mod_setofgrid Module Reference

Module for storing data needed for a specific conformation.
store all grids and position of atoms. More...

Data Types
type	sogrid
	Store all grids ( UHBD type), and "charges": charges, accessibility and their position. More...

Functions/Subroutines
subroutine	allocate_sogrid (this)
	Initialze sogrid with the total number of grid declared in mod_gridtype.f90. More...
subroutine	delete_sogrid (this)
	Delete sogrid. More...
subroutine	load_grid (this, filename, t_grid, scfct_opt, iform_opt)
	Load one grid or one "charge", can read binary or ascii format Add analytical interactions ( negative grid number ) More...
subroutine	load_ljgrid (this, type_to_load, lj_filename, pdb_filename, opt_fct)
	allocate and load lj_grid, should be done only once need more option, only one of lj / atom should be allocated keep one function, need type_to_load : 1 or 2, both are array of characters More...
subroutine	set_analytic (this, name_type, list_rad, bin_size, max_size, surf_prefct, gouy_chapman, opt_extra_param)
	Initialize one analytic array. More...
subroutine	allocate_charge (this, nat)
	Allocate charge array and square of the charges for electrostatic desolvation. More...
subroutine	allocate_acc_surf (this, nat2)
	Allocate accessibility and list_atom_surface array. More...
subroutine	read_charge (this, echa_filename)
	Function to read charges, and make charge_square. More...
real(kind=8) function	get_max_debye (this)
	Used ?? More...
subroutine	write_accessibility (this, access_filename, center_prot, vdw, max_vdw, max_dist, param_probe)
	Write acceessibility into a file. More...
subroutine	read_accessibility (this, access_filename, center_prot, vdw, max_vdw, max_dist, param_probe, opt_recalculate)
	Read accessibility file. More...
subroutine	set_ofgrid_info (this)
	Print info of this set_of_grid. More...

Detailed Description

Module for storing data needed for a specific conformation.
store all grids and position of atoms.

Function/Subroutine Documentation

allocate_acc_surf()

subroutine mod_setofgrid::allocate_acc_surf	(	type ( sogrid ), intent(inout), pointer	this,
		integer, intent(in)	nat2
	)

Allocate accessibility and list_atom_surface array.

Parameters

this	: pointer to an instance of sogrid ( why pointer ?)
nat2	: number of accessibility atoms

allocate_charge()

subroutine mod_setofgrid::allocate_charge	(	type ( sogrid )	this,
		integer, intent(in)	nat
	)

Allocate charge array and square of the charges for electrostatic desolvation.

Parameters

this	: instance of sogrid
nat	: number of charges

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allocate_sogrid()

subroutine mod_setofgrid::allocate_sogrid

(

type ( sogrid )

this

)

Initialze sogrid with the total number of grid declared in mod_gridtype.f90.

The array of grid has a fixed sized

Parameters

this	: instance of sogrid

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delete_sogrid()

subroutine mod_setofgrid::delete_sogrid

(

type ( sogrid )

this

)

Delete sogrid.

Parameters

this	: instance of sogrid

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get_max_debye()

real ( kind=8 ) function mod_setofgrid::get_max_debye

(

type ( sogrid )

this

)

Used ??

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load_grid()

subroutine mod_setofgrid::load_grid	(	type ( sogrid ), intent(inout)	this,
		character*128	filename,
		integer, intent(in)	t_grid,
		real ( kind=8 ), optional	scfct_opt,
		integer, intent(in), optional	iform_opt
	)

Load one grid or one "charge", can read binary or ascii format Add analytical interactions ( negative grid number )

Parameters

this	: instance of sogrid
filename	: name of the file
t_grid	: type of the grid from 1 to 9, see mod_gridtype.f90
scfct_opt	: optionaly the multiplicative factor to apply ( default 0.)
iform_opt	: optionaly, ascii or binary

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load_ljgrid()

subroutine mod_setofgrid::load_ljgrid	(	type ( sogrid )	this,
		integer, intent(in)	type_to_load,
		character, dimension(*)	lj_filename,
		character, dimension(*)	pdb_filename,
		real ( kind=8 ), optional	opt_fct
	)

allocate and load lj_grid, should be done only once need more option, only one of lj / atom should be allocated keep one function, need type_to_load : 1 or 2, both are array of characters

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read_accessibility()

subroutine mod_setofgrid::read_accessibility	(	type ( sogrid )	this,
		character*128	access_filename,
		real ( kind=8 ), dimension ( 3 )	center_prot,
		real ( kind=8 ), dimension ( : ), pointer	vdw,
		real ( kind=8 )	max_vdw,
		real ( kind=8 )	max_dist,
		type ( probe_type )	param_probe,
		logical, optional	opt_recalculate
	)

Read accessibility file.

Optional but save lots of time to not recompute solva for large system
Read as well vwd, max_vdw and max_dist computed previously

Parameters

this	: input, instance of sogrid
access_filename	: input, name of the file, p1.access
center_prot	: output, center of geometry of the solute
vdw	: output, list of the Van der Walls radius
max_vdw	: output, maximum value of the vdw array
max_dist	: output, maximum radius of the protein distance_max
param_probe	: input, instance of probe_type, for checking whether the re-calculation is needed
opt_recalculate	: optional, input, if param_probe values are different than in the file, stop reading (default: .true.)

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read_charge()

subroutine mod_setofgrid::read_charge	(	type ( sogrid )	this,
		character *128	echa_filename
	)

Function to read charges, and make charge_square.

Parameters

this	: instance of sogrid
echa_filename	: effective charge (*.echa) filename

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set_analytic()

subroutine mod_setofgrid::set_analytic	(	type ( sogrid )	this,
		character, dimension(*), intent(in)	name_type,
		real (kind=8), dimension(:)	list_rad,
		real(kind=8)	bin_size,
		real(kind=4)	max_size,
		real(kind=8)	surf_prefct,
		logical	gouy_chapman,
		real(kind=4), optional	opt_extra_param
	)

Initialize one analytic array.

Can be done only after cut_off has been computed and other stoke_radius known

Parameters

this	: instance of sogrid
name_type	: string name debye-huckel or crowder
list_rad	: list all radii by type of proteins NJB: could be various types
bin_size	: of the precomputed array
max_size	: size of cut-off, already corrected in case of box
opt_extra_param	: optional, ionic stength at the moment

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set_ofgrid_info()

subroutine mod_setofgrid::set_ofgrid_info

(

type ( sogrid )

this

)

Print info of this set_of_grid.

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write_accessibility()

subroutine mod_setofgrid::write_accessibility	(	type ( sogrid )	this,
		character*128	access_filename,
		real ( kind=8 ), dimension ( 3 )	center_prot,
		real ( kind=8 ), dimension ( : )	vdw,
		real ( kind=8 )	max_vdw,
		real ( kind=8 )	max_dist,
		type ( probe_type )	param_probe
	)

Write acceessibility into a file.

It allows to be computed only once, and only read for the next simulations
Store a maximum of information, the pdb does not even need to be read
It is called by prepare_atom_protein()

Parameters

this	: instance of sogrid
access_filename	: name of the file, p1.access
center_prot	: center of geometry of the solute
vdw	: list of the Van der Walls radius
max_vdw	: maximum value of the vdw array
max_dist	: maximum radius of the protein distance_max
param_probe	: the value of the probe used to compute the accessibility

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