mod_reactioncriteria Module Reference

Module to define reaction criteria
More informations on the reaction criteria page. More...

Data Types
type	react_criter
	react_criter deals mainly with the reaction criteria positions and distances More...

Functions/Subroutines
subroutine	allocate_react_criter (this, type_reaction_string, filename, et1f, et2f, nnons, nwrec, sdamd)
	Allocate arrays. More...
subroutine	delete_react_criter (this)
	Delete the arrays. More...
subroutine	allocate_rate (this, win0, nwin, dwin, nb_contact, b, c, dm, ibootsp, ifpt, stop_traj, anal_corr, stoke_rad_sum, real_net_charge_product, ionic)
	Initilialize the association_rate pointer. More...
subroutine	read_rxna (this, filename)
	Read the reaction criteria file, usually *.rxna file. More...
subroutine	read_et_rxna (this, et1f, et2f)
	Read reaction criteria for electron transfert calculation. More...
subroutine	make_independent (this, dind)
	Make the list of independent pairs. More...
subroutine	check_add_criteria (this, counter, nb_atom, xv, tmp_rcriter_pos, status_incl)
	Test when reading reaction criteria, called by read_pdb. More...
subroutine	write_to_logfile (this, io_unit)
	Write information to a log file. More...

Variables
integer, parameter	docking = 1
	Enumeration, associated with type_rection. More...
integer, parameter	assoc_rate = 2
integer, parameter	elec_transfer = 3
integer, parameter	all = 4
integer, parameter	off_rc = 5

Detailed Description

Module to define reaction criteria
More informations on the reaction criteria page.

Function/Subroutine Documentation

allocate_rate()

subroutine mod_reactioncriteria::allocate_rate	(	type ( react_criter )	this,
		real ( kind=4 ), intent(in)	win0,
		integer, intent(in)	nwin,
		real ( kind=4 ), intent(in)	dwin,
		integer, intent(in)	nb_contact,
		real ( kind=4 ), intent(in)	b,
		real ( kind=4 ), intent(in)	c,
		real ( kind=8 ), intent(in)	dm,
		logical	ibootsp,
		logical	ifpt,
		logical	stop_traj,
		logical	anal_corr,
		real ( kind=8 ), intent(in), optional	stoke_rad_sum,
		real ( kind=8 ), intent(in), optional	real_net_charge_product,
		real ( kind=4 ), intent(in), optional	ionic
	)

Initilialize the association_rate pointer.

Create the object and initiliaze the internal pointer p_assoc_rate

Parameters

this	: instance of react_criter
win0,nwin,dwin	: first_window, number and width of windows
nb_contact	: the maximum number of contact to record
b,c	: b and c surface
dm	: translational diffusion coefficient of the solute 2
ibootsp,ifpt	: if bootstrap for association rate or first tpassage time must be applied
stop_traj	: should current traj stop when most strict reaction criteria met

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allocate_react_criter()

subroutine mod_reactioncriteria::allocate_react_criter	(	type ( react_criter )	this,
		character*128, intent(in)	type_reaction_string,
		character*128, intent(in)	filename,
		character*128, intent(in)	et1f,
		character*128, intent(in)	et2f,
		integer, intent(in)	nnons,
		integer, intent(in)	nwrec,
		integer, intent(in)	sdamd
	)

Allocate arrays.

It sets up parameters and calls the function read_rxna or read_et_rxna for reading the reaction criteria The association_rate pointer may be then initilized with allocate_rate

Parameters

this	: instance of react_criter
type_reaction_string	: "docking" / "asociation" / "electron_transfert" / "all" / "off_rc"
filename	: name of the file with the reaction criteria
et1f,et2f	: in case of electron transfert the reaction criteria are defined in theses files
nnons	: minimum number of nonspecific criteria to valid for accepting complexes
nwrec	: in case of association rate, the specific window where reaction criteria are checked

Todo:

check initialization of dind

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check_add_criteria()

subroutine mod_reactioncriteria::check_add_criteria	(	type ( react_criter )	this,
		integer	counter,
		integer, intent(in)	nb_atom,
		real ( kind=8 ), dimension( 3 ), intent(in)	xv,
		real ( kind=8 ), dimension(:,:), pointer	tmp_rcriter_pos,
		logical, intent(out)	status_incl
	)

Test when reading reaction criteria, called by read_pdb.

Used when one solute is flexible, search for the correct atom number
Check than the atom number of this particular conformation corresponds to the atom number of the initial reaction criteria

Parameters

this	: instance of react_criter
counter	: identifier of the solute
nb_atom	: atom number
xv	: position of the atom
tmp_rcriter_pos	: return the position of the atom corresponding to the atom number
status_incl	: return true if the atom has been included in the array of reaction criteria

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delete_react_criter()

subroutine mod_reactioncriteria::delete_react_criter

(

type ( react_criter )

this

)

Delete the arrays.

Delete all allocated arrays and the association_rate object

Parameters

this	: instance of react_criter

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make_independent()

subroutine mod_reactioncriteria::make_independent	(	type ( react_criter )	this,
		real (kind=4), intent(in)	dind
	)

Make the list of independent pairs.

Todo:

Need to think about independent pairs in case of flexible/multi-proteins

Independent pairs apply only to associaiton rates
independence is check only for each pos_atom 1 and 2 separately but stored in matrix ( 1, 2 ) => no problem of center of mass

Parameters

this	: instance of react_criter
dind	: distance to use for indepence ( in Angstrom ), Default 6 A

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read_et_rxna()

subroutine mod_reactioncriteria::read_et_rxna	(	type ( react_criter )	this,
		character*128, intent(in)	et1f,
		character*128, intent(in)	et2f
	)

Read reaction criteria for electron transfert calculation.

Called by allocate_react_criter

Parameters

this	: instance of react_criter
et1f,et2f	: file names where the reaction criteria are defined

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read_rxna()

subroutine mod_reactioncriteria::read_rxna	(	type ( react_criter )	this,
		character*128, intent(in)	filename
	)

Read the reaction criteria file, usually *.rxna file.

Called by allocate_react_criter
Do not check for independence, default ind_pairs is false , done optionaly by make_independent
Should be called the first time, if nb criteria are identical use update rxna
Data stored in arrays drc and drc2 in the order 1,nspec and nspec+1, nspec+1+aspec,..nspec+aspec+1+nnonspec

Parameters

this	: instance of react_criter
filename	: name of the reaction criteria file

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write_to_logfile()

subroutine mod_reactioncriteria::write_to_logfile	(	type ( react_criter )	this,
		integer, intent(in)	io_unit
	)

Write information to a log file.

io_unit is given by read_input_file, egal to fort.52

Parameters

this	: instance of react_criter
io_unit	: file descriptor of the log file

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Variable Documentation

all

integer, parameter mod_reactioncriteria::all = 4

assoc_rate

integer, parameter mod_reactioncriteria::assoc_rate = 2

docking

integer, parameter mod_reactioncriteria::docking = 1

Enumeration, associated with type_rection.

elec_transfer

integer, parameter mod_reactioncriteria::elec_transfer = 3

off_rc

integer, parameter mod_reactioncriteria::off_rc = 5