SDA (SDA flex)  7.2
Simulation of Diffusional Association
Functions/Subroutines | Variables
mod_sda_input Module Reference

Functions/Subroutines

subroutine read_input_sda (tab_prot, filename, tmp_p_list, all_filename_pdb, iflex, iload_pdb, extend_array, opt_all_prot)
 Function for reading the sda input file. More...
 
subroutine load_pdb (psgrid, filename, opt_center_prot, opt_van, opt_return_center)
 
subroutine load_all_pdbs (tab_prot, filename, nb_prot_group, onedim_filename_pdb, total_conf, extend_array)
 Laod all pdbs in case of flexibility, save with the intermediate of tab_prot and flexibility. More...
 
subroutine read_listconf_pdb (prot, filename, onedim_filename_pdb, total_conf, bool_extend)
 Read the list of conformations if flexible. More...
 

Variables

integer, parameter maxconf =200
 
integer, parameter maxgrid =5
 

Function/Subroutine Documentation

◆ load_all_pdbs()

subroutine mod_sda_input::load_all_pdbs ( type ( array_protein_type tab_prot,
character*64  filename,
integer  nb_prot_group,
character*64, dimension ( maxconf onedim_filename_pdb,
integer  total_conf,
logical  extend_array 
)

Laod all pdbs in case of flexibility, save with the intermediate of tab_prot and flexibility.

Parameters
tab_prot: instance of array_protein_type
filename: name of the listconformation file
nb_prot_group: number of group of solutes
onedim_filename_pdb:
total_conf: number of conformation
extend_array: if the array for the pdb need to be extended ( to a maximum size, case of flexibility )
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◆ load_pdb()

subroutine mod_sda_input::load_pdb ( type ( sogrid ), pointer  psgrid,
character*64  filename,
logical, optional  opt_center_prot,
real ( kind= 8 ), dimension ( : ), optional, allocatable  opt_van,
real ( kind= 8 ), dimension ( 3 ), optional  opt_return_center 
)
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◆ read_input_sda()

subroutine mod_sda_input::read_input_sda ( type ( array_protein_type tab_prot,
character*64  filename,
type ( param_list tmp_p_list,
character*64, dimension(:,:), allocatable  all_filename_pdb,
logical  iflex,
logical  iload_pdb,
logical  extend_array,
logical, optional  opt_all_prot 
)

Function for reading the sda input file.

Can read any parameters ( just need to extend ). Always read Type_Calculation, and create the array_protein. Can load pdb files if load_pdb is True

Parameters
tab_prot: instance of array_protein_type
filename: name of the sda input file
tmp_p_list: define all parameters in param_list
all_filename_pdb: to store all pdb filenames
iflex: if some solutes are flexible
iload_pdb: if the pdb need to be loaded
extend_array: if the array for the pdb need to be extended ( to a maximum size, case of flexibility )
opt_all_prot: boolean, whether to read all molecule types or not in sda_2protein mode - default: false

use general parameters, same as sda

allocate array

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◆ read_listconf_pdb()

subroutine mod_sda_input::read_listconf_pdb ( type ( protein prot,
character*64  filename,
character*64, dimension ( maxconf onedim_filename_pdb,
integer  total_conf,
logical  bool_extend 
)

Read the list of conformations if flexible.

particular version for this tool. may merged to common module

Parameters
prot: instance of protein
filename: name of the list of conformations
onedim_filename_pdb: will store the pdb names
total_conf: will store the number of conformations
bool_extend: if the arrays must be extended to all have the same size ( dcd format )
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Variable Documentation

◆ maxconf

integer, parameter mod_sda_input::maxconf =200

◆ maxgrid

integer, parameter mod_sda_input::maxgrid =5
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