mod_flexibility Module Reference

Module for flexibility. More...

Data Types
type	flexible
	Main class owned by each protein to allow a change in conformation. More...
type	list_flex_type
	List of set of grid. More...
type	nodeflex
	Define nodes of list_flex, internal use. More...

Functions/Subroutines
subroutine	new_flexible (this, plist_flex)
	Constructor flexible .
subroutine	delete_flexible (this)
	Destructor flexible.
subroutine	init_flexible_freq (this)
	Initialize or reinitialze the time for the next change in conformation : time_next_flex.
subroutine	new_list_flex (this, flex_method_str, list_conf_fname, total_conf, initial_conf, nearest_ngb, frequence, std_freq, internal_energy, imarkov)
	Constructor of list_flexible.
subroutine	delete_listflex (this)
	Delete the full list and the associated sogrid.
subroutine	correct_transitionmatrix (this)
	Checks mod_flexibilty::list_flex_type::transition_matrix for correct input only used when imarkov only for a square transition matrix.
subroutine	correct_stationarydistribution (this)
	Checks mod_flexibilty::list_flex_type::stationary_distribution for correct inputs and normalizes used when the internal energy calculation option turned on the stationary_distribution corresponds to weights (markovian=false) or to the eigenvector (with eigenvalue=1) of the mod_flexibilty::list_flex_type::transition_matrix (markovian=true)
subroutine	correct_weights (this)
	Goes through sogrid list and correct the conf_weights depending on single values and/or the sum of all values.
subroutine	delete_last_dataflex (this, status)
	Deleta the last node of the list and the associated sogrid.
subroutine	delete_first_dataflex (this, status)
	not used until now, to delete ??
subroutine	insert_sogrid (this, p_sogrid, head, status)
	Insert a new sogrid and create a new node.
recursive integer function	associate_to_conformation (this, pnew_node, nb_conf, counter, shift_conf)
	Associate pointer pnew_node to the conformation number.
subroutine	change_conf_flex (this, conf_nb, shift_conf_opt)
	Update the p_current_node of flex to conformation nb_conf (== -1 random ) or shift_conf ( +/- 1 )

Variables
integer, parameter	flex_intern = 0
	enumeration of node's state for the list
integer, parameter	flex_first = 1
integer, parameter	flex_last = 2
integer, parameter	flex_random = 0
	enumeration for the algorithm
integer, parameter	flex_metropolis = 1
integer, parameter	flex_minimum = 2
integer, parameter	flex_time = 3

Detailed Description

Module for flexibility.

Manage a list of possible conformation ( list of set_of_grid ). define type for flexibility : NodeFlex, list_flex_type and flexible

Function/Subroutine Documentation

associate_to_conformation()

recursive integer function mod_flexibility::associate_to_conformation	(	type ( nodeflex ), target	this,
		type ( nodeflex ), pointer	pnew_node,
		integer, intent(in)	nb_conf,
		integer, intent(out)	counter,
		integer, intent(in)	shift_conf
	)

Associate pointer pnew_node to the conformation number.

set pnew_node to nb_conf or shift ( previous or next ) called by change_conf_flex only, which deals with random numbers

if shift_opt is given moved to a neighbour. if shift not given and nb_conf /= -1, moved to nb_conf using recursive function, needed to loop throught the list.

Parameters

this	: instance of NodeFlex
pnew_node	: pointer to the NodeFlex, associated if status == 0
nb_conf	: specify the conformation number, used if shift_conf == 0
counter	: return the current conformation in the case nb_conf is specified explictely
shift_conf	: if 1 or -1, points to the next or previous node. if 0 use nb_conf

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change_conf_flex()

subroutine mod_flexibility::change_conf_flex	(	type ( flexible )	this,
		integer, intent(in)	conf_nb,
		integer, optional	shift_conf_opt
	)

Update the p_current_node of flex to conformation nb_conf (== -1 random ) or shift_conf ( +/- 1 )

if shift_conf_opt present ( +1 / -1) limited to +/- 1 not present, do not use shift both cases if conf_nb == -1 random if shift ( can be the same) full random (can be the same ) if conf_nb /= -1 and shift_conf is not present : specify the conformation number exactly

Parameters

this	: instance of flexible
conf_nb	: new conformation number
conf_nb	: conformation number, if == -1, random
shift_conf_opt	: optionaly if conf_nb different of -1 (=0) apply the given shift

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correct_stationarydistribution()

subroutine mod_flexibility::correct_stationarydistribution

(

type ( list_flex_type )

this

)

Checks mod_flexibilty::list_flex_type::stationary_distribution for correct inputs and normalizes used when the internal energy calculation option turned on the stationary_distribution corresponds to weights (markovian=false) or to the eigenvector (with eigenvalue=1) of the mod_flexibilty::list_flex_type::transition_matrix (markovian=true)

Parameters

this	instance of a mod_flexibility::list_flex_type

correct_transitionmatrix()

subroutine mod_flexibility::correct_transitionmatrix

(

type ( list_flex_type )

this

)

Checks mod_flexibilty::list_flex_type::transition_matrix for correct input only used when imarkov only for a square transition matrix.

Parameters

this	instance of a mod_flexibility::list_flex_type

correct_weights()

subroutine mod_flexibility::correct_weights

(

type ( list_flex_type)

this

)

Goes through sogrid list and correct the conf_weights depending on single values and/or the sum of all values.

Parameters

this	instance of a list_flex_type

delete_first_dataflex()

subroutine mod_flexibility::delete_first_dataflex	(	type ( list_flex_type )	this,
		integer, intent(out)	status
	)

not used until now, to delete ??

delete_flexible()

subroutine mod_flexibility::delete_flexible

(

type ( flexible )

this

)

Destructor flexible.

Deallocate array for statistics, nullify the pointer ( no deletion of sogrid )

Parameters

this	: instance of a flexible

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delete_last_dataflex()

subroutine mod_flexibility::delete_last_dataflex	(	type ( list_flex_type )	this,
		integer, intent(out)	status
	)

Deleta the last node of the list and the associated sogrid.

Parameters

this	: instance of list_flex_type
status	: for error report

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delete_listflex()

subroutine mod_flexibility::delete_listflex

(

type ( list_flex_type )

this

)

Delete the full list and the associated sogrid.

Parameters

this	: instance of a list_flex_type

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init_flexible_freq()

subroutine mod_flexibility::init_flexible_freq

(

type ( flexible )

this

)

Initialize or reinitialze the time for the next change in conformation : time_next_flex.

if std_freq_random > 0, add a random variable else use exactly frequence

Parameters

this	: instance of a flexible

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insert_sogrid()

subroutine mod_flexibility::insert_sogrid	(	type ( list_flex_type )	this,
		type ( sogrid ), pointer	p_sogrid,
		logical, intent(in)	head,
		integer	status
	)

Insert a new sogrid and create a new node.

Could increment the size here

Parameters

this	: instance of list_flex_type
p_sogrid	: pointer to the sogrid to insert
head	: if true insert first position, if false last position
status	: for error report, not used

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new_flexible()

subroutine mod_flexibility::new_flexible	(	type ( flexible )	this,
		type ( list_flex_type ), target	plist_flex
	)

Constructor flexible
.

Called by mod_protein::set_flexible
The list of conformation should be independently created with new_list_flex
Allocate the array for the statistics

Parameters

this	: instance of a flexible
plist_flex	: the list of sogrid to associate to flexible

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new_list_flex()

subroutine mod_flexibility::new_list_flex	(	type ( list_flex_type )	this,
		character ( 128 )	flex_method_str,
		character ( 128 )	list_conf_fname,
		integer	total_conf,
		integer	initial_conf,
		logical	nearest_ngb,
		real ( kind=4 )	frequence,
		real ( kind=4 )	std_freq,
		logical	internal_energy,
		logical	imarkov
	)

Constructor of list_flexible.

Parameters

this	: instance of a list_flex_type
flex_method_str	: "metropolis", "random", "time" or "minimum"
list_conf_fname	: name of the input file with all conformations
total_conf	: total number of conformations
initial_conf	: specifies if a particular conformation is choosen at the start of a new trajectory
nearest_ngb	: logical, nearest neigbour only
frequence	: time for changing conformation
std_freq	: variance in the frequence
internal_energy	: logical, calculate internal energy
imarkov	: logical, use transition matrix

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Variable Documentation

flex_first

integer, parameter mod_flexibility::flex_first = 1

flex_intern

integer, parameter mod_flexibility::flex_intern = 0

enumeration of node's state for the list

flex_last

integer, parameter mod_flexibility::flex_last = 2

flex_metropolis

integer, parameter mod_flexibility::flex_metropolis = 1

flex_minimum

integer, parameter mod_flexibility::flex_minimum = 2

flex_random

integer, parameter mod_flexibility::flex_random = 0

enumeration for the algorithm

flex_time

integer, parameter mod_flexibility::flex_time = 3