Module for storing data needed for a specific conformation.
store all grids and position of atoms.
More...
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type | sogrid |
| Store all grids ( UHBD type), and "charges": charges, accessibility and their position. More...
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subroutine | allocate_sogrid (this) |
| Initialze sogrid with the total number of grid declared in mod_gridtype.f90. More...
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subroutine | delete_sogrid (this) |
| Delete sogrid. More...
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subroutine | load_grid (this, filename, t_grid, scfct_opt, iform_opt) |
| Load one grid or one "charge", can read binary or ascii format Add analytical interactions ( negative grid number ) More...
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subroutine | load_ljgrid (this, type_to_load, lj_filename, pdb_filename, opt_fct) |
| allocate and load lj_grid, should be done only once need more option, only one of lj / atom should be allocated keep one function, need type_to_load : 1 or 2, both are array of characters
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subroutine | set_analytic (this, name_type, list_stoke, bin_size, max_size, opt_extra_param) |
| Initialize one analytic array. More...
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subroutine | allocate_charge (this, nat) |
| Allocate charge array and square of the charges for electrostatic desolvation. More...
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subroutine | allocate_acc_surf (this, nat2) |
| Allocate accessibility and list_atom_surface array. More...
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subroutine | read_charge (this, echa_filename) |
| Function to read charges, and make charge_square. More...
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real(kind=8) function | get_max_debye (this) |
| Used ??
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subroutine | write_accessibility (this, access_filename, center_prot, vdw, max_vdw, max_dist, param_probe) |
| Write acceessibility into a file. More...
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subroutine | read_accessibility (this, access_filename, center_prot, vdw, max_vdw, max_dist, param_probe, opt_recalculate) |
| Read accessibility file. More...
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subroutine | set_ofgrid_info (this) |
| Print info of this set_of_grid.
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Module for storing data needed for a specific conformation.
store all grids and position of atoms.
subroutine mod_setofgrid::allocate_acc_surf |
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type ( sogrid ), intent(inout), pointer |
this, |
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integer, intent(in) |
nat2 |
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Allocate accessibility and list_atom_surface array.
- Parameters
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this | : pointer to an instance of sogrid ( why pointer ?) |
nat2 | : number of accessibility atoms |
subroutine mod_setofgrid::allocate_charge |
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type ( sogrid ) |
this, |
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integer, intent(in) |
nat |
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Allocate charge array and square of the charges for electrostatic desolvation.
- Parameters
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this | : instance of sogrid |
nat | : number of charges |
subroutine mod_setofgrid::allocate_sogrid |
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type ( sogrid ) |
this | ) |
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Initialze sogrid with the total number of grid declared in mod_gridtype.f90.
The array of grid has a fixed sized
- Parameters
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subroutine mod_setofgrid::delete_sogrid |
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type ( sogrid ) |
this | ) |
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Delete sogrid.
- Parameters
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subroutine mod_setofgrid::load_grid |
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type ( sogrid ), intent(inout) |
this, |
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character*128 |
filename, |
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integer, intent(in) |
t_grid, |
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real ( kind=8 ), optional |
scfct_opt, |
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integer, intent(in), optional |
iform_opt |
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) |
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Load one grid or one "charge", can read binary or ascii format Add analytical interactions ( negative grid number )
- Parameters
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this | : instance of sogrid |
filename | : name of the file |
t_grid | : type of the grid from 1 to 9, see mod_gridtype.f90 |
scfct_opt | : optionaly the multiplicative factor to apply ( default 0.) |
iform_opt | : optionaly, ascii or binary |
subroutine mod_setofgrid::read_accessibility |
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type ( sogrid ) |
this, |
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character*128 |
access_filename, |
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real ( kind=8 ), dimension ( 3 ) |
center_prot, |
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real ( kind=8 ), dimension ( : ), pointer |
vdw, |
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real ( kind=8 ) |
max_vdw, |
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real ( kind=8 ) |
max_dist, |
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type ( probe_type ) |
param_probe, |
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logical, optional |
opt_recalculate |
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Read accessibility file.
Optional but save lots of time to not recompute solva for large system
Read as well vwd, max_vdw and max_dist computed previously
- Parameters
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this | : input, instance of sogrid |
access_filename | : input, name of the file, p1.access |
center_prot | : output, center of geometry of the solute |
vdw | : output, list of the Van der Walls radius |
max_vdw | : output, maximum value of the vdw array |
max_dist | : output, maximum radius of the protein distance_max |
param_probe | : input, instance of probe_type, for checking whether the re-calculation is needed |
opt_recalculate | : optional, input, if param_probe values are different than in the file, stop reading (default: .true.) |
subroutine mod_setofgrid::read_charge |
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type ( sogrid ) |
this, |
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character *128 |
echa_filename |
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Function to read charges, and make charge_square.
- Parameters
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this | : instance of sogrid |
echa_filename | : effective charge (*.echa) filename |
subroutine mod_setofgrid::set_analytic |
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type ( sogrid ) |
this, |
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character, dimension(*), intent(in) |
name_type, |
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real (kind=8), dimension(:) |
list_stoke, |
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real(kind=8) |
bin_size, |
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real(kind=4) |
max_size, |
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real(kind=4), optional |
opt_extra_param |
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) |
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Initialize one analytic array.
Can be done only after cut_off has been computed and other stoke_radius known
- Parameters
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this | : instance of sogrid |
name_type | : string name debye-huckel or crowder |
list_stoke | : list all stoke radius by type of proteins |
bin_size | : of the precomputed array |
max_size | : size of cut-off, already corrected in case of box |
opt_extra_param | : optional, ionic stength at the moment |
subroutine mod_setofgrid::write_accessibility |
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type ( sogrid ) |
this, |
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character*128 |
access_filename, |
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real ( kind=8 ), dimension ( 3 ) |
center_prot, |
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real ( kind=8 ), dimension ( : ) |
vdw, |
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real ( kind=8 ) |
max_vdw, |
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real ( kind=8 ) |
max_dist, |
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type ( probe_type ) |
param_probe |
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) |
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Write acceessibility into a file.
It allows to be computed only once, and only read for the next simulations
Store a maximum of information, the pdb does not even need to be read
It is called by prepare_atom_protein()
- Parameters
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this | : instance of sogrid |
access_filename | : name of the file, p1.access |
center_prot | : center of geometry of the solute |
vdw | : list of the Van der Walls radius |
max_vdw | : maximum value of the vdw array |
max_dist | : maximum radius of the protein distance_max |
param_probe | : the value of the probe used to compute the accessibility |
The documentation for this module was generated from the following file: