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SDA (SDA flex)
7.2
Simulation of Diffusional Association
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SDA (SDA flex)
7.2
Simulation of Diffusional Association
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Data Types | |
| type | mod_record::nodecomplexe |
| Define one Node for the ListComplexe . More... | |
| type | mod_record::listcomplexe |
| Complexes implemented as a list, fast insertion and deletion To define a list, we use type NodeComplexe which contains one object Can extend the description here. More... | |
| type | mod_record::trajectory |
| Implemented as an array, fixed size and append data only at the end. More... | |
| type | mod_record::record |
| Main "base" class All derived can be created from this one. More... | |
Modules | |
| module | mod_record |
| MODULE mod_record Define type record and subtypes Trajectory and ListComplexe. | |
Functions/Subroutines | |
| subroutine, public | mod_record::new_record (this, type_record_string, type_calc, nb_max_complexe, filename_out, io_compl, opt_sum, box_info, ntraj_rec, freq_print, rmsd_min, one_run, one_conf, format_ascii, nb_types) |
| for creation, copy and deletion More... | |
| subroutine, public | mod_record::init_record (this, opt_iocmx) |
| A simpler initialization, used when reading an existing file nullify the pointers mainly new add opt_iocmx if want to force. More... | |
| subroutine, public | mod_record::initialize_record (this, tab_prot, opt_read, opt_nb_protein, opt_large_traj) |
| Finalize the creation of a record. Setup the bits for variable fields, assign tab_prot and writes the header, except if opt_read is true. This function has been improved and allocate basic trajectory / list_complexe automatically if not done before Usefull for tools, shoud make tab_prot an option also ( want to use easy construction without tab_prot ) More... | |
| subroutine, public | mod_record::delete_record (this, opt_donot_check_array) |
| Delete record : complexe or trajectory Only nullify the pointer to ptab_protein, do not delete the object. More... | |
| subroutine, public | mod_record::copy_record (this, p_copy, opt_header, opt_newsizemax) |
| Make a copy of a record Note : it is a copy of all data members, the content of the array or list is not copied. Use by tools, and by parallelisation to assign a complexe to each thread test if p_copy is already associated ( tool ), or create one ( OpenMP ) More... | |
| subroutine | mod_record::extract_version_number (version_str, int_version) |
| Get version from the header string. More... | |
| character *10 function | mod_record::create_version_str (int_version) |
| Create the string for the versino number. More... | |
| subroutine | mod_record::set_bit_energy (this, position) |
| Set bit of bit_energy or bit_integer to 1 Better for internal usage, or Should consider than the order will not change in futur. More... | |
| subroutine | mod_record::set_bit_integer (this, position) |
| subroutine | mod_record::set_variable_field (this) |
| Set the size of the variable field ( energy and integer ) nb_int and nb_real Convenient function to call set_nb_int and set_nb_real at once. Need the bits to be set correclty before the call Adviced to use this function from sda and external ( tools ). . More... | |
| subroutine | mod_record::set_nb_int (this) |
| For internal use. Call set_variable_field adviced. More... | |
| subroutine | mod_record::set_nb_real (this) |
| For internal use. Call set_variable_field adviced. More... | |
| subroutine | mod_record::return_compatible_array_wrap (this, array_int, array_real, array_other, opt_p_onecomplexe) |
| Function wrapper to mod_onecomplexe::return_compatible_array. More... | |
| subroutine, public | mod_record::set_onecomplexe_wrap (this, position, box, orient_x, orient_y, array_int_compl, array_real_compl, other_real, opt_p_onecomplexe) |
| Function wrapper to mod_onecomplexe::set_onecomplexe. More... | |
| integer function | mod_record::get_max_bit_energy (this) |
| Return the maximum indice used for energy. used to set size array_energy of sda_2proteins correctly. Order of array_energy is fixed. More... | |
| integer function | mod_record::get_nbterms_energy_compatible (this, opt_force_split) |
| Get the minimum size of the array to contain the energy terms. More... | |
| integer function, public | mod_record::get_nbterms_integer_compatible (this) |
| Similar for integer terms. . More... | |
| subroutine, public | mod_record::reset_position (this, opt_status) |
| Reset the current pointer of trajectory or complexe to the first element Kind of rewind. More... | |
| subroutine, public | mod_record::getnext (this, status, opt_step, opt_p_onecomplexe) |
| Update the current pointers to the next position. Update the current node p_current and and the pointer on a one_complexe to the next element of the list or array. Usefull for traversing complexe or trajectory records. More... | |
| subroutine, public | mod_record::compute_all_occurencies (this, total_occur) |
| Compute the sum of all occurencies in the complex file Used mainly by sda_2proteins and sda_koff. If trajectory return the size of the array. Occurrencies are always stored at the first index of other_real_ocompl. More... | |
| subroutine | mod_record::write_header_record (this) |
| Function to write only the header to the output file Called by write_record. More... | |
| subroutine | mod_record::make_format_header_ascii (this, to_write, opt_version) |
| Make the format string for the header, for reading and writing the header. More... | |
| subroutine | mod_record::make_header_ascii (this) |
| subroutine | mod_record::make_header_energy_ascii (this, if_var) |
| header with variance, used by tools More... | |
| subroutine | mod_record::make_header_int_pairs_ascii (this, if_var) |
| ?? More... | |
| subroutine | mod_record::make_format_string_ascii (this) |
| Make format for all one_complexe instances, for read and write. Common to trajectory and complexes. For internal use normally. to check if used correctly, should be called only once ! here works for read and write. More... | |
| subroutine | mod_record::write_header_ascii (this) |
| Write header in ascii format. More... | |
| subroutine | mod_record::write_header_bin (this) |
| Write header in binary format, always print cm. More... | |
| subroutine, public | mod_record::read_header_record (this, filename, opt_cm, opt_nb_record, opt_summary) |
| Read the header of the record, call appropriate ascii or binary sub-functions Setup internal variables with inforamtion from the header. Adviced to use this function directly. . More... | |
| subroutine | mod_record::read_header_binary (this, type_calc, int_type_record, nb_prot, nb_type, bit_integer, bit_real, nb_other_real, opt_sum, box_info, cm, int_version) |
| Internal use. . More... | |
| subroutine | mod_record::read_header_ascii (this, type_calc, int_type_record, nb_prot, nb_type, bit_integer, bit_real, nb_other_real, opt_sum, box_info, cm, int_version) |
| Internal use. . More... | |
| subroutine, public | mod_record::add_record (this, array_prot, ntraj, nstep, array_energy, time, opt_nconf) |
| Add a new entry into the record Creates a new one_complexe if needed ( in case of complex ) This function is not thread-safe, critical sections are needed. More... | |
| integer function | mod_record::get_indice_ntraj (this) |
| Function to get the indice of the trajectory number. . More... | |
| integer function | mod_record::get_indice_nconf (this) |
| Same for conformation number. More... | |
| subroutine | mod_record::print_bits (this, opt_for_choice) |
| Print info about bits. More... | |
| subroutine | mod_record::print_record (this, opt_recompute_dispersion) |
| Print infos about the record. for complexes can ask to recompute the dispersion when printing. More... | |
| subroutine, public | mod_record::write_record (this, opt_recompute_dispersion) |
| Main function to write the record. Make internal call to write header. . More... | |
| subroutine, public | mod_record::read_file_record (this, opt_rebuild_sum_square) |
| Read the record and fill the array or list with the data. More... | |
| subroutine | mod_record::count_records (this, nb_line) |
| Function to count the number of lines. Tricky for binary : need to read data without saving, read in temporary variables . More... | |
| subroutine | mod_record::test_binary (this, filename, version) |
| Test if a file is in binary or ascii format. Called internally test version not used yet \TODO NJB: Make check for ascii/binary more robust. See check used for grid files. More... | |
| subroutine | mod_record::new_trajectory (this, nb_max_complexe) |
| Allocate a trajectory. More... | |
| subroutine | mod_record::initialize_trajectory (this, basecl, opt_large_traj) |
| Finalize the creation of a trajectory. More... | |
| subroutine | mod_record::delete_trajectory (this, basecl, donot_check_array) |
| Delete trajectory. More... | |
| subroutine | mod_record::write_array (this, basecl, opt_last_conf) |
| Write trajectory files. . More... | |
| subroutine | mod_record::write_part_array (this, basecl, first, last) |
| this is the real writing to disk part other More... | |
| subroutine | mod_record::read_string_trajectory (this, basecl, io_err) |
| subroutine | mod_record::print_array (this, basecl) |
| subroutine | mod_record::new_listcomplexe (this, rmsd_min, one_run, one_conf) |
| Allocate the ListComplexe. More... | |
| subroutine | mod_record::delete_listcomplexe (this, opt_clean) |
| Delete the ListComplex. More... | |
| subroutine | mod_record::merge_complexe (this, p_copy) |
| Merge 2 records into 1 unique Implemented only for "ListComplexe" ( DO NOT USE with trajectory ! ) More... | |
| subroutine | mod_record::delete_last_data (this, status) |
| Delete the last data of the list. More... | |
| subroutine | mod_record::fill_listcomplexe (this, basecl, position, orient_x, orient_y, array_energy, array_integer, dist_max, opt_other_real) |
| Create and insert a new one_complexe into the list Normally called by add_record, but can be filled manually. More... | |
| subroutine | mod_record::read_string_complexe (this, basecl, rebuild_sum_square, io_err) |
| Read a binary or ascii line from a complexe file. More... | |
| subroutine | mod_record::insert_new_node (this, pnew_onecomplexe) |
| Allocate and insert a new NodeComplexe always BEFORE this one. More... | |
| subroutine | mod_record::insert_node (this, pnew_node) |
| Insert an existing node before this one. More... | |
| subroutine | mod_record::delete_onecomplexe_fromlist (this) |
| Delete one_complexe from the list. More... | |
| subroutine | mod_record::write_listcomplexe (this, basecl, recompute_dispersion) |
| Write the entire list of complexes to the disk. More... | |
| subroutine | mod_record::print_listcomplexe (this, recompute_dispersion) |
| Only for test keep as example of recursive function for dealing with a list. More... | |
| recursive integer function | mod_record::print_node_list (this, recompute_dispersion) |
| Only for test. More... | |
| subroutine | mod_record::rms_complexe (rmsd2, dist_max, r1, y11, y12, r2, y21, y22) |
| Compute an approximation of the root mean square difference between 2 complexes. If rmsd2 < "rmsd_min", the complexe with the minimum energy will conserved. The other deleted Only an approximation for rigid body protein, we use only the orientation axis for the computation Typical values should be rmsd_min <= 2 when a large number of binding sites want to be recorded and <= 1 for more accuracy close to a binding site . More... | |
Variables | |
| integer, parameter | mod_record::last_version_rec = 2 |
| Versioning. More... | |
| integer, parameter | mod_record::intern = 0 |
| enumeration for the state of the node More... | |
| integer, parameter | mod_record::first = 1 |
| integer, parameter | mod_record::last = 2 |
| integer, parameter | mod_record::trajectory_enum =1 |
| enumeration for type_record More... | |
| integer, parameter | mod_record::complexe_enum =2 |
| integer, parameter | mod_record::off_record = 3 |
| character(13), dimension(8) | mod_record::ener_colnames = (/ character(13):: 'TotEn', 'El', 'ED', 'HD', 'rLJ', 'LJ', 'ImgChg', 'MetDes' /) |
| names of the energy terms for the output More... | |
| character(13), dimension(8) | mod_record::var_colnames = (/ character(13):: 'varTotEn', 'varEl', 'varED', 'varHD', 'varRLJ', 'varLJ', 'varImgChg', 'varMetDes' /) |
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References: see also http://mcm.h-its.org/sda7/do:c/doc_sda7/references.html:
Brownian dynamics simulation of protein-protein diffusional encounter. (1998) Methods, 14, 329-341.
SDA 7: A modular and parallel implementation of the simulation of diffusional association software. Journal of computational chemistry 36.21 (2015): 1631-1645.
Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, X. Yu, M. Ozboyaci, M. Reinhardt, P. Friedrich, R.R.Gabdoulline, S.Richter and R.C.Wade
Module for reading and writing trajectories and complexes files
most general type is record, subtypes are complex and trajectory
1.9.1
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