SDA  7.1
Simulation of Diffusional Association
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Functions/Subroutines
check_reaction_pair.f90 File Reference

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

Functions/Subroutines

subroutine check_reaction_pair (prot1, prot2, rcriteria, visited_windows, escape, sum_time, first_time, time, dtnow, close)
 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.
. More...
 
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. More...
 

Detailed Description

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

Version
{version 7.1 (2015)}

Copyright (c) 2009, 2010, 2015 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) formerly EML Research gGmbH (EML-R ) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

Copyright (c) 2000, 2003 European Molecular Biology Laboratory Meyerhofstr. 1, Postfach 10.2209 D-69012, 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/doc/doc_sda7/references.html):

Brownian dynamics simulation of protein-protein diffusional encounter.

(1998) Methods, 14, 329-341.

Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, R.R.Gabdoulline, M. Ozboyaci, S.Richter and R.C.Wade


Function/Subroutine Documentation

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 
)

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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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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