mod_array_protein Module Reference

Module to define an array of proteins. More...

Data Types
type	array_protein_type
	Main class which owns all subgroups : protein and sogrid, see UMLshema_archi. More...

Functions/Subroutines
subroutine	new_array_protein (this, size, nb_grids)
	Allocate the arrays. More...
subroutine	delete_array_protein (this, opt_copy_omp)
	Deallocate arrays array and set_of_protein. More...
subroutine	copy_array_protein (this, ptab_dest, type_calc, param_metaldesolv)
	Make a copy of the array. More...
integer function	get_type (this, prot_nb)
	Function to get the protein type. More...
subroutine	print_info_array_protein (this, opt_check_associated)
	Print array information. More...

Detailed Description

Module to define an array of proteins.

Function/Subroutine Documentation

copy_array_protein()

subroutine mod_array_protein::copy_array_protein	(	type ( array_protein_type )	this,
		type ( array_protein_type ), pointer	ptab_dest,
		type ( type_calculation ), intent(in)	type_calc,
		type ( parameter_metaldesolv ), intent(in)	param_metaldesolv
	)

Make a copy of the array.

Used with OpenMP, makes pointer easier with older specification
Parameter type_calc to force sda_2proteins and solute 2 with local copy
Sdamm not used yet, to see later

Parameters

this	: instance of array_protein_type, source of the copy
ptab_dest	: pointer to the target of the copy
type_calc	: instance of type_calculation
param_metaldesolv	: instance of type com_sda::parameter_metaldesolv

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delete_array_protein()

subroutine mod_array_protein::delete_array_protein	(	type ( array_protein_type )	this,
		logical, optional	opt_copy_omp
	)

Deallocate arrays array and set_of_protein.

By default, delete all proteins and associated flexible and/or sogrid associated
Deletion of the sogrid is optional, needed only with sda_2proteins and OpenMP

Parameters

this	: instance of array_protein_type
opt_copy_omp	: optionaly do not delete the associated sogrid and flexible. Default delete all

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get_type()

integer function mod_array_protein::get_type	(	type ( array_protein_type ), intent(in)	this,
		integer, intent(in)	prot_nb
	)

Function to get the protein type.

Should not be used inside heavy computational code
Usefull for tools and initialization
If too slow make an array during initilisation, this choice was prefered with set_of_protein

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new_array_protein()

subroutine mod_array_protein::new_array_protein	(	type ( array_protein_type )	this,
		integer	size,
		integer	nb_grids
	)

Allocate the arrays.

Parameters

this	: instance of array_protein_type
size	: total number of solutes
nb_grids	: total number of grids ( in fact nb of sogrid), a flexible solute accounts for only one grid ( it uses only one flexible )

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print_info_array_protein()

subroutine mod_array_protein::print_info_array_protein	(	type ( array_protein_type )	this,
		logical, optional	opt_check_associated
	)

Print array information.

Set opt false for tools for instance, in sda stop because there is an error in initialization

Parameters

this	: instance of array_protein_type, source of the copy
opt_check_associated	optional, stop if so_grid of proteins are not associated

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