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) | 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. More... | |

real(kind=8) | vol_radius |

Radius used to define volume occupancies in HI calculation. More... | |

real(kind=8) | rep_radius |

Radius used to define soft core repulsion in crowder model. More... | |

logical | idebye |

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

logical | dh_only |

logical | idh_imgchg |

logical | ihom_charged_surf |

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

real(kind=8) | surface_charge_dens |

Charge density on the surface. 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 |

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 )

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

logical mod_setofgrid::sogrid::alloc_which_at_surf |

should this array be allocated? default: false

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

value of the effective charge, and square value for desolvation

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

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

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.

logical mod_setofgrid::sogrid::dh_only |

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

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

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

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

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

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

parameter for exclusion, put it here even if not implemented

keep old format because old subroutine

logical mod_setofgrid::sogrid::idebye |

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

logical mod_setofgrid::sogrid::idh_imgchg |

logical mod_setofgrid::sogrid::ihom_charged_surf |

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

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

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

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

Largest cut off in cut2_array.

integer mod_setofgrid::sogrid::nb_atom_surface |

integer mod_setofgrid::sogrid::nb_charge |

integer mod_setofgrid::sogrid::nb_reaction_criteria |

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

pointer to exclusion grid

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

pointer to module mod_ljgrid, include all grids, all atoms

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

position of the effective charge

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

fixed size array which contains pointers to analytical 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

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 ( 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.

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

Radius used to define soft core repulsion in crowder model.

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

Charge density on the surface.

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

Radius used to define volume occupancies in HI calculation.

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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