mod_protein Module Reference

Module to define one protein (position, orientation, is surface?)
. More...

Data Types
type	protein
	Define properties of one solute / protein. More...

Functions/Subroutines
subroutine	new_protein (this, irot, isurf, iflex, iimg_chg, id, vert_excl, opt_imdesolv)
	Allocate one protein.
subroutine	set_flexible (this, plist_flexible)
	Allocate a flexible and assign the plist_flexible.
subroutine	allocate_array_mdesolv (this, param_metaldesolv)
subroutine	delete_protein (this)
	Destructor, normally not called directly but by mod_array_protein add new variable local_copy, simpler and allow easier for flex.
subroutine	update_rot_orientation (this, mrot)
	rotate orientation axis version with explicit terms, faster
subroutine	update_rotation_protein (this, matrix_rot)
	Rotate the position of atoms/ charges / etc. version with explicit rotation, faster now use the pointer, either points to a sogrid copy, or rotate the local copy.
subroutine	info_protein (this)
	Print info.
subroutine	init_movable_array (this, sgrid, make_local_copy)
	Make the copy of the atomic position to protein if make_local_copy is true Otherwise points to sogrid why sgrid ? already associated ? Not if flex to check.
subroutine	copy_movable_array (this, opt_mat)
	Copy movable atoms from sogrid arrays to a local copy in the protein. Needed in case of flexibility (keep a copy of the initial position), certianly sda_pmf (with option opt_mat)\ Check if local copy is true, otherwise do nothing Optional opt_mat will load the initial position locally and apply the matrix of rotation. .
subroutine	select_charge (grid_number, prot1, prot2, nq1, nq2, p_charge1, p_charge2, p_charge_position1, p_charge_position2, dummy_array)
	First version, fastest version, do not check for asymetry. .
subroutine	select_charge2 (grid_number, prot1, prot2, nq1, nq2, p_charge1, p_charge2, p_charge_position1, p_charge_position2, dummy_array, opt_pgrid1, opt_pgrid2, opt_subgrid)
	Select correct pointer for charges ( and optionaly subgrids : only lennard-jones now ). .
subroutine	initialize_conformation (this, opt_conf_nb)
	Initialize the conformation in case of flexible. replace change_conformation::init_conformation .
subroutine	update_visited_conf (this, timestep)
	update array statistics for sda_flex, use timestep rather than integer, may change
subroutine	merge_visited_conf (this, to_merge)
subroutine	print_visited_conf (this)

Detailed Description

Module to define one protein (position, orientation, is surface?)
.

Function/Subroutine Documentation

allocate_array_mdesolv()

subroutine mod_protein::allocate_array_mdesolv	(	type ( protein )	this,
		type ( parameter_metaldesolv )	param_metaldesolv
	)

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copy_movable_array()

subroutine mod_protein::copy_movable_array	(	type ( protein )	this,
		real(kind=8), dimension(3,3), optional	opt_mat
	)

Copy movable atoms from sogrid arrays to a local copy in the protein. Needed in case of flexibility (keep a copy of the initial position), certianly sda_pmf (with option opt_mat)\ Check if local copy is true, otherwise do nothing
Optional opt_mat will load the initial position locally and apply the matrix of rotation.
.

Precondition

To be called after init_movable_array

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delete_protein()

subroutine mod_protein::delete_protein

(

type ( protein )

this

)

Destructor, normally not called directly but by mod_array_protein add new variable local_copy, simpler and allow easier for flex.

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info_protein()

subroutine mod_protein::info_protein

(

type ( protein ), intent(in)

this

)

Print info.

init_movable_array()

subroutine mod_protein::init_movable_array	(	type ( protein )	this,
		type ( sogrid ), pointer	sgrid,
		logical	make_local_copy
	)

Make the copy of the atomic position to protein if make_local_copy is true Otherwise points to sogrid why sgrid ? already associated ? Not if flex to check.

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initialize_conformation()

subroutine mod_protein::initialize_conformation	(	type ( protein )	this,
		integer, optional	opt_conf_nb
	)

Initialize the conformation in case of flexible.
replace change_conformation::init_conformation
.

Parameters

this	: instance of protein
opt_conf_nb	:: optional, indicates which conformation. If zero chosses a random one

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merge_visited_conf()

subroutine mod_protein::merge_visited_conf	(	type ( protein )	this,
		type ( protein )	to_merge
	)

new_protein()

subroutine mod_protein::new_protein	(	type ( protein )	this,
		logical, intent(in)	irot,
		logical, intent(in)	isurf,
		logical, intent(in)	iflex,
		logical, intent(in)	iimg_chg,
		integer, intent(in)	id,
		logical, intent(in)	vert_excl,
		logical, optional	opt_imdesolv
	)

Allocate one protein.

Parameters

this	: instance of protein
irot	: if the solute rotates
isurf	: if the solute is a surface ( no rotation, no translation, different PBC )
iflex	: if the solute is flexible
iimg_chg	: if solute should compute image_charge forces and energies
id	: identifier, depreceated
vert_excl	: should decision on whether to make an excluded volume check depend on vertical height
opt_imdesolv	: optional, global object mdesolv

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print_visited_conf()

subroutine mod_protein::print_visited_conf

(

type ( protein )

this

)

select_charge()

subroutine mod_protein::select_charge	(	integer, intent(in)	grid_number,
		type ( protein ), intent(in), target	prot1,
		type ( protein ), intent(in), target	prot2,
		integer, intent(out)	nq1,
		integer, intent(out)	nq2,
		real ( kind = 8 ), dimension ( : ), intent(out), pointer	p_charge1,
		real ( kind = 8 ), dimension ( : ), intent(out), pointer	p_charge2,
		real ( kind=8 ), dimension(:,:), intent(out), pointer	p_charge_position1,
		real ( kind=8 ), dimension(:,:), intent(out), pointer	p_charge_position2,
		real ( kind = 8 ), dimension ( : ), target	dummy_array
	)

First version, fastest version, do not check for asymetry.
.

Can be called by sdamm, because an additional check is done in compute_force/energy

Assign pointer to the correct grid / charge.

Parameters

grid_number	: grid to select
prot1,prot2	: protein
nq1,nq2	: number of "charges"
p_charge1,p_charge2	: pointer to the "charge" value
p_charge_position1,p_charge_position2	: pointer to the "charge" positions
dummy_array	: sned the dummy array adress, used by hydrophobic and lennard-jones

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select_charge2()

subroutine mod_protein::select_charge2	(	integer, intent(in)	grid_number,
		type ( protein ), intent(in), target	prot1,
		type ( protein ), intent(in), target	prot2,
		integer, intent(out)	nq1,
		integer, intent(out)	nq2,
		real ( kind = 8 ), dimension ( : ), intent(out), pointer	p_charge1,
		real ( kind = 8 ), dimension ( : ), intent(out), pointer	p_charge2,
		real ( kind=8 ), dimension(:,:), intent(out), pointer	p_charge_position1,
		real ( kind=8 ), dimension(:,:), intent(out), pointer	p_charge_position2,
		real ( kind = 8 ), dimension ( : ), target	dummy_array,
		type ( type_grid ), intent(out), optional, pointer	opt_pgrid1,
		type ( type_grid ), intent(out), optional, pointer	opt_pgrid2,
		integer, intent(in), optional	opt_subgrid
	)

Select correct pointer for charges ( and optionaly subgrids : only lennard-jones now ).
.

Include lennard-jones grids
Check if associated, allow asymetric computation
Could replace select_charge, need benchmark.

Parameters

grid_number	: grid to select
prot1,prot2	: protein
nq1,nq2	: number of "charges"
p_charge1,p_charge2	: pointer to the "charge" value
p_charge_position1,p_charge_position2	: pointer to the "charge" positions
dummy_array	: sned the dummy array adress, used by hydrophobic and lennard-jones
opt_pgrid1,opt_pgrid2	: optional, pointer to the grid, can be lennard-jones
opt_subgrid	: optional, the subgrid number ( only lj now )

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set_flexible()

subroutine mod_protein::set_flexible	(	type ( protein )	this,
		type ( list_flex_type )	plist_flexible
	)

Allocate a flexible and assign the plist_flexible.

Parameters

this	: instance of protein
plist_flexible	: pointer to a list_flex_type

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update_rot_orientation()

subroutine mod_protein::update_rot_orientation	(	type ( protein )	this,
		real ( kind=8 ), dimension(3,3), intent(in)	mrot
	)

rotate orientation axis version with explicit terms, faster

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update_rotation_protein()

subroutine mod_protein::update_rotation_protein	(	type ( protein )	this,
		real ( kind=8 ), dimension(3,3), intent(in)	matrix_rot
	)

Rotate the position of atoms/ charges / etc. version with explicit rotation, faster now use the pointer, either points to a sogrid copy, or rotate the local copy.

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update_visited_conf()

subroutine mod_protein::update_visited_conf	(	type ( protein )	this,
		real ( kind=4 )	timestep
	)

update array statistics for sda_flex, use timestep rather than integer, may change