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