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Diffstat (limited to 'include/tng_io.hpp')
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diff --git a/include/tng_io.hpp b/include/tng_io.hpp deleted file mode 100644 index 12172e5..0000000 --- a/include/tng_io.hpp +++ /dev/null @@ -1,1703 +0,0 @@ -/* This code is part of the tng binary trajectory format. - * - * 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 |