mod_protein::protein Type Reference

Define properties of one solute / protein. More...

Collaboration diagram for mod_protein::protein:

Public Attributes
integer, dimension(3)	box
	keep trace of the box position, needed for sdamm More...
real(kind=8), dimension(3)	position
	real position for sdamm, relative position for sda_2proteins More...
real(kind=8), dimension(3)	center_protein
	center of geometry from the pdb file More...
integer	id
	may be used by mod_record, keep it More...
real(kind=8)	real_net_charge
	Local copy of real net charge (total charge) More...
real(kind=8)	surface_charge_dens
type(sogrid), pointer	p_sogrid
	pointer to the associated set of grid (sogrid) More...
type(flexible), pointer	p_flex
	pointer to a flexible, only one of these two pointers should be initalized More...
logical	local_copy
	If a local copy of the movable atoms is needed. More...
integer, dimension(:), pointer	p_which_atom_surface
	one-dimensional array listing the atoms which are on the surface (order as in the orig.PDB file) More...
type(type_ljgrid), pointer	p_pos_lenjones
	pointer to movable arrays for lennard-jones, contains all grids and position More...
real(kind=8), dimension(3)	orientation_x
	For langevin integrator, not implementd. More...
real(kind=8), dimension(3)	orientation_y
real(kind=8), dimension(3)	orientation_z
real(kind=8)	diff_trans
	local copy of diffusion coefficient. Maybe be modified by Hydrodynamic Interactions More...
real(kind=8)	diff_rotat
logical	surface
	General variable of the properties of the solute. More...
logical	iflex
logical	rotate
logical	iimg_chg
logical	vert_excl
integer	nb_charge
	In case of local copy, size of the arrays. More...
integer	nb_atom_surface
integer	nb_rcriteria
logical	imetaldesolv
	Parameter specific to metaldesolvation, grid owned by each protein. More...
real(kind=8), dimension(:,:), pointer	array_mdesolv
integer	size_metal
real(kind=8), dimension(:,:), pointer	p_pos_charge
	pointers to the movable arrays if there is no local copy, they point to sogrid arrays if there is a local copy needed, they allocate their own arrays More...
real(kind=8), dimension(:,:), pointer	p_list_atom_surface
real(kind=4), dimension(:,:), pointer	p_pos_rcriteria

Detailed Description

Define properties of one solute / protein.

Contains :

• geometric center
• position and orientation
• pointer to one sogrid, if the solute is not flexible is associated
  
• pointeur to one flexible, if the solute is flexible ( one flexible by protein)
• optional an internal copy of the movable_atoms ( effective charges, accessibility atoms and reaction criteria ), when an independent copy from the sogrid is needed ( sdamm, sda_2proteins with OpenMP )
• new added a copy of type_ljgrid, contains movable atoms and points to the unique array of grid

Member Data Documentation

array_mdesolv

real ( kind=8 ), dimension(:,:), pointer mod_protein::protein::array_mdesolv

box

integer, dimension ( 3 ) mod_protein::protein::box

keep trace of the box position, needed for sdamm

Todo:

check if still needed

center_protein

real ( kind=8 ), dimension(3) mod_protein::protein::center_protein

center of geometry from the pdb file

diff_rotat

real ( kind=8 ) mod_protein::protein::diff_rotat

diff_trans

real ( kind=8 ) mod_protein::protein::diff_trans

local copy of diffusion coefficient. Maybe be modified by Hydrodynamic Interactions

id

integer mod_protein::protein::id

may be used by mod_record, keep it

iflex

logical mod_protein::protein::iflex

iimg_chg

logical mod_protein::protein::iimg_chg

imetaldesolv

logical mod_protein::protein::imetaldesolv

Parameter specific to metaldesolvation, grid owned by each protein.

local_copy

logical mod_protein::protein::local_copy

If a local copy of the movable atoms is needed.

nb_atom_surface

integer mod_protein::protein::nb_atom_surface

nb_charge

integer mod_protein::protein::nb_charge

In case of local copy, size of the arrays.

nb_rcriteria

integer mod_protein::protein::nb_rcriteria

orientation_x

real ( kind=8 ), dimension(3) mod_protein::protein::orientation_x

For langevin integrator, not implementd.

orientation of the solute, store vector for the 3 axis

orientation_y

real ( kind=8 ), dimension(3) mod_protein::protein::orientation_y

orientation_z

real ( kind=8 ), dimension(3) mod_protein::protein::orientation_z

p_flex

type ( flexible ), pointer mod_protein::protein::p_flex

pointer to a flexible, only one of these two pointers should be initalized

p_list_atom_surface

real ( kind = 8 ), dimension(:,:), pointer mod_protein::protein::p_list_atom_surface

p_pos_charge

real ( kind = 8 ), dimension(:,:), pointer mod_protein::protein::p_pos_charge

pointers to the movable arrays if there is no local copy, they point to sogrid arrays
if there is a local copy needed, they allocate their own arrays

p_pos_lenjones

type ( type_ljgrid ), pointer mod_protein::protein::p_pos_lenjones

pointer to movable arrays for lennard-jones, contains all grids and position

p_pos_rcriteria

real ( kind = 4 ), dimension(:,:), pointer mod_protein::protein::p_pos_rcriteria

p_sogrid

type ( sogrid ), pointer mod_protein::protein::p_sogrid

pointer to the associated set of grid (sogrid)

p_which_atom_surface

integer, dimension(:), pointer mod_protein::protein::p_which_atom_surface

one-dimensional array listing the atoms which are on the surface (order as in the orig.PDB file)

position

real ( kind=8 ), dimension(3) mod_protein::protein::position

real position for sdamm, relative position for sda_2proteins

real_net_charge

real ( kind=8 ) mod_protein::protein::real_net_charge

Local copy of real net charge (total charge)

rotate

logical mod_protein::protein::rotate

size_metal

integer mod_protein::protein::size_metal

surface

logical mod_protein::protein::surface

General variable of the properties of the solute.

surface_charge_dens

real ( kind=8 ) mod_protein::protein::surface_charge_dens

vert_excl

logical mod_protein::protein::vert_excl

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

• mod_protein.f90