Store all grids ( UHBD type), and "charges": charges, accessibility and their position. More...
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(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) | 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. | |
logical | idebye |
Save if debye-huckel / analytical interaction is activated Needed because full load done only later by param_force_energy. | |
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), 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 |
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 |
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 )