SDA (SDA flex)  7.2
Simulation of Diffusional Association
Data Types | Functions/Subroutines | Variables
mod_record Module Reference

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

Data Types

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  nodecomplexe
 Define one Node for the ListComplexe
. More...
 
type  record
 Main "base" class
All derived can be created from this one. More...
 
type  trajectory
 Implemented as an array, fixed size and append data only at the end. 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)
 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. 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

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.

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 
)

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 )
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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

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.

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' /)
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