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SDA (SDA flex)
7.2
Simulation of Diffusional Association
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SDA (SDA flex)
7.2
Simulation of Diffusional Association
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Data Types | |
| type | mod_grid::type_uhbd_grid |
| type | mod_grid::type_dtgrid |
| type | mod_grid::type_grid |
| Contains all data related to grid. More... | |
Modules | |
| module | mod_grid |
| Module for dealing with 3 dimensional grids. | |
Functions/Subroutines | |
| subroutine | mod_grid::allocate_grid (this, xmax, ymax, zmax, opt_logical) |
| Allocate grid. More... | |
| subroutine | mod_grid::allocate_grid_uhbd (this, xmax, ymax, zmax, be_logical) |
| Allocate the 3d imensional uhbd grid. More... | |
| subroutine | mod_grid::allocate_dtgrid (this, filename, scfct, be_logical) |
| subroutine | mod_grid::delete_grid (this) |
| Delete the grid. More... | |
| subroutine | mod_grid::delete_uhbd_grid (this) |
| Delete UHBD grid Called by delete_grid. More... | |
| subroutine | mod_grid::delete_dtgrid (this, be_logical) |
| logical function | mod_grid::is_associated (this) |
| function to test if the 3d grid is correctly initiliazed More... | |
| integer function | mod_grid::is_associated_int (this) |
| function to test the type of grid variant return type_of_grid More... | |
| subroutine | mod_grid::read_grid (this, filename, grid_type_opt, scfct_opt, read_header_only_opt, iform_opt) |
| Read grid file. More... | |
| real(kind=8) function | mod_grid::get_value_real_uhbd (this, i, j, k) |
| Test for uhbd and dtgrid. More... | |
| real(kind=8) function | mod_grid::get_value_dtgrid (this, i, j, k) |
| Get the value at a point of a dtgrid. More... | |
| logical function | mod_grid::get_value_exclusion_dtgrid (this, i, j, k) |
| subroutine | mod_grid::get_voxel_dtgrid (this, i, j, k, voxel) |
| real(kind=8) function | mod_grid::get_value (this, i, j, k) |
| Test function. More... | |
| subroutine | mod_grid::copy_grid (this, outgrid, opt_form) |
| Copy a grid. More... | |
| subroutine | mod_grid::grid_scale (this, scaling) |
| Multiply all grid points by a scaling factor. More... | |
| subroutine | mod_grid::exclude (this, exclud_grid) |
| Exclude potential interior of grid solute. More... | |
| subroutine | mod_grid::make_sphere (this) |
| Set to 0. all points further than a cutoff. The cutoff is the maximum shpere we can include inside the cube. More... | |
| subroutine | mod_grid::set_grid_zero (this) |
| subroutine | mod_grid::test_format_grid (this, io_unit) |
| Error in make ep_grid, grdflag is a good variable for binary or ascii, but works only if created by module no rules for uhbd ( 1 ) or apbs ( -1 ) use title of electrostatic grid to decide by default in sda, force to read in binary, can be changed now. More... | |
| subroutine | mod_grid::read_header_grid (this, io_unit, status) |
| Read header of the file. More... | |
| subroutine | mod_grid::write_grid (this, filename, opt_modif_name, opt_pgrid4) |
| Write a grid to a file. More... | |
| subroutine | mod_grid::write_uhbd_grid (this, base, filename, opt_pgrid4) |
| Write UHBD grid to a file Called by write_grid. More... | |
| subroutine | mod_grid::read_excl_grid (this, filename, prot_cm, param_probe, status) |
| Specific function for reading an exclusion grid. More... | |
| subroutine | mod_grid::write_excl_grid (this, filename, prot_cm, param_probe) |
| Write exclusion grid. More... | |
| subroutine | mod_grid::write_grid_dx (this, filename, opt_modif_name) |
| Write grid to dx format. More... | |
| subroutine | mod_grid::print_grid (this, io_unit) |
| Print information about the grid into a log file. More... | |
| integer function | mod_grid::get_gridtype (this) |
| Return the grid type as defined in mod_gridtype. More... | |
| subroutine | mod_grid::shift_origin (this, center) |
| Shift the origin of the grid to the given position. More... | |
| subroutine | mod_grid::print_origin (this) |
| Print origin, for debug. More... | |
| subroutine | mod_grid::info_grid (this) |
| Print information about the grid, may extend. More... | |
Variables | |
| integer, parameter | mod_grid::enum_uhbd = 1 |
| integer, parameter | mod_grid::enum_dtgrid = 2 |
Copyright (c) 2009, 2010, 2015, 2016, 2019 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany
Please send your contact address to get information on updates and new features to "mcmsoft@h-its.org". Questions will be answered as soon as possible.
References: see also http://mcm.h-its.org/sda7/do:c/doc_sda7/references.html:
Brownian dynamics simulation of protein-protein diffusional encounter. (1998) Methods, 14, 329-341.
SDA 7: A modular and parallel implementation of the simulation of diffusional association software. Journal of computational chemistry 36.21 (2015): 1631-1645.
Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, X. Yu, M. Ozboyaci, M. Reinhardt, P. Friedrich, R.R.Gabdoulline, S.Richter and R.C.Wade
Define 3D UHBD
1.9.1
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