SDA (SDA flex)  7.2
Simulation of Diffusional Association
Public Attributes | List of all members
mod_setofgrid::sogrid Type Reference

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 More...
 
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 !! More...
 
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 More...
 
type(analytic), dimension(:), pointer pset_analytic_grid
 fixed size array which contains pointers to analytical grid More...
 
type(type_grid_excl), pointer p_excl_grid
 pointer to exclusion grid More...
 
type(type_ljgrid), pointer p_ljgrid
 pointer to module mod_ljgrid, include all grids, all atoms More...
 
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
More...
 
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. More...
 
real(kind=8) stoke_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. More...
 
logical idebye
 Save if debye-huckel / analytical interaction is activated Needed because full load done only later by param_force_energy. More...
 
real(kind=4), dimension(:,:), allocatable cut2_array
 Array to store cut off for each grid in sogrid with equivalent in all other sogrids. More...
 
real(kind=4) max_cut2
 Largest cut off in cut2_array. More...
 
real(kind=8), dimension(:), allocatable charge_grid
 value of the effective charge, and square value for desolvation More...
 
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() More...
 
real(kind=8), dimension(:), allocatable accessibility
 
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 More...
 
logical alloc_which_at_surf
 should this array be allocated? default: false More...
 
real(kind=8) hexcl
 parameter for exclusion, put it here even if not implemented
keep old format because old subroutine More...
 
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

◆ 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.

◆ 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

◆ 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.

◆ 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_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.

◆ stoke_radius

real(kind=8) mod_setofgrid::sogrid::stoke_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.

◆ 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:
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