SDA (SDA flex)  7.2
Simulation of Diffusional Association
Functions/Subroutines
read_record.f90 File Reference

tools for reading / modifying records ( complexes file or trajectory ) More...

Functions/Subroutines

program read_record
 Program read_record. More...
 
subroutine convert_tomm (filename, o_record)
 convert_tomm – no longer used. Now new tool convert_traj_SDAMM More...
 
subroutine convert_format (filename, o_record)
 Convert from ascii to binary or inverse. More...
 
subroutine extract_terms (o_record, nb_record)
 Extract and sum up energies. More...
 
subroutine split_conformation (o_record, nb_conf)
 Split multiple conformation complexes. More...
 
subroutine format_cluster (o_record, filename, large_traj_nb)
 Make the format compatible to the cluster program. More...
 
subroutine extract_no_from_file (o_record, filename_no_comp, filename)
 Read a list of complexes belonging to the smae cluster. More...
 
logical function is_in_array (array_no, size_array, count_in)
 Utility function. More...
 
subroutine read_array_no (filename, array_no)
 Utility function. More...
 
subroutine initialize_record_cluster_format (record_comp, o_record, large_traj_nb)
 Initialize destination array for cluster_format could be used in more than 1 function general subroutine, initialize a empty record with default values for cluster format Used internally to read_record. More...
 
subroutine sum_energy_terms (o_record, array_real)
 
subroutine concatenate_traj (o_record, traj_concat_f)
 
subroutine extract_frames (i_record, extr_fr_beg, extr_fr_end, large_traj_nb)
 
subroutine extract_dist (i_record, max_c2c_dist, large_traj_nb)
 
integer function get_index (val, array)
 

Detailed Description

tools for reading / modifying records ( complexes file or trajectory )

Version
{version 7.2.3 (2019)}

Copyright (c) 2009, 2010, 2015, 2016, 2019 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

Please send your contact address to get information on updates and new features to "mcmsoft@h-its.org". Questions will be answered as soon as possible.

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


Function/Subroutine Documentation

◆ concatenate_traj()

subroutine concatenate_traj ( type ( record ), intent(inout)  o_record,
character ( 256 ), dimension (:), intent(in)  traj_concat_f 
)
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◆ convert_format()

subroutine convert_format ( character *64  filename,
type ( record o_record 
)

Convert from ascii to binary or inverse.

The output filename is automaticaly created ( append .bin or .ascii )

Parameters
filename: name of the input file
o_record: instance of record
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◆ convert_tomm()

subroutine convert_tomm ( character *64  filename,
type ( record o_record 
)

convert_tomm – no longer used. Now new tool convert_traj_SDAMM

◆ extract_dist()

subroutine extract_dist ( type( record ), intent(in)  i_record,
real( kind = 8 )  max_c2c_dist,
logical, intent(in)  large_traj_nb 
)
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◆ extract_frames()

subroutine extract_frames ( type ( record ), intent(in)  i_record,
integer, intent(inout)  extr_fr_beg,
integer, intent(inout)  extr_fr_end,
logical, intent(in)  large_traj_nb 
)
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◆ extract_no_from_file()

subroutine extract_no_from_file ( type ( record o_record,
character *64  filename_no_comp,
character *64  filename 
)

Read a list of complexes belonging to the smae cluster.

Used for recursive clustering. The format is very simple : one integer by line ( compatible with cluster_details )

Parameters
o_record: instance of record
filename_no_comp: file name from where to extract the list of number
filename: name of the initial complexe file
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◆ extract_terms()

subroutine extract_terms ( type ( record o_record,
integer  nb_record 
)

Extract and sum up energies.

Used for sdamm, can extract specific terms or the total energy
Note the electrostatic energy is correct

Parameters
o_record: instance of record
nb_record: total number of lines ( the number of steps will be computed inside the function
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◆ format_cluster()

subroutine format_cluster ( type ( record o_record,
character *64  filename,
logical  large_traj_nb 
)

Make the format compatible to the cluster program.

Simply delete additional data ( nprotein, nconf ) data will be lost and 0 to the missing data cannot fully follow the orignal version, but can limit changes 2 integer : ntraj, nstep, 9 coordinates, fixe the rest at : total_energy, ep, ed, hd, lj, occu, average, std_dev general function, copy o_record parameters, modify accordingly to the out

Parameters
o_record: instance of record
filename: input file name
large_traj_nb: bool, indicates if the integer field should be printed larger (in case of large step number)
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◆ get_index()

integer function get_index ( integer  val,
integer, dimension(:)  array 
)

◆ initialize_record_cluster_format()

subroutine initialize_record_cluster_format ( type ( record ), target  record_comp,
type ( record o_record,
logical, intent(in)  large_traj_nb 
)

Initialize destination array for cluster_format could be used in more than 1 function general subroutine, initialize a empty record with default values for cluster format Used internally to read_record.

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◆ is_in_array()

logical function is_in_array ( integer, dimension( size_array ), intent(in)  array_no,
integer, intent(in)  size_array,
integer, intent(in)  count_in 
)

Utility function.

Parameters
array_no: input array
size_array: size of input array
count_in: value to check if present in array
Returns
b_in : boolean true or false

◆ read_array_no()

subroutine read_array_no ( character *64  filename,
integer, dimension(:), allocatable  array_no 
)

Utility function.

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◆ split_conformation()

subroutine split_conformation ( type ( record o_record,
integer  nb_conf 
)

Split multiple conformation complexes.

Always complex by default, should not be too much work for traj, but why to do it ??
Will create nb_conf output files

Parameters
o_record: instance of record
nb_conf: the total number of conformations
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◆ sum_energy_terms()

subroutine sum_energy_terms ( type ( record ), target  o_record,
real ( kind=8 ), dimension (:)  array_real 
)
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