read_record.f90 File Reference

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

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

---

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

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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