MODULE mod_record
Define type record and subtypes Trajectory and ListComplexe. More...

Data Types
type	nodecomplexe
	Define one Node for the ListComplexe . More...

type	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	trajectory
	Implemented as an array, fixed size and append data only at the end. More...

type	record
	Main "base" class All derived can be created from this one. More...

Functions/Subroutines
subroutine, public	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	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	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	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	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	extract_version_number (version_str, int_version)
	Get version from the header string. More...

character *10 function	create_version_str (int_version)
	Create the string for the versino number. More...

subroutine	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	set_bit_integer (this, position)

subroutine	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	set_nb_int (this)
	For internal use. Call set_variable_field adviced. More...

subroutine	set_nb_real (this)
	For internal use. Call set_variable_field adviced. More...

subroutine	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	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	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	get_nbterms_energy_compatible (this, opt_force_split)
	Get the minimum size of the array to contain the energy terms. More...

integer function, public	get_nbterms_integer_compatible (this)
	Similar for integer terms. . More...

subroutine, public	reset_position (this, opt_status)
	Reset the current pointer of trajectory or complexe to the first element Kind of rewind. More...

subroutine, public	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	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	write_header_record (this)
	Function to write only the header to the output file Called by write_record. More...

subroutine	make_format_header_ascii (this, to_write, opt_version)
	Make the format string for the header, for reading and writing the header. More...

subroutine	make_header_ascii (this)

subroutine	make_header_energy_ascii (this, if_var)
	header with variance, used by tools More...

subroutine	make_header_int_pairs_ascii (this, if_var)
	?? More...

subroutine	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	write_header_ascii (this)
	Write header in ascii format. More...

subroutine	write_header_bin (this)
	Write header in binary format, always print cm. More...

subroutine, public	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	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	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	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	get_indice_ntraj (this)
	Function to get the indice of the trajectory number. . More...

integer function	get_indice_nconf (this)
	Same for conformation number. More...

subroutine	print_bits (this, opt_for_choice)
	Print info about bits. More...

subroutine	print_record (this, opt_recompute_dispersion)
	Print infos about the record. for complexes can ask to recompute the dispersion when printing. More...

subroutine, public	write_record (this, opt_recompute_dispersion)
	Main function to write the record. Make internal call to write header. . More...

subroutine, public	read_file_record (this, opt_rebuild_sum_square)
	Read the record and fill the array or list with the data. More...

subroutine	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	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	new_trajectory (this, nb_max_complexe)
	Allocate a trajectory. More...

subroutine	initialize_trajectory (this, basecl, opt_large_traj)
	Finalize the creation of a trajectory. More...

subroutine	delete_trajectory (this, basecl, donot_check_array)
	Delete trajectory. More...

subroutine	write_array (this, basecl, opt_last_conf)
	Write trajectory files. . More...

subroutine	write_part_array (this, basecl, first, last)
	this is the real writing to disk part other More...

subroutine	read_string_trajectory (this, basecl, io_err)

subroutine	print_array (this, basecl)

subroutine	new_listcomplexe (this, rmsd_min, one_run, one_conf)
	Allocate the ListComplexe. More...

subroutine	delete_listcomplexe (this, opt_clean)
	Delete the ListComplex. More...

subroutine	merge_complexe (this, p_copy)
	Merge 2 records into 1 unique Implemented only for "ListComplexe" ( DO NOT USE with trajectory ! ) More...

subroutine	delete_last_data (this, status)
	Delete the last data of the list. More...

subroutine	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	read_string_complexe (this, basecl, rebuild_sum_square, io_err)
	Read a binary or ascii line from a complexe file. More...

subroutine	insert_new_node (this, pnew_onecomplexe)
	Allocate and insert a new NodeComplexe always BEFORE this one. More...

subroutine	insert_node (this, pnew_node)
	Insert an existing node before this one. More...

subroutine	delete_onecomplexe_fromlist (this)
	Delete one_complexe from the list. More...

subroutine	write_listcomplexe (this, basecl, recompute_dispersion)
	Write the entire list of complexes to the disk. More...

subroutine	print_listcomplexe (this, recompute_dispersion)
	Only for test keep as example of recursive function for dealing with a list. More...

recursive integer function	print_node_list (this, recompute_dispersion)
	Only for test. More...

subroutine	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	last_version_rec = 2
	Versioning. More...

integer, parameter	intern = 0
	enumeration for the state of the node More...

integer, parameter	first = 1

integer, parameter	last = 2

integer, parameter	trajectory_enum =1
	enumeration for type_record More...

integer, parameter	complexe_enum =2

integer, parameter	off_record = 3

character(13), dimension(8)	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)	var_colnames = (/ character(13):: 'varTotEn', 'varEl', 'varED', 'varHD', 'varRLJ', 'varLJ', 'varImgChg', 'varMetDes' /)

Detailed Description

MODULE mod_record
Define type record and subtypes Trajectory and ListComplexe.

Used for dealing with trajectories and complexes
They both store mod_onecomplexe objects, and then share the same format and rules for output
Trajectory is a fixed array of one_complexe, the size can be fixed for output optimisation
ListComplexe is a list implemenation of one_necomplexe ( fast insertion and deletion whatever the position ), but has a max_nb_complexe to limit the size

All records can read/writen in ascii or binary format
Output are variable:
Maximum 4 integer : ntraj(nrun), nstep, nprotein, nconf
Maximum 20 real for energy: total energy, electrostatic,...
But the content can be modified at run-time ( do not store or print what is not used )

Function/Subroutine Documentation

◆ add_record()

subroutine, public mod_record::add_record	(	type ( record )	this,
		type ( protein ), dimension ( : ), intent(in)	array_prot,
		integer, intent(in)	ntraj,
		integer, intent(in)	nstep,
		real ( kind=8 ), dimension ( :, : ), intent(in)	array_energy,
		real ( kind=4 ), intent(in)	time,
		integer, intent(in), optional	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.

Parameters

this	: an instance of record
array_prot	: an instance of array_protein_type
ntraj	: the current trajectory number
nstep	: the current step number
array_energy	: input array which contains energies terms
time	: the current time
opt_nconf	: optionaly the current conformation

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◆ compute_all_occurencies()

subroutine, public mod_record::compute_all_occurencies	(	type ( record )	this,
		integer, intent(out)	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.

Parameters

this	: an instance of record
total_occur	: sum of occurencies

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◆ copy_record()

subroutine, public mod_record::copy_record	(	type ( record )	this,
		type ( record ), pointer	p_copy,
		logical, optional	opt_header,
		integer, optional	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 )

Parameters

this	: an instance of record
p_copy	: a pointer to the destination record
opt_header	: optional copy the header informations or initialize them
opt_newsizemax	: optional fixe the value of nb_max_complexe of the destination record to opt_newsizemax or copy the value from the source

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◆ count_records()

subroutine mod_record::count_records	(	type ( record )	this,
		integer, intent(out)	nb_line
	)

Function to count the number of lines.
Tricky for binary : need to read data without saving, read in temporary variables
.

Parameters

this	: an instance of record
nb_line	: return the number of lines

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◆ create_version_str()

character*10 function mod_record::create_version_str ( integer, intent(in) int_version )

Create the string for the versino number.

Parameters

int_version : version as integer

Returns: str_version : string with version number, formated for header

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◆ delete_last_data()

subroutine mod_record::delete_last_data	(	type ( listcomplexe )	this,
		integer, intent(out)	status
	)

Delete the last data of the list.

Used when the size of complexes exceeds the maximum and for deleting all the list

Parameters

this	: an instance of ListComplexe
status	: return 0 if the data have correctly deleted

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◆ delete_listcomplexe()

subroutine mod_record::delete_listcomplexe	(	type ( listcomplexe )	this,
		logical, optional	opt_clean
	)

Delete the ListComplex.

Parameters

this	: an instance of ListComplexe
opt_clean	: optionaly reset member data nb_complexe ?? to check

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◆ delete_onecomplexe_fromlist()

subroutine mod_record::delete_onecomplexe_fromlist ( type ( nodecomplexe ), target this )

Delete one_complexe from the list.

Delete the content ( one_complexe ) and rearrange the pointers of the list
The deallocation of the node itself must be done by an other function ( cannot delete itself )

Parameters

this	: an instance of NodeComplexe

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◆ delete_record()

subroutine, public mod_record::delete_record	(	type ( record )	this,
		logical, optional	opt_donot_check_array
	)

Delete record : complexe or trajectory
Only nullify the pointer to ptab_protein, do not delete the object.

Parameters

this	: an instance of record
opt_donot_check_array	: by default write on disk the last configurations in trajectory before deleting it. Set to true to deactivate ( tool or restart )

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◆ delete_trajectory()

subroutine mod_record::delete_trajectory	(	type ( trajectory )	this,
		type ( record )	basecl,
		logical	donot_check_array
	)

Delete trajectory.

For some tools we want to desable automatic writing of array when finishing the program

Parameters

this	: an instance of Trajectory
basecl	: an instance of record
donot_check_array	: bool if true do not write the last in the array into the disk

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◆ extract_version_number()

subroutine mod_record::extract_version_number	(	character, dimension(*), intent(in)	version_str,
		integer	int_version
	)

Get version from the header string.

Parameters

version_str	: string to parse
int_version	: the version number as integer

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◆ fill_listcomplexe()

subroutine mod_record::fill_listcomplexe	(	type ( listcomplexe )	this,
		type ( record )	basecl,
		real ( kind=8 ), dimension ( 3 ), intent(in)	position,
		real ( kind=8 ), dimension ( 3 ), intent(in)	orient_x,
		real ( kind=8 ), dimension ( 3 ), intent(in)	orient_y,
		real ( kind=8 ), dimension ( : ), intent(in)	array_energy,
		integer, dimension ( 4 ), intent(in)	array_integer,
		real ( kind=8 ), intent(in)	dist_max,
		real ( kind=8 ), dimension ( : ), optional	opt_other_real
	)

Create and insert a new one_complexe into the list
Normally called by add_record, but can be filled manually.

The instance one_complexe is inserted according to its total energy
A check is performed if a previous one is closer than rmsd_min. See doc for the complete story

Todo:: Check the logic, tested but could make simpler ( maybe faster )

Parameters

this	: an instance of ListComplexe
basecl	: an instance of record
position	: position of the solute
orient_x,orient_y	: orientation of the axis
array_energy	: store energy terms in the expected order
array_integer	: correspond to ntraj, nstep,...
dist_max	: maximal radius of the protein 2, sogrid % distance_max
opt_other_real	: optionaly the array other_real_ocompl, default (0.,0.,0.)

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◆ get_indice_nconf()

integer function mod_record::get_indice_nconf ( type ( record ) this )

Same for conformation number.

Parameters

this	: an instance of record

Returns: indice : indice where to get the conformation number from onecomplexe::array_int, return 0 if not present

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◆ get_indice_ntraj()

integer function mod_record::get_indice_ntraj ( type ( record ) this )

Function to get the indice of the trajectory number.
.

Function to use in collaboration with return_compatible_array, return_array_int and return_array_real Safer to use than directly access the data, easier to maintain when there will be modification.

Parameters

this	: an instance of record

Returns: indice : indice where to get the trajectory number from onecomplexe::array_int, return 0 if not present

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◆ get_max_bit_energy()

integer function mod_record::get_max_bit_energy ( type ( record ) this )

Return the maximum indice used for energy.
used to set size array_energy of sda_2proteins correctly. Order of array_energy is fixed.

Todo:: combine with get_nbterms_X, easier to use.

Parameters

this	: an instance of record

Returns: nb_bits : integer, return the maximum used indice

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◆ get_nbterms_energy_compatible()

integer function mod_record::get_nbterms_energy_compatible	(	type ( record )	this,
		logical, optional	opt_force_split
	)

Get the minimum size of the array to contain the energy terms.

Normally for reading, but if force_split get the minimum size of array_1d ( sda_2proteins ) or for sdamm if opt_sum of record is one

Parameters

this	: an instance of record
opt_force_split	: force the size to take account than the energy terms are splitted

Returns: nb_terms : size

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◆ get_nbterms_integer_compatible()

integer function, public mod_record::get_nbterms_integer_compatible ( type ( record ) this )

Similar for integer terms.
.

Parameters

this	: an instance of record

Returns: nb_terms : size

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◆ getnext()

subroutine, public mod_record::getnext	(	type ( record )	this,
		integer	status,
		integer, intent(in), optional	opt_step,
		type ( one_complexe ), optional, pointer	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.

Parameters

this	: an instance of record
status	: return 1 if no data are present, otherwise 0
opt_step	: optional, specify how many complexes should the jump omit (default: 1)
opt_p_onecomplexe	: optional, will point to the same than adress than p_onecompl, used for shortcut to p_onecompl

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◆ init_record()

subroutine, public mod_record::init_record	(	type (record )	this,
		integer, optional	opt_iocmx
	)

A simpler initialization, used when reading an existing file nullify the pointers mainly new add opt_iocmx if want to force.

Parameters

this	: an instance of record
opt_iocmx	: optional, gives a file descriptor, usefull if more than 1 record opened at the same time

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◆ initialize_record()

subroutine, public mod_record::initialize_record	(	type (record )	this,
		type ( array_protein_type ), optional, target	tab_prot,
		logical, intent(in), optional	opt_read,
		integer, intent(in), optional	opt_nb_protein,
		logical, intent(in), optional	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 )

the bit_integer and bit_energy should have been set before the call
need to be separate, because need to set value of bits before

Parameters

this	: an instance of record
tab_prot	: optional, an instance of array_protein_type
opt_read	: optional, open the record for reading, will not write the header file
opt_nb_protein	: optional, indicates the number of the number of proteins, by default use the size of array_protein
opt_large_traj	: optional, boolean: if the trajectory file is large, it will be read one by one, instead of allocating the entire trajectory at once

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◆ initialize_trajectory()

subroutine mod_record::initialize_trajectory	(	type ( trajectory )	this,
		type ( record )	basecl,
		logical, intent(in), optional	opt_large_traj
	)

Finalize the creation of a trajectory.

Called by initialize_record
To call after initialisation of bit energy and bit_integer of type record
by default use nb_max_complexe of basecl, could add optional size ( for large file )

Parameters

this	: an instance of Trajectory
basecl	: an instance of record
opt_large_traj	: optional, boolean: if the trajectory is large, it will be read one by one

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◆ insert_new_node()

subroutine mod_record::insert_new_node	(	type ( nodecomplexe ), target	this,
		type ( one_complexe ), pointer	pnew_onecomplexe
	)

Allocate and insert a new NodeComplexe always BEFORE this one.

Associate the pointer to the one_complexe to the new created node

Parameters

this	: an instance of NodeComplexe
pnew_onecomplexe	: pointer to a rencently created one_complexe

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◆ insert_node()

subroutine mod_record::insert_node	(	type ( nodecomplexe ), target	this,
		type ( nodecomplexe ), pointer	pnew_node
	)

Insert an existing node before this one.

Parameters

this	: an instance of NodeComplexe
pnew_node	: pointer one_complexe

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◆ make_format_header_ascii()

subroutine mod_record::make_format_header_ascii	(	type ( record )	this,
		logical	to_write,
		integer, optional	opt_version
	)

Make the format string for the header, for reading and writing the header.

Parameters

this	: an instance of record
to_write	: if true make the format for writing, otherwise for reading
opt_version	: optional, force the version number

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◆ make_format_string_ascii()

subroutine mod_record::make_format_string_ascii ( type ( record ) 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.

Parameters

this	: an instance of record

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◆ make_header_ascii()

subroutine mod_record::make_header_ascii ( type ( record ) this )

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◆ make_header_energy_ascii()

subroutine mod_record::make_header_energy_ascii	(	type ( record )	this,
		logical	if_var
	)

header with variance, used by tools

Parameters

this	: an instance of record
if_var	: true will add column for variance of the energy terms

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◆ make_header_int_pairs_ascii()

subroutine mod_record::make_header_int_pairs_ascii	(	type ( record ), intent(inout)	this,
		logical, intent(in)	if_var
	)

??

Parameters

this	: an instance of record
if_var	: true will add column for variance of the energy terms

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◆ merge_complexe()

subroutine mod_record::merge_complexe	(	type ( record )	this,
		type ( record )	p_copy
	)

Merge 2 records into 1 unique
Implemented only for "ListComplexe" ( DO NOT USE with trajectory ! )

Respect the energetic order when doing the merging
The total size will not exceed the size of this % nb_max_complexe, the other data will be deleted
Used with OpenMP for merging the complexes of different threads

Parameters

this	: an instance of record
p_copy	: pointer to the record to be merged into this

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◆ new_listcomplexe()

subroutine mod_record::new_listcomplexe	(	type ( listcomplexe )	this,
		real ( kind=8 )	rmsd_min,
		logical	one_run,
		logical	one_conf
	)

Allocate the ListComplexe.

Create the nodes necessary for the ListComplexe management

Parameters

this	: an instance of "ListComplexe"
rmsd_min	: parameter for the recording of complexes
one_run	: parameter for the recording of complexes
one_conf	: parameter for the recording of complexes

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◆ new_record()

subroutine, public mod_record::new_record	(	type ( record )	this,
		character, dimension(*)	type_record_string,
		type ( type_calculation )	type_calc,
		integer	nb_max_complexe,
		character ( 128 )	filename_out,
		integer	io_compl,
		logical	opt_sum,
		logical	box_info,
		integer	ntraj_rec,
		integer	freq_print,
		real ( kind=8 )	rmsd_min,
		logical	one_run,
		logical	one_conf,
		logical	format_ascii,
		integer, optional	nb_types
	)

for creation, copy and deletion

Allocate a object record : complexe or trajectory
allocate a list_complexe or an array for trajectory and open the output file with the correct format
The obect is not fully ready to use at this stage
It needs correct "bit_integer" and "bit_energy" and a call to initialize_trajectory

Parameters

this	: an instance of record
type_record_string	: "complexe" or "trajectory"
type_calc	: instance of type_calculation
nb_max_complexe	: fixe the size of array for trajectory, or the maximum size of a list
filename_out	: filename of output
io_compl	: file descriptor
opt_sum	: bool indicates if the energy terms should be added ( ep1_2+ep2_1 ) or separated in the output. Internally always splitted, influences only the output
box_info	: bool if box information is present ( used only for sdamm )
ntraj_rec	: the trajectory number to record
freq_print	: the frequence in steps (not in time ) with which the trajectory is written
rmsd_min	: value used for complexes output
one_run	: value used for complexes output
one_conf	: value used for complexes output
format_ascii	: bool, if true ascii output, else bunary output
nb_types	: number of different types of proteins

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◆ new_trajectory()

subroutine mod_record::new_trajectory	(	type ( trajectory )	this,
		integer	nb_max_complexe
	)

Allocate a trajectory.

Allocate the array with instances of empty one_complexe
Need to give nb_max_complexe for allocating the array

Parameters

this	: an instance of "Trajectory"
nb_max_complexe	: size of the array to allocate

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◆ print_array()

subroutine mod_record::print_array	(	type ( trajectory )	this,
		type ( record )	basecl
	)

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◆ print_bits()

subroutine mod_record::print_bits	(	type ( record )	this,
		logical, optional	opt_for_choice
	)

Print info about bits.

Parameters

this	: an instance of record
opt_for_choice	: bool if true less output used in tool when a choice is expected, default false

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◆ print_listcomplexe()

subroutine mod_record::print_listcomplexe	(	type ( listcomplexe )	this,
		logical	recompute_dispersion
	)

Only for test
keep as example of recursive function for dealing with a list.

Function crash if recursivity > 10 000 approx.

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◆ print_node_list()

recursive integer function mod_record::print_node_list	(	type ( nodecomplexe )	this,
		logical	recompute_dispersion
	)

Only for test.

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◆ print_record()

subroutine mod_record::print_record	(	type ( record )	this,
		logical, optional	opt_recompute_dispersion
	)

Print infos about the record.
for complexes can ask to recompute the dispersion when printing.

Parameters

this	: an instance of record
opt_recompute_dispersion	: optionaly recompute the dispersion ( only for complexes ). Default true.

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◆ read_file_record()

subroutine, public mod_record::read_file_record	(	type ( record )	this,
		logical, optional	opt_rebuild_sum_square
	)

Read the record and fill the array or list with the data.

The file is first "rewinded"

Parameters

this	: an instance of record
opt_rebuild_sum_square	: optional, if the square energy must be recomputed (restart complexe)

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◆ read_header_ascii()

subroutine mod_record::read_header_ascii	(	type ( record )	this,
		type ( type_calculation )	type_calc,
		integer	int_type_record,
		integer, intent(inout)	nb_prot,
		integer, intent(inout)	nb_type,
		integer ( kind=2 ), intent(inout)	bit_integer,
		integer ( kind=2 ), intent(inout)	bit_real,
		integer, intent(inout)	nb_other_real,
		logical, intent(out)	opt_sum,
		logical, intent(out)	box_info,
		real ( kind = 8 ), dimension ( 2, 3 )	cm,
		integer	int_version
	)

Internal use.
.

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◆ read_header_binary()

subroutine mod_record::read_header_binary	(	type ( record )	this,
		type ( type_calculation )	type_calc,
		integer	int_type_record,
		integer, intent(inout)	nb_prot,
		integer, intent(inout)	nb_type,
		integer ( kind=2 ), intent(inout)	bit_integer,
		integer ( kind=2 ), intent(inout)	bit_real,
		integer, intent(inout)	nb_other_real,
		logical, intent(out)	opt_sum,
		logical, intent(out)	box_info,
		real ( kind = 8 ), dimension ( 2, 3 )	cm,
		integer	int_version
	)

Internal use.
.

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◆ read_header_record()

subroutine, public mod_record::read_header_record	(	type ( record )	this,
		character(len=*), intent(in)	filename,
		real ( kind = 8 ), dimension ( 2, 3 ), intent(out), optional	opt_cm,
		integer, intent(out), optional	opt_nb_record,
		logical, intent(in), optional	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.
.

Parameters

this	: an instance of record
filename	: file to read
opt_cm	: optionaly read the center of proteins ( only for sda_2proteins ). Safe with sdamm : do nothing
opt_nb_record	: optionaly as input, count the number of lines ( set opt_nb_record for return and nb_max_complexe )
opt_summary	: should summary data be written to output

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◆ read_string_complexe()

subroutine mod_record::read_string_complexe	(	type ( listcomplexe )	this,
		type ( record )	basecl,
		logical	rebuild_sum_square,
		integer	io_err
	)

Read a binary or ascii line from a complexe file.

Create a new one_complexe and insert in the list

Todo:: combine with read_string_trajectory if possible, check why io_err !
Check if line is not empty, and really read some data

Parameters

this	: an instance of "ListComplexe"
basecl	: an instance of record
rebuild_sum_square	: logicalm if the square of energy needs to be recomputed ( complex as restart )
io_err	: used as status ??

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◆ read_string_trajectory()

subroutine mod_record::read_string_trajectory	(	type ( trajectory )	this,
		type ( record )	basecl,
		integer	io_err
	)

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◆ reset_position()

subroutine, public mod_record::reset_position	(	type ( record )	this,
		integer, intent(out), optional	opt_status
	)

Reset the current pointer of trajectory or complexe to the first element
Kind of rewind.

Parameters

this	: an instance of record
opt_status	: optional, return 1 if the list is empty

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◆ return_compatible_array_wrap()

subroutine mod_record::return_compatible_array_wrap	(	type ( record )	this,
		integer, dimension(:)	array_int,
		real( kind=8 ), dimension(:)	array_real,
		real( kind=8 ), dimension(:)	array_other,
		type ( one_complexe ), optional, pointer	opt_p_onecomplexe
	)

Function wrapper to mod_onecomplexe::return_compatible_array.

Easier to use, in combination with getNext(). Most of parameters come from record.
by default use use internal p_onecompl pointer to one_complexe, but can pass an other pointer as an option.

Parameters

this	: an instance of record
array_int,array_real,array_other	: array to fill with data
opt_p_onecomplexe	: optional, use this pointer to retrieve the data

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◆ rms_complexe()

subroutine mod_record::rms_complexe	(	real ( kind=8 ), intent(out)	rmsd2,
		real ( kind=8 ), intent(in)	dist_max,
		real ( kind=8 ), dimension ( 3 )	r1,
		real ( kind=8 ), dimension ( 3 )	y11,
		real ( kind=8 ), dimension ( 3 )	y12,
		real ( kind=8 ), dimension ( 3 )	r2,
		real ( kind=8 ), dimension ( 3 )	y21,
		real ( kind=8 ), dimension ( 3 )	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
.

Parameters

rmsd2	: return mean square difference between 2 complexes
dist_max	: maximal radius of the protein 2, sogrid % distance_max
r1	: position of complex 1
y11,y12	: orientation of complex 1
r2	: position of complex 2
y21,y22	: orientation of complex 2

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◆ set_bit_energy()

subroutine mod_record::set_bit_energy	(	type ( record )	this,
		integer	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.

Parameters

this	: an instance of record
position	: bit position to set {@

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◆ set_bit_integer()

subroutine mod_record::set_bit_integer	(	type ( record )	this,
		integer	position
	)

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◆ set_nb_int()

subroutine mod_record::set_nb_int ( type ( record ) this )

For internal use. Call set_variable_field adviced.

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◆ set_nb_real()

subroutine mod_record::set_nb_real ( type ( record ) this )

For internal use. Call set_variable_field adviced.

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◆ set_onecomplexe_wrap()

subroutine, public mod_record::set_onecomplexe_wrap	(	type ( record )	this,
		real ( kind=8 ), dimension( 3 ), intent(in)	position,
		integer, dimension ( 3 ), intent(in)	box,
		real ( kind=8 ), dimension( 3 ), intent(in)	orient_x,
		real ( kind=8 ), dimension( 3 ), intent(in)	orient_y,
		integer, dimension ( : ), intent(in)	array_int_compl,
		real ( kind=8 ), dimension( : ), intent(in)	array_real_compl,
		real ( kind=8 ), dimension( : ), intent(in)	other_real,
		type ( one_complexe ), optional, pointer	opt_p_onecomplexe
	)

Function wrapper to mod_onecomplexe::set_onecomplexe.

same idea than return_compatible_array, easy to use with getNext() function. for sdamm must be called in a loop, maybe to extend later ( in the wrapper for simplicity ) add optional opt_p_onecomplexe, to set a new onecomplexe before it is inserted inside the record

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◆ set_variable_field()

subroutine mod_record::set_variable_field ( type ( record ) 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 ).
.

Parameters

this	: an instance of record

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◆ test_binary()

subroutine mod_record::test_binary	(	type ( record )	this,
		character(len=*)	filename,
		character*10	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.

Parameters

this	: an instance of record
filename	: name of the file
version	: not used yet

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◆ write_array()

subroutine mod_record::write_array	(	type ( trajectory )	this,
		type ( record )	basecl,
		logical, optional	opt_last_conf
	)

Write trajectory files.
.

Called when the array is full and for writing the restart file ( last conformation ). Size array can be of any size for the trajectory, but for restart need to be larger than nb_proteins.

Parameters

this	: an instance of trajectory
basecl	: an instance of record
opt_last_conf	: optionaly write only the last configuration ( for write_restart )

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◆ write_header_ascii()

subroutine mod_record::write_header_ascii ( type ( record ) this )

Write header in ascii format.

Parameters

this	: an instance of record

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◆ write_header_bin()

subroutine mod_record::write_header_bin ( type ( record ) this )

Write header in binary format, always print cm.

Parameters

this	: an instance of record

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◆ write_header_record()

subroutine mod_record::write_header_record ( type ( record ) this )

Function to write only the header to the output file
Called by write_record.

Parameters

this	: an instance of record

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◆ write_listcomplexe()

subroutine mod_record::write_listcomplexe	(	type ( listcomplexe )	this,
		type ( record )	basecl,
		logical, intent(in)	recompute_dispersion
	)

Write the entire list of complexes to the disk.

Called by write_record Only the sum of the square of the total energy is stored during the computation
The dispersion is computed only before writing to disk

Parameters

this	: an instance of mod_record::listcomplexe "ListComplexe"
basecl	: an instance of record
recompute_dispersion	: bool if true compute the dispersion

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◆ write_part_array()

subroutine mod_record::write_part_array	(	type ( trajectory )	this,
		type ( record )	basecl,
		integer, intent(in)	first,
		integer, intent(in)	last
	)

this is the real writing to disk part other

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◆ write_record()

subroutine, public mod_record::write_record	(	type ( record )	this,
		logical, optional	opt_recompute_dispersion
	)

Main function to write the record.
Make internal call to write header.
.

Parameters

this	: an instance of record
opt_recompute_dispersion	: optionaly recompute the dispersion ( only for complexes ). Default true.

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Variable Documentation

◆ complexe_enum

integer, parameter mod_record::complexe_enum =2

◆ ener_colnames

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

◆ first

integer, parameter mod_record::first = 1

◆ intern

integer, parameter mod_record::intern = 0

enumeration for the state of the node

◆ last

integer, parameter mod_record::last = 2

◆ last_version_rec

integer, parameter mod_record::last_version_rec = 2

Versioning.

◆ off_record

integer, parameter mod_record::off_record = 3

◆ trajectory_enum

integer, parameter mod_record::trajectory_enum =1

enumeration for type_record

◆ var_colnames

character ( 13 ), dimension ( 8 ) mod_record::var_colnames = (/ character(13):: 'varTotEn', 'varEl', 'varED', 'varHD', 'varRLJ', 'varLJ', 'varImgChg', 'varMetDes' /)

Data Types

Functions/Subroutines

Variables

Detailed Description

Function/Subroutine Documentation

◆ add_record()

◆ compute_all_occurencies()

◆ copy_record()

◆ count_records()

◆ create_version_str()

◆ delete_last_data()

◆ delete_listcomplexe()

◆ delete_onecomplexe_fromlist()

◆ delete_record()

◆ delete_trajectory()

◆ extract_version_number()

◆ fill_listcomplexe()

◆ get_indice_nconf()

◆ get_indice_ntraj()

◆ get_max_bit_energy()

◆ get_nbterms_energy_compatible()

◆ get_nbterms_integer_compatible()

◆ getnext()

◆ init_record()

◆ initialize_record()

◆ initialize_trajectory()

◆ insert_new_node()

◆ insert_node()

◆ make_format_header_ascii()

◆ make_format_string_ascii()

◆ make_header_ascii()

◆ make_header_energy_ascii()

◆ make_header_int_pairs_ascii()

◆ merge_complexe()

◆ new_listcomplexe()

◆ new_record()

◆ new_trajectory()

◆ print_array()

◆ print_bits()

◆ print_listcomplexe()

◆ print_node_list()

◆ print_record()

◆ read_file_record()

◆ read_header_ascii()

◆ read_header_binary()

◆ read_header_record()

◆ read_string_complexe()

◆ read_string_trajectory()

◆ reset_position()

◆ return_compatible_array_wrap()

◆ rms_complexe()

◆ set_bit_energy()

◆ set_bit_integer()

◆ set_nb_int()

◆ set_nb_real()

◆ set_onecomplexe_wrap()

◆ set_variable_field()

◆ test_binary()

◆ write_array()

◆ write_header_ascii()

◆ write_header_bin()

◆ write_header_record()

◆ write_listcomplexe()

◆ write_part_array()

◆ write_record()

Variable Documentation

◆ complexe_enum

◆ ener_colnames

◆ first

◆ intern

◆ last

◆ last_version_rec

◆ off_record

◆ trajectory_enum

◆ var_colnames