check_reaction_pair.f90 File Reference

Functions/Subroutines
subroutine	check_reaction_pair (prot1, prot2, rcriteria, visited_windows, escape, sum_time, first_time, time, dtnow, close, geom)
	Check the reaction criteria from the solute's position for all calculations. Account for any contact number in association rate calculation. Modification of sda6 when checking independent distance : Use same as in bootstrap : record only the minimum window visited for each contact. .
subroutine	check_reaction_pair_sdamm (tab_protein, set1, set2, rcriteria, geom, sum_time, dtnow, array_close, nclose, close)
	Make separate version for testing, maybe merged into the common function later on.

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

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Check if the reaction pairs are satisfied between protein 1 and 2.
Include all cases : docking, association rate and electron transfert

Function/Subroutine Documentation

check_reaction_pair()

subroutine check_reaction_pair	(	type ( protein ), intent(in)	prot1,
		type ( protein ), intent(in)	prot2,
		type ( react_criter )	rcriteria,
		integer, dimension(:)	visited_windows,
		real ( kind=8 ), dimension (:,:)	escape,
		real ( kind=4 ), dimension(:,:)	sum_time,
		real ( kind=4 ), dimension(:,:)	first_time,
		real ( kind=4 )	time,
		real ( kind=4 )	dtnow,
		logical, intent(out)	close,
		type ( geometry ), intent(in)	geom
	)

Check the reaction criteria from the solute's position for all calculations.
Account for any contact number in association rate calculation.
Modification of sda6 when checking independent distance :
Use same as in bootstrap : record only the minimum window visited for each contact.
.

Parameters

prot1	: protein1, fixed in sda
prot2	: protein2, mobil
rcriteria	: instance of a reaction_criteria object, mod_ReactionCriteria include mod_rate_calculation
visited_windows	: array for assocaiton and first passage time
escape	: update escape array for one trajectory
sum_time	: array use for
first_time	: array for first passage time
time	: actual time of one trajectory
dtnow	: timestep ( variable in sda )
close	: bolean true if the distance < rhit

is docking, may add more like electron transfer

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check_reaction_pair_sdamm()

subroutine check_reaction_pair_sdamm	(	type ( array_protein_type )	tab_protein,
		integer	set1,
		integer	set2,
		type ( react_criter )	rcriteria,
		type ( geometry )	geom,
		real ( kind=4 ), dimension(:,:)	sum_time,
		real ( kind=4 )	dtnow,
		integer, dimension (:,:)	array_close,
		integer	nclose,
		logical, intent(out)	close
	)

Make separate version for testing, maybe merged into the common function later on.

similar code than normal version, only recopy part for association rate, sum_time not needed as input Record sum_time for all windows, contacts specified in input Check if close ( criteria nwrec and nnons ), will save complexess and write in record

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