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

Collaboration diagram for mod_setofgrid::sogrid:

Public Attributes
real(kind=8), dimension(:,:), allocatable	position_charge
	position of the effective charge

real(kind=4), dimension(:,:), allocatable	reaction_criteria_pos
	reaction criteria associated to this set of grid make sense for sda flex, for sdamm ?? by default associated to protein2 change associate to all proteins we want to consider possible criteria seems easier to store only array of position for sda_flex and sdamm, limitation if HOMODIMER !!

type(type_grid), dimension(:), pointer	pset_grid
	fixed size array which contains pointers to grid objects ( uhbd type): electrostatic, desolvation, hydrophobic, lennard-jones repulsive ( sdamm ), lennar-jones

type(analytic), dimension(:), pointer	pset_analytic_grid
	fixed size array which contains pointers to analytical grid

type(crowder), pointer	p_crowder
	Crowder interactions use intermediate object that points to analytical grids at moment.

type(type_grid_excl), pointer	p_excl_grid
	pointer to exclusion grid

type(type_ljgrid), pointer	p_ljgrid
	pointer to module mod_ljgrid, include all grids, all atoms

real(kind=8)	charge_total

integer	nb_charge

integer	nb_atom_surface

integer	nb_reaction_criteria

real(kind=8)	diffusion_trans
	rotation and translation diffusion coefficients, as read in the input file

real(kind=8)	diffusion_rotat

real(kind=8)	real_net_charge
	Charge calculations up to SDA 7 solely based on effective charges Real net charge, that is used for Debye-Huckel calculations can be used by setting value in the input file.

real(kind=8)	dh_radius
	In case of hydrodynamic interaction stoke_radius must be > 0. Used by Debye-Huckel also now, need to correct / test for HI, explict hi variable needed NJB: No longer used!! Now separate radii for DH, HI and spherical crowder repulsion.

real(kind=8)	vol_radius
	Radius used to define volume occupancies in HI calculation.

real(kind=8)	rep_radius
	Radius used to define soft core repulsion in crowder model.

logical	idebye
	Save if debye-huckel / analytical interaction is activated Needed because full load done only later by param_force_energy.

logical	dh_only

logical	idh_imgchg

logical	isphere_crowd
	Are the solutes described by this sogrid crowders. Added by Neil Bruce and adapted by Abraham.

logical	ishape_crowd

logical	ihom_charged_surf
	Save if type is a homogeneously charged non-conducting surface.

real(kind=8)	surface_charge_dens
	Charge density on the surface.

real(kind=4), dimension(:,:), allocatable	cut2_array
	Array to store cut off for each grid in sogrid with equivalent in all other sogrids.

real(kind=4)	max_cut2
	Largest cut off in cut2_array.

real(kind=8)	conf_weight
	parameter for internal energy calculations Used to distinguish the internal energy different conformations of a solute for equienergetic conformations, weight turned of by setting to -1


real(kind=8), dimension(:), allocatable	charge_grid
	value of the effective charge, and square value for desolvation

real(kind=8), dimension(:), allocatable	charge_square_grid


real(kind=8), dimension(:,:), allocatable	list_atom_surface
	accessibility position of the atoms at the surface, computed by solva()

real(kind=8), dimension(:), allocatable	accessibility

real(kind=8), dimension(:), allocatable	hd_sasa

integer, dimension(:), allocatable	which_atom_surface
	array listing which atoms from the entire PDB list are the surface atoms (i.e., accessible) - used only in tools

logical	alloc_which_at_surf
	should this array be allocated? default: false


real(kind=8)	hexcl
	parameter for exclusion, put it here even if not implemented keep old format because old subroutine

real(kind=8)	distance_max

Detailed Description

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

Pointer to exclusion grid as well, see mod_exclusion_grid.f90
Many proteins may refer to the same instance of sogrid ( case of sdamm )

Member Data Documentation

◆ accessibility

real ( kind = 8 ), dimension(:), allocatable mod_setofgrid::sogrid::accessibility

◆ alloc_which_at_surf

logical mod_setofgrid::sogrid::alloc_which_at_surf

should this array be allocated? default: false

◆ charge_grid

real ( kind = 8 ), dimension(:), allocatable mod_setofgrid::sogrid::charge_grid

value of the effective charge, and square value for desolvation

◆ charge_square_grid

real ( kind = 8 ), dimension(:), allocatable mod_setofgrid::sogrid::charge_square_grid

◆ charge_total

real ( kind=8 ) mod_setofgrid::sogrid::charge_total

◆ conf_weight

real(kind=8) mod_setofgrid::sogrid::conf_weight

parameter for internal energy calculations Used to distinguish the internal energy different conformations of a solute for equienergetic conformations, weight turned of by setting to -1

◆ cut2_array

real(kind=4), dimension (:,:), allocatable mod_setofgrid::sogrid::cut2_array

Array to store cut off for each grid in sogrid with equivalent in all other sogrids.

◆ dh_only

logical mod_setofgrid::sogrid::dh_only

◆ dh_radius

real(kind=8) mod_setofgrid::sogrid::dh_radius

In case of hydrodynamic interaction stoke_radius must be > 0. Used by Debye-Huckel also now, need to correct / test for HI, explict hi variable needed NJB: No longer used!! Now separate radii for DH, HI and spherical crowder repulsion.

Radius used to define cavity in DH calculation

◆ diffusion_rotat

real ( kind=8 ) mod_setofgrid::sogrid::diffusion_rotat

◆ diffusion_trans

real ( kind=8 ) mod_setofgrid::sogrid::diffusion_trans

rotation and translation diffusion coefficients, as read in the input file

◆ distance_max

real ( kind=8 ) mod_setofgrid::sogrid::distance_max

◆ hd_sasa

real ( kind = 8 ), dimension(:), allocatable mod_setofgrid::sogrid::hd_sasa

◆ hexcl

real ( kind=8 ) mod_setofgrid::sogrid::hexcl

parameter for exclusion, put it here even if not implemented
keep old format because old subroutine

◆ idebye

logical mod_setofgrid::sogrid::idebye

Save if debye-huckel / analytical interaction is activated Needed because full load done only later by param_force_energy.

◆ idh_imgchg

logical mod_setofgrid::sogrid::idh_imgchg

◆ ihom_charged_surf

logical mod_setofgrid::sogrid::ihom_charged_surf

Save if type is a homogeneously charged non-conducting surface.

◆ ishape_crowd

logical mod_setofgrid::sogrid::ishape_crowd

◆ isphere_crowd

logical mod_setofgrid::sogrid::isphere_crowd

Are the solutes described by this sogrid crowders. Added by Neil Bruce and adapted by Abraham.

◆ list_atom_surface

real ( kind = 8 ), dimension(:,:), allocatable mod_setofgrid::sogrid::list_atom_surface

accessibility position of the atoms at the surface, computed by solva()

◆ max_cut2

real(kind=4) mod_setofgrid::sogrid::max_cut2

Largest cut off in cut2_array.

◆ nb_atom_surface

integer mod_setofgrid::sogrid::nb_atom_surface

◆ nb_charge

integer mod_setofgrid::sogrid::nb_charge

◆ nb_reaction_criteria

integer mod_setofgrid::sogrid::nb_reaction_criteria

◆ p_crowder

type(crowder), pointer mod_setofgrid::sogrid::p_crowder

Crowder interactions use intermediate object that points to analytical grids at moment.

could have other interaction types as well

◆ p_excl_grid

type ( type_grid_excl ), pointer mod_setofgrid::sogrid::p_excl_grid

pointer to exclusion grid

◆ p_ljgrid

type ( type_ljgrid ), pointer mod_setofgrid::sogrid::p_ljgrid

pointer to module mod_ljgrid, include all grids, all atoms

◆ position_charge

real ( kind = 8 ), dimension(:,:), allocatable mod_setofgrid::sogrid::position_charge

position of the effective charge

◆ pset_analytic_grid

type ( analytic ), dimension(:), pointer mod_setofgrid::sogrid::pset_analytic_grid

fixed size array which contains pointers to analytical grid

◆ pset_grid

type ( type_grid ), dimension(:), pointer mod_setofgrid::sogrid::pset_grid

fixed size array which contains pointers to grid objects ( uhbd type): electrostatic, desolvation, hydrophobic, lennard-jones repulsive ( sdamm ), lennar-jones

◆ reaction_criteria_pos

real ( kind=4 ), dimension (:,:), allocatable mod_setofgrid::sogrid::reaction_criteria_pos

reaction criteria associated to this set of grid make sense for sda flex, for sdamm ?? by default associated to protein2 change associate to all proteins we want to consider possible criteria seems easier to store only array of position for sda_flex and sdamm, limitation if HOMODIMER !!

◆ real_net_charge

real ( kind=8 ) mod_setofgrid::sogrid::real_net_charge

Charge calculations up to SDA 7 solely based on effective charges Real net charge, that is used for Debye-Huckel calculations can be used by setting value in the input file.

◆ rep_radius

real(kind=8) mod_setofgrid::sogrid::rep_radius

Radius used to define soft core repulsion in crowder model.

◆ surface_charge_dens

real(kind=8) mod_setofgrid::sogrid::surface_charge_dens

Charge density on the surface.

◆ vol_radius

real(kind=8) mod_setofgrid::sogrid::vol_radius

Radius used to define volume occupancies in HI calculation.

◆ which_atom_surface

integer, dimension(:), allocatable mod_setofgrid::sogrid::which_atom_surface

array listing which atoms from the entire PDB list are the surface atoms (i.e., accessible) - used only in tools

The documentation for this type was generated from the following file:

mod_setofgrid.f90

Public Attributes