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 |
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.
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 ) |
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 | ||
) |
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
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
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
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 ) |
integer, parameter mod_sda_input::maxconf =200 |
integer, parameter mod_sda_input::maxgrid =5 |