocks must be written separately and iteratively in chunks
    * to fit in memory.
    * @details tng_data->output_file_path
    * specifies which file to write to. If the file (output_file) is not open it
    * will be opened.
    * @param hash_mode is an option to decide whether to use the md5 hash or not.
    * If hash_mode == TNG_USE_HASH an md5 hash for each header block will be generated.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status writeFileHeaders(const tng_hash_mode hash_mode)
    {
        return status = tng_file_headers_write(traj, hash_mode);
    }



    /**
    * @brief Read one (the next) block (of any kind) from the input_file of tng_data.
    * which file to read from. If the file (input_file) is not open it will be
    * opened.
    * @param block_data is a pointer to the struct which will be populated with the
    * data.
    * @details If block_data->input_file_pos > 0 it is the position from where the
    * reading starts otherwise it starts from the current position.
    * @param hash_mode is an option to decide whether to use the md5 hash or not.
    * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be
    * compared to the md5 hash of the read contents to ensure valid data.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status readNextBlock(const tng_hash_mode hash_mode, tng_gen_block_t block_data)
    {
        return status = tng_block_read_next(traj,block_data, hash_mode);
    }



    /**
    * @brief Read one (the next) frame set, including mapping and related data blocks
    * from the input_file of tng_data.
    * which file to read from. If the file (input_file) is not open it will be
    * opened.
    * @param hash_mode is an option to decide whether to use the md5 hash or not.
    * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be
    * compared to the md5 hash of the read contents to ensure valid data.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status readNextFrameSet(const tng_hash_mode hash_mode)
    {
        return status = tng_frame_set_read_next(traj, hash_mode);
    }


    /**
    * @brief Write one frame set, including mapping and related data blocks
    * to the output_file of tng_data.
    * @details  tng_data->output_file_path specifies
    * which file to write to. If the file (output_file) is not open it will be
    * opened.
    * @param hash_mode is an option to decide whether to use the md5 hash or not.
    * If hash_mode == TNG_USE_HASH an md5 hash for each header block will be generated.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status writeFrameSet(const tng_hash_mode hash_mode)
    {
        return status = tng_frame_set_write(traj, hash_mode);
    }


    /**
    * @brief Create and initialise a frame set.
    * @param first_frame is the first frame of the frame set.
    * @param n_frames is the number of frames in the frame set.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status newFrameSet(const int64_t first_frame,
        const int64_t n_frames)
    {
        return status =  tng_frame_set_new(traj, first_frame, n_frames);
    }


    /**
    * @brief Create and initialise a frame set with the time of the first frame
    * specified.
    * @param first_frame is the first frame of the frame set.
    * @param n_frames is the number of frames in the frame set.
    * @param first_frame_time is the time stamp of the first frame (in seconds).
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status newFrameSetWithTime
                (const int64_t first_frame,
                 const int64_t n_frames,
                 const double first_frame_time)
    {
        return status =  tng_frame_set_with_time_new(traj,
                                                     first_frame, n_frames,
                                                     first_frame_time);
    }


    /**
    * @brief Set the time stamp of the first frame of the current frame set.
    * @param first_frame_time is the time stamp of the first frame in the
    * frame set.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status setTimeOfFirstFrameOfFrameSet
                    (const double first_frame_time)
    {
        return status = tng_frame_set_first_frame_time_set(traj,
                                                           first_frame_time);
    }

    /**
    * @brief Add a non-particle dependent data block.
    * @param id is the block ID of the block to add.
    * @param block_name is a descriptive name of the block to add
    * @param datatype is the datatype of the data in the block (e.g. int/float)
    * @param block_type_flag indicates if this is a non-trajectory block (added
    * directly to tng_data) or if it is a trajectory block (added to the
    * frame set)
    * @param n_frames is the number of frames of the data block (automatically
    * set to 1 if adding a non-trajectory data block)
    * @param n_values_per_frame is how many values a stored each frame (e.g. 9
    * for a box shape block)
    * @param stride_length is how many frames are between each entry in the
    * data block
    * @param codec_id is the ID of the codec to compress the data.
    * @param new_data is an array of data values to add.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status addDataBlock(const int64_t id,
        const char *block_name,
        const tng_data_type datatype,
        const tng_block_type block_type_flag,
        int64_t n_frames,
        const int64_t n_values_per_frame,
        const int64_t stride_length,
        const int64_t codec_id,
        void *new_data)
    {
        return status = tng_data_block_add(traj, id,block_name,
            datatype,block_type_flag, n_frames,
            n_values_per_frame, stride_length,
            codec_id, new_data);
    }


    /**
    * @brief Add a particle dependent data block.
    * @param id is the block ID of the block to add.
    * @param block_name is a descriptive name of the block to add
    * @param datatype is the datatype of the data in the block (e.g. int/float)
    * @param block_type_flag indicates if this is a non-trajectory block (added
    * directly to tng_data) or if it is a trajectory block (added to the
    * frame set)
    * @param n_frames is the number of frames of the data block (automatically
    * set to 1 if adding a non-trajectory data block)
    * @param n_values_per_frame is how many values a stored each frame (e.g. 9
    * for a box shape block)
    * @param stride_length is how many frames are between each entry in the
    * data block
    * @param first_particle_number is the number of the first particle stored
    * in this data block
    * @param n_particles is the number of particles stored in this data block
    * @param codec_id is the ID of the codec to compress the data.
    * @param new_data is an array of data values to add.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status addParticleDataBlock(const int64_t id,
        const char *block_name,
        const tng_data_type datatype,
        const tng_block_type block_type_flag,
        int64_t n_frames,
        const int64_t n_values_per_frame,
        const int64_t stride_length,
        const int64_t first_particle_number,
        const int64_t n_particles,
        const int64_t codec_id,
        void *new_data)
    {
        return status = tng_particle_data_block_add(traj,id,    block_name,
            datatype, block_type_flag, n_frames,n_values_per_frame,
            stride_length,first_particle_number,n_particles,
            codec_id, new_data);
    }


    /**
    * @brief Write data of one trajectory frame to the output_file of tng_data.
    * @param frame_nr is the index number of the frame to write.
    * @param block_id is the ID of the data block to write the data to.
    * @param data is an array of data to write. The length of the array should
    * equal n_values_per_frame.
    * @param hash_mode is an option to decide whether to use the md5 hash or not.
    * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be
    * compared to the md5 hash of the read contents to ensure valid data.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status writeFrameData(const int64_t frame_nr,
        const int64_t block_id,
        const void *data,
        const tng_hash_mode hash_mode)
    {
        return status = tng_frame_data_write(traj,frame_nr,block_id,data,hash_mode);
    }


    /**
    * @brief Write particle data of one trajectory frame to the output_file of
    * tng_data.
    * @param frame_nr is the index number of the frame to write.
    * @param block_id is the ID of the data block to write the data to.
    * @param val_first_particle is the number of the first particle in the data
    * array.
    * @param val_n_particles is the number of particles in the data array.
    * @param data is a 1D-array of data to write. The length of the array should
    * equal n_particles * n_values_per_frame.
    * @param hash_mode is an option to decide whether to use the md5 hash or not.
    * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be
    * compared to the md5 hash of the read contents to ensure valid data.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status writeFrameParticleData(const int64_t frame_nr,
        const int64_t block_id,
        const int64_t val_first_particle,
        const int64_t val_n_particles,
        const void *data,
        const tng_hash_mode hash_mode)
    {
        return status = tng_frame_particle_data_write(traj,frame_nr,block_id,val_first_particle,val_n_particles,data,hash_mode);
    }


    /**
    * @brief Free data is an array of values (2D).
    * @param values is the 2D array to free and will be set to 0 afterwards.
    * @param n_frames is the number of frames in the data array.
    * @param n_values_per_frame is the number of values per frame in the data array.
    * @param type is the data type of the data in the array (e.g. int/float/char).
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status freeDataValues(union data_values **values,
        const int64_t n_frames,
        const int64_t n_values_per_frame,
        const tng_data_type type)
    {
        return status = tng_data_values_free(traj, values, n_frames,n_values_per_frame,type);
    }


    /**
    * @brief Free data is an array of values (3D).
    * @param values is the array to free and will be set to 0 afterwards.
    * @param n_frames is the number of frames in the data array.
    * @param n_particles is the number of particles in the data array.
    * @param n_values_per_frame is the number of values per frame in the data array.
    * @param type is the data type of the data in the array (e.g. int/float/char).
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status freeParticleDataValues(union data_values ***values,
        const int64_t n_frames,
        const int64_t n_particles,
        const int64_t n_values_per_frame,
        const tng_data_type type)
    {
        return status = tng_particle_data_values_free(traj, values,n_frames,n_particles,n_values_per_frame,type);
    }


    /**
    * @brief Retrieve non-particle data, from the last read frame set. Obsolete!
    * which file to read from. If the file (input_file) is not open it will be
    * opened.
    * @param block_id is the id number of the particle data block to read.
    * @param values is a pointer to a 2-dimensional array (memory unallocated), which
    * will be filled with data. The array will be sized
    * (n_frames * n_values_per_frame).
    * Since ***values is allocated in this function it is the callers
    * responsibility to free the memory.
    * @param n_frames is set to the number of particles in the returned data. This is
    * needed to properly reach and/or free the data afterwards.
    * @param n_values_per_frame is set to the number of values per frame in the data.
    * This is needed to properly reach and/or free the data afterwards.
    * @param type is set to the data type of the data in the array.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status getData(const int64_t block_id,
        union data_values ***values,
        int64_t *n_frames,
        int64_t *n_values_per_frame,
        char *type)
    {
        return status = tng_data_get(traj, block_id, values, n_frames,
                                     n_values_per_frame, type);
    }

    /**
    * @brief Retrieve a vector (1D array) of non-particle data, from the last read frame set.
    * @param block_id is the id number of the particle data block to read.
    * @param values is a pointer to a 1-dimensional array (memory unallocated), which
    * will be filled with data. The length of the array will be (n_frames * n_values_per_frame).
    * Since **values is allocated in this function it is the callers
    * responsibility to free the memory.
    * @param n_frames is set to the number of particles in the returned data. This is
    * needed to properly reach and/or free the data afterwards.
    * @param stride_length is set to the stride length of the returned data.
    * @param n_values_per_frame is set to the number of values per frame in the data.
    * This is needed to properly reach and/or free the data afterwards.
    * @param type is set to the data type of the data in the array.
    * @details This does only work for numerical (int, float, double) data.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status getDataVector
                (const int64_t block_id,
                 void **values,
                 int64_t *n_frames,
                 int64_t *stride_length,
                 int64_t *n_values_per_frame,
                 char *type)
    {
        return status = tng_data_vector_get(traj, block_id, values, n_frames,
                                            stride_length, n_values_per_frame,
                                            type);
    }

    /**
    * @brief Read and retrieve non-particle data, in a specific interval. Obsolete!
    * which file to read from. If the file (input_file) is not open it will be
    * opened.
    * @param block_id is the id number of the particle data block to read.
    * @param start_frame_nr is the index number of the first frame to read.
    * @param end_frame_nr is the index number of the last frame to read.
    * @param hash_mode is an option to decide whether to use the md5 hash or not.
    * If hash_mode == TNG_USE_HASH the md5 hash in the file will be
    * compared to the md5 hash of the read contents to ensure valid data.
    * @param values is a pointer to a 2-dimensional array (memory unallocated), which
    * will be filled with data. The array will be sized
    * (n_frames * n_values_per_frame).
    * Since ***values is allocated in this function it is the callers
    * responsibility to free the memory.
    * @param n_values_per_frame is set to the number of values per frame in the data.
    * This is needed to properly reach and/or free the data afterwards.
    * @param type is set to the data type of the data in the array.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status getDataInterval(const int64_t block_id,
        const int64_t start_frame_nr,
        const int64_t end_frame_nr,
        const tng_hash_mode hash_mode,
        union data_values ***values,
        int64_t *n_values_per_frame,
        char *type)
    {
        return status = tng_data_interval_get(traj, block_id, start_frame_nr,
                                              end_frame_nr, hash_mode, values,
                                              n_values_per_frame, type);
    }


    /**
    * @brief Read and retrieve a vector (1D array) of non-particle data,
    * in a specific interval.
    * @param block_id is the id number of the particle data block to read.
    * @param start_frame_nr is the index number of the first frame to read.
    * @param end_frame_nr is the index number of the last frame to read.
    * @param hash_mode is an option to decide whether to use the md5 hash or not.
    * If hash_mode == TNG_USE_HASH the md5 hash in the file will be
    * compared to the md5 hash of the read contents to ensure valid data.
    * @param values is a pointer to a 1-dimensional array (memory unallocated), which
    * will be filled with data. The length of the array will be (n_frames * n_values_per_frame).
    * Since **values is allocated in this function it is the callers
    * responsibility to free the memory.
    * @param stride_length is set to the stride length (writing frequency) of
    * the data.
    * @param n_values_per_frame is set to the number of values per frame in the data.
    * This is needed to properly reach and/or free the data afterwards.
    * @param type is set to the data type of the data in the array.
    * @details This does only work for numerical (int, float, double) data.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status getDataVectorInterval
                (const int64_t block_id,
                 const int64_t start_frame_nr,
                 const int64_t end_frame_nr,
                 const char hash_mode,
                 void **values,
                 int64_t *stride_length,
                 int64_t *n_values_per_frame,
                 char *type)
    {
        return status = tng_data_vector_interval_get(traj, block_id,
                                                     start_frame_nr,
                                                     end_frame_nr,
                                                     hash_mode, values,
                                                     stride_length,
                                                     n_values_per_frame,
                                                     type);
    }

    /**
    * @brief Retrieve particle data, from the last read frame set. Obsolete!
    * @details The particle dimension of the returned values array is translated
    * to real particle numbering, i.e. the numbering of the actual molecular
    * system.
    * specifies which file to read from. If the file (input_file) is not open it
    * will be opened.
    * @param block_id is the id number of the particle data block to read.
    * @param values is a pointer to a 3-dimensional array (memory unallocated), which
    * will be filled with data. The array will be sized
    * (n_frames * n_particles * n_values_per_frame).
    * Since ****values is allocated in this function it is the callers
    * responsibility to free the memory.
    * @param n_frames is set to the number of particles in the returned data. This is
    * needed to properly reach and/or free the data afterwards.
    * @param n_particles is set to the number of particles in the returned data. This is
    * needed to properly reach and/or free the data afterwards.
    * @param n_values_per_frame is set to the number of values per frame in the data.
    * This is needed to properly reach and/or free the data afterwards.
    * @param type is set to the data type of the data in the array.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status getParticleData(const int64_t block_id,
        union data_values ****values,
        int64_t *n_frames,
        int64_t *n_particles,
        int64_t *n_values_per_frame,
        char *type)
    {
        return status = (tng_particle_data_get(traj, block_id, values, n_frames,
            n_particles, n_values_per_frame, type));
    }


    /**
    * @brief Retrieve a vector (1D array) of particle data, from the last read frame set.
    * @details The particle dimension of the returned values array is translated
    * to real particle numbering, i.e. the numbering of the actual molecular
    * system.
    * @param block_id is the id number of the particle data block to read.
    * @param values is a pointer to a 1-dimensional array (memory unallocated), which
    * will be filled with data. The length of the array will be
    * (n_frames * n_particles * n_values_per_frame).
    * Since **values is allocated in this function it is the callers
    * responsibility to free the memory.
    * @param n_frames is set to the number of frames in the returned data. This is
    * needed to properly reach and/or free the data afterwards.
    * @param stride_length is set to the stride length of the returned data.
    * @param n_particles is set to the number of particles in the returned data. This is
    * needed to properly reach and/or free the data afterwards.
    * @param n_values_per_frame is set to the number of values per frame in the data.
    * This is needed to properly reach and/or free the data afterwards.
    * @param type is set to the data type of the data in the array.
    * @details This does only work for numerical (int, float, double) data.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status getParticleDataVector
                (const int64_t block_id,
                 void **values,
                 int64_t *n_frames,
                 int64_t *stride_length,
                 int64_t *n_particles,
                 int64_t *n_values_per_frame,
                 char *type)
    {
        return status = tng_particle_data_vector_get(traj, block_id,
                                                     values, n_frames,
                                                     stride_length,
                                                     n_particles,
                                                     n_values_per_frame, type);
    }


    /**
    * @brief Read and retrieve particle data, in a specific interval. Obsolete!
    * @details The particle dimension of the returned values array is translated
    * to real particle numbering, i.e. the numbering of the actual molecular
    * system.
    * @param block_id is the id number of the particle data block to read.
    * @param start_frame_nr is the index number of the first frame to read.
    * @param end_frame_nr is the index number of the last frame to read.
    * @param hash_mode is an option to decide whether to use the md5 hash or not.
    * If hash_mode == TNG_USE_HASH the md5 hash in the file will be
    * compared to the md5 hash of the read contents to ensure valid data.
    * @param values is a pointer to a 3-dimensional array (memory unallocated), which
    * will be filled with data. The array will be sized
    * (n_frames * n_particles * n_values_per_frame).
    * Since ****values is allocated in this function it is the callers
    * responsibility to free the memory.
    * @param n_particles is set to the number of particles in the returned data. This is
    * needed to properly reach and/or free the data afterwards.
    * @param n_values_per_frame is set to the number of values per frame in the data.
    * This is needed to properly reach and/or free the data afterwards.
    * @param type is set to the data type of the data in the array.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status getParticleDataInterval(const int64_t block_id,
        const int64_t start_frame_nr,
        const int64_t end_frame_nr,
        const tng_hash_mode hash_mode,
        union data_values ****values,
        int64_t *n_particles,
        int64_t *n_values_per_frame,
        char *type)
    {
        return status = (tng_particle_data_interval_get(traj, block_id, start_frame_nr,
            end_frame_nr, hash_mode, values,
            n_particles, n_values_per_frame,
            type));
    }


    /**
    * @brief Read and retrieve a vector (1D array) particle data, in a
    * specific interval.
    * @details The particle dimension of the returned values array is translated
    * to real particle numbering, i.e. the numbering of the actual molecular
    * system.
    * @param block_id is the id number of the particle data block to read.
    * @param start_frame_nr is the index number of the first frame to read.
    * @param end_frame_nr is the index number of the last frame to read.
    * @param hash_mode is an option to decide whether to use the md5 hash or not.
    * If hash_mode == TNG_USE_HASH the md5 hash in the file will be
    * compared to the md5 hash of the read contents to ensure valid data.
    * @param values is a pointer to a 1-dimensional array (memory unallocated), which
    * will be filled with data. The length of the array will be
    * (n_frames * n_particles * n_values_per_frame).
    * Since **values is allocated in this function it is the callers
    * responsibility to free the memory.
    * @param stride_length is set to the stride length (writing frequency) of
    * the data.
    * @param n_particles is set to the number of particles in the returned data. This is
    * needed to properly reach and/or free the data afterwards.
    * @param n_values_per_frame is set to the number of values per frame in the data.
    * This is needed to properly reach and/or free the data afterwards.
    * @param type is set to the data type of the data in the array.
    * @details This does only work for numerical (int, float, double) data.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status getParticleDataVectorInterval
                (const int64_t block_id,
                 const int64_t start_frame_nr,
                 const int64_t end_frame_nr,
                 const tng_hash_mode hash_mode,
                 void **values,
                 int64_t *n_particles,
                 int64_t *stride_length,
                 int64_t *n_values_per_frame,
                 char *type)
    {
        return status = tng_particle_data_vector_interval_get(traj, block_id,
                                                              start_frame_nr,
                                                              end_frame_nr,
                                                              hash_mode,
                                                              values,
                                                              n_particles,
                                                              stride_length,
                                                              n_values_per_frame,
                                                              type);
    }


    /** @brief Get the date and time of initial file creation in ISO format (string).
    *  @param time is a pointer to the string in which the date will be stored. Memory
    must be reserved beforehand.
    * @return TNG_SUCCESS (0) if successful.
    */
    tng_function_status getTimeStr(char *time)
    {
        return status = tng_time_get_str(traj, time);
    }


};





class Molecule
{
private:

    tng_molecule_t mol;
    Trajectory * traj;
    tng_function_status status;
public:
    tng_function_status addChain(const char *name, Chain *chain);
    tng_function_status findChain(const char *name, int64_t id, Chain *chain);
    friend class Trajectory;
    //Constructor
    Molecule(Trajectory * trajectory)
    {
        traj = trajectory;

        //status = tng_molecule_init(traj->traj,mol);
    }
    /**
     *@Dose nothing, use ~TngMolecule()
    */
    ~Molecule()
    {
        status = tng_molecule_destroy(traj->traj,mol);
    }
        //! Status
    tng_function_status getStatus()
    { return status; }


    /**
    * @brief Set the name of a molecule.
    * @param new_name is a string containing the wanted name.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setName(const char *new_name)
    {
        return status = tng_molecule_name_set(traj->traj,mol,new_name);
    }

    /**
    * @brief Get the count of a molecule.
    * @param cnt is a pointer to the variable to be populated with the count.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status getCnt(int64_t *cnt)
    {
        return status = tng_molecule_cnt_get(traj->traj,mol,cnt);
    }

    /**
    * @brief Set the count of a molecule.
    * @param cnt is the number of instances of this molecule.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
    * has occurred or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status setCnt(int64_t cnt)
    {
        return status = tng_molecule_cnt_set(traj->traj,mol,cnt);
    }

};

    tng_function_status Trajectory::addMolecule(const char *name, Molecule_t molecule)
{
    return status = tng_molecule_add(traj,name, &molecule->mol);
}

    tng_function_status Trajectory::addMoleculeWithId
                (const char *name,
                 const int64_t id,
                 Molecule_t molecule)
{
    return status = tng_molecule_w_id_add(traj, name, id, &molecule->mol);
}

/**
* @brief Find a molecule.
* @param tng_data is the trajectory data container containing the molecule.
* @param name is a string containing the name of the molecule. If name is empty
* only id will be used for finding the molecule.
* @param id is the id of the molecule to look for. If id is -1 only the name of
* the molecule will be used for finding the molecule.
* @param molecule is a pointer to the molecule if it was found - otherwise 0.
* @return TNG_SUCCESS (0) if the molecule is found or TNG_FAILURE (1) if the
* molecule is not found.
* @details If name is an empty string and id is -1 the first molecule will be
* found.
*/
tng_function_status Trajectory::findMolecule
                (const char *name,
                int64_t id,
                Molecule_t molecule)
{
    return status = tng_molecule_find(traj, name, id,
                            &molecule->mol);
}


class Atom
{
private:
    tng_atom_t atom;
    Trajectory * traj;
    tng_function_status status;
public:
    friend class Residue;
    //constructor
    Atom(Trajectory * trajectory)
    {
        traj = trajectory;
    }
    //deonstructor
    /**
     *@Dose nothing, use ~TngMolecule()
    */
        ~Atom()
    {
        //delete atom;
    }
            //! Status
    tng_function_status getStatus()
    { return status; }
    /**
    * @brief Set the name of an atom.
    * @param new_name is a string containing the wanted name.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setName(const char *new_name)
    {
        return status = tng_atom_name_set(traj->traj, atom , new_name);
    }

    /**
    * @param new_type is a string containing the atom type.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setType(const char *new_type)
    {
        return status = tng_atom_type_set(traj->traj, atom, new_type);
    }
};

class Residue
{
    private:
    tng_residue_t residue;
    Trajectory * traj;
    tng_function_status status;
public:
    friend class Chain;
    //constructor
    Residue(Trajectory  * trajectory)
    {
        traj = trajectory;
    }
    //deonstructor
    /**
     *@Dose nothing, use ~TngMolecule()
    */
        ~Residue()
    {
        //delete residue;
    }
    //! Status
    tng_function_status getStatus()
    { return status; }
    /**
    * @brief Set the name of a residue.
    * @param residue is the residue to rename.
    * @param new_name is a string containing the wanted name.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setName(const char *new_name)
    {
        return status = tng_residue_name_set(traj->traj, residue,new_name);
    }

    /**
    * @brief Add an atom to a residue.
    * @param atom_name is a string containing the name of the atom.
    * @param atom_type is a string containing the atom type of the atom.
    * @param atom is a pointer to the newly created atom.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status addAtom(const char *atom_name,
        const char *atom_type,
        Atom * atom)
    {
        return status = tng_residue_atom_add(traj->traj, residue, atom_name,
                                             atom_type, &atom->atom);
    }


    /**
    * @brief Add an atom with a specific ID to a residue.
    * @param atom_name is a string containing the name of the atom.
    * @param atom_type is a string containing the atom type of the atom.
    * @param id is the ID of the created atom.
    * @param atom is a pointer to the newly created atom.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could
    * not be set properly or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status addAtomWithId
                (const char *atom_name,
                 const char *atom_type,
                 const int64_t id,
                 Atom * atom)
    {
        return status = tng_residue_atom_w_id_add(traj->traj, residue,
                                                  atom_name, atom_type,
                                                  id, &atom->atom);
    }

};

class Chain
{
    private:
    tng_chain_t chain;
    Trajectory * traj;
    tng_function_status status;
public:
    friend class Molecule;
    //constructor
    Chain(Trajectory * trajectory)
    {
        traj = trajectory;
    }
    //deonstructor
    /**
     *@Dose nothing, use ~TngMolecule()
    */
        ~Chain()
    {
        //delete chain;
    }
    //! Status
    tng_function_status getStatus()
    { return status; }
    /**
    * @brief Set the name of a chain.
    * @param new_name is a string containing the wanted name.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status setName(const char *new_name)
    {
        return status  = tng_chain_name_set(traj->traj, chain, new_name);
    }


    /**
    * @brief Find a residue in a chain.
    * @param name is a string containing the name of the residue.
    * @param id is the id of the residue to find. If id == -1 the first residue
    * that matches the specified name will be found.
    * @param residue is a pointer to the residue if it was found - otherwise 0.
    * @return TNG_SUCCESS (0) if the residue is found or TNG_FAILURE (1) if the
    * residue is not found.
    * @details If name is an empty string the first residue will be found.
    */
    tng_function_status findResidue
                (const char *name,
                 int64_t id,
                 Residue *residue)
    {
        return status = tng_chain_residue_find(traj->traj, chain, name,
                                               id, &residue->residue);
    }

    /**
    * @brief Add a residue to a chain.
    * @param name is a string containing the name of the residue.
    * @param residue is a pointer to the newly created residue.
    * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
    * error has occured.
    */
    tng_function_status addResidue(const char *name,
        Residue * residue)
    {
        return status = tng_chain_residue_add(traj->traj, chain,
                                              name, &residue->residue);
    }

    /**
    * @brief Add a residue with a specific ID to a chain.
    * @param name is a string containing the name of the residue.
    * @param id is the ID of the created residue.
    * @param residue is a pointer to the newly created residue.
    * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could
    * not be set properly or TNG_CRITICAL (2) if a major error has occured.
    */
    tng_function_status addResidueWithId
                (const char *name,
                 const int64_t id,
                 Residue * residue)
    {
        return status = tng_chain_residue_w_id_add(traj->traj, chain,
                                                   name, id, &residue->residue);
    }
};

/**
* @brief Add a chain to a molecule.
* @param name is a string containing the name of the chain.
* @param chain s a pointer to the newly created chain.
* @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major
* error has occured.
*/
tng_function_status Molecule::addChain(const char *name, Chain *chain)
{
    return status = tng_molecule_chain_add(traj->traj,mol,name,&chain->chain);
}

/**
* @brief Find a chain in a molecule.
* @param name is a string containing the name of the chain. If name is empty
* only id will be used for finding the chain.
* @param id is the id of the chain to look for. If id is -1 only the name of
* the chain will be used for finding the chain.
* @param chain is a pointer to the chain if it was found - otherwise 0.
* @return TNG_SUCCESS (0) if the chain is found or TNG_FAILURE (1) if the
* chain is not found.
* @details If name is an empty string and id is -1 the first chain will be
* found.
*/
tng_function_status Molecule::findChain
                (const char *name,
                int64_t id,
                Chain *chain)
{
    return status = tng_molecule_chain_find(traj->traj, mol, name, id,
                                            &chain->chain);
}

}
#endif