SDA  7.1
Simulation of Diffusional Association
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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
 
real(kind=8), dimension(3) center_protein
 center of geometry from the pdb file
 
integer id
 may be used by mod_record, keep it
 
type(sogrid), pointer p_sogrid
 pointer to the associated set of grid (sogrid)
 
type(flexible), pointer p_flex
 pointer to a flexible, only one of these two pointers should be initalized
 
logical local_copy
 If a local copy of the movable atoms is needed.
 
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)
 
type(type_ljgrid), pointer p_pos_lenjones
 pointer to movable arrays for lennard-jones, contains all grids and position
 
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
 
real(kind=8) diff_rotat
 
logical surface
 General variable of the properties of the solute.
 
logical iflex
 
logical rotate
 
logical iimg_chg
 
integer nb_charge
 In case of local copy, size of the arrays.
 
integer nb_atom_surface
 
integer nb_rcriteria
 
logical imetaldesolv
 Parameter specific to metaldesolvation, grid owned by each protein.
 
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

 
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 :

Member Data Documentation

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

keep trace of the box position, needed for sdamm

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


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