SDA
7.1
Simulation of Diffusional Association
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- a -
alloc_which_at_surf :
mod_setofgrid::sogrid
array :
mod_array_protein::array_protein_type
array_boot_fpt :
mod_rate_calculation::association_rate
array_bootstrap :
mod_rate_calculation::association_rate
array_bootstrap_real :
mod_rate_calculation::association_rate
array_grid_calc :
mod_force_energy::type_force_energy
array_img_chg :
mod_force_energy::type_force_energy
array_ljgrid :
mod_ljgrid::type_ljgrid
array_mfpt :
mod_rate_calculation::association_rate
array_position_atom_lj :
mod_ljgrid::type_ljgrid
array_prot_type :
mod_force_energy::type_force_energy
array_trajectory :
mod_record::trajectory
atom_nb1 :
mod_reactioncriteria::react_criter
- b -
beta :
mod_rate_calculation::association_rate
bit_energy :
mod_record::record
bool_par :
mod_type_calc::type_calculation
bootstrap :
mod_rate_calculation::association_rate
box :
mod_onecomplexe::one_complexe
,
mod_protein::protein
brate :
mod_rate_calculation::association_rate
- c -
c :
mod_input_parameter::param_list
c_surface :
mod_geometry::sphere
center_protein :
mod_protein::protein
charge_grid :
mod_setofgrid::sogrid
clock_max :
alltimer::mytimer
computation :
mod_input_parameter::param_list
counter :
alltimer::mytimer
couple_eldes :
mod_force_energy::type_force_energy
cpu_start :
alltimer::mytimer
current_conf :
mod_flexibility::flexible
cut2_array :
mod_setofgrid::sogrid
- d -
delta_clock :
alltimer::mytimer
delta_cpu :
alltimer::mytimer
dependent_pairs :
mod_reactioncriteria::react_criter
description_column_str :
mod_record::record
diff_trans :
mod_protein::protein
diffusion_trans :
mod_setofgrid::sogrid
dind :
mod_reactioncriteria::react_criter
dist_rc :
mod_reactioncriteria::react_criter
distance_max :
mod_flexibility::list_flex_type
docking :
mod_reactioncriteria
dseed :
mod_input_parameter::param_list
dt1 :
com_sda::parameter_timestep
dt2f :
com_sda::parameter_timestep
- e -
ener_colnames :
mod_record
enum_grid_force_calc :
mod_gridtype
enum_rt :
mod_residencetime::residence_time
enum_sphere :
mod_geometry
enum_type_calc :
mod_type_calc::type_calculation
epfct :
mod_input_parameter::param_list
epsilon_scale :
mod_force_energy::type_force_energy
escape :
mod_geometry::geometry
escape_prob :
mod_rate_calculation::association_rate
- f -
factor :
mod_grid::type_grid
fast_computation :
mod_force_energy::type_force_energy
first_window :
mod_rate_calculation::association_rate
fixe_bin_size :
mod_input_parameter::param_list
fixed_bin_size :
mod_residencetime::residence_time
flex_intern :
mod_flexibility
flex_random :
mod_flexibility
format_ascii :
mod_record::record
format_boot :
mod_rate_calculation::association_rate
format_header_ascii :
mod_record::record
format_resid3d :
mod_residencetime::residence_time
format_string_ascii :
mod_record::record
frequence :
mod_flexibility::list_flex_type
- g -
grid_type :
mod_grid::type_grid
- h -
h :
mod_grid::type_grid
header_str :
mod_record::record
hexcl :
mod_setofgrid::sogrid
hpin :
mod_grid::type_grid
- i -
ianalytic :
mod_force_energy::type_force_energy
ibox :
mod_onecomplexe::one_complexe
id :
mod_protein::protein
idebye :
mod_setofgrid::sogrid
iform :
mod_grid::type_grid
imetaldesolv :
mod_force_energy::type_force_energy
,
mod_input_parameter::param_list
,
mod_protein::protein
implicit :
mod_flexibility::list_flex_type
ind_pairs :
mod_reactioncriteria::react_criter
indice_ntraj :
mod_record::record
inputf :
com_sda
int_ocompl :
mod_onecomplexe::one_complexe
intern :
mod_record
io_bootstp :
mod_rate_calculation::association_rate
io_compl :
mod_record::record
ionic :
mod_input_parameter::param_list
ipmf :
mod_input_parameter::param_list
is_logical :
mod_grid::type_grid
itimestep :
mod_input_parameter::param_list
- k -
ki :
mod_analytic::analytic
- l -
last_version_rec :
mod_record
list_atom_surface :
mod_setofgrid::sogrid
list_conf_fname :
mod_flexibility::list_flex_type
local_copy :
mod_protein::protein
- m -
max_cut2 :
mod_setofgrid::sogrid
max_fields :
mod_record::record
max_nb_integer_bit :
com_sda
max_size_movable_charge :
mod_flexibility::list_flex_type
method_flex :
mod_flexibility::list_flex_type
- n -
nb_charge :
mod_protein::protein
nb_complexe :
mod_record::listcomplexe
nb_grid :
mod_force_energy::type_force_energy
nb_grids :
mod_array_protein::array_protein_type
nb_int :
mod_record::record
nb_ljgrid :
mod_ljgrid::type_ljgrid
nb_max_complexe :
mod_record::record
nb_pos_atom :
mod_ljgrid::type_position_atom
nb_window :
mod_rate_calculation::association_rate
nbbin :
mod_analytic::analytic
nbtypes :
mod_analytic::analytic
nnons_min :
mod_reactioncriteria::react_criter
npx :
mod_grid::type_grid
nspec :
mod_reactioncriteria::react_criter
- o -
one_run :
mod_record::listcomplexe
optimize_exit :
com_sda::parameter_timestep
orientation_x :
mod_protein::protein
origin :
mod_grid::type_grid
other_real_ocompl :
mod_onecomplexe::one_complexe
- p -
p_assoc_rate :
mod_reactioncriteria::react_criter
p_current :
mod_record::listcomplexe
p_current_node :
mod_flexibility::flexible
p_data :
mod_record::nodecomplexe
p_excl_grid :
mod_setofgrid::sogrid
p_first :
mod_flexibility::list_flex_type
,
mod_record::listcomplexe
p_flex :
mod_protein::protein
p_grid :
mod_grid::type_grid
p_ljgrid :
mod_setofgrid::sogrid
p_next :
mod_record::nodecomplexe
p_onecompl :
mod_record::record
p_pos_charge :
mod_protein::protein
p_pos_lenjones :
mod_protein::protein
p_position_atom :
mod_ljgrid::type_position_atom
p_previous :
mod_record::nodecomplexe
p_sogrid :
mod_protein::protein
p_which_atom_surface :
mod_protein::protein
pair_proteins :
mod_residencetime::residence_time
parray_nrj :
mod_analytic::analytic
pbox :
mod_geometry::geometry
pcomplexe :
mod_record::record
pdb_filename :
mod_input_parameter::param_list
pgrid :
mod_exclusion_grid::type_grid_excl
plist_flex :
mod_flexibility::flexible
pos_atom1 :
mod_reactioncriteria::react_criter
position :
mod_onecomplexe::one_complexe
,
mod_protein::protein
position_charge :
mod_setofgrid::sogrid
pset_analytic_grid :
mod_setofgrid::sogrid
pset_grid :
mod_setofgrid::sogrid
pshere :
mod_geometry::geometry
ptab_prot :
mod_record::record
ptrajectory :
mod_record::record
- r -
rcnst :
com_sda
rdf :
mod_residencetime::residence_time
reaction_criteria_pos :
mod_setofgrid::sogrid
real_ocompl :
mod_onecomplexe::one_complexe
record_type_calc :
mod_record::record
resid_3d :
mod_residencetime::residence_time
resid_dist :
mod_residencetime::residence_time
resid_plan :
mod_residencetime::residence_time
restart_filename :
mod_input_parameter::param_list
rmsd_min :
mod_input_parameter::param_list
rxna12f :
mod_input_parameter::param_list
- s -
scfct :
mod_grid::type_grid
sda_2proteins :
mod_type_calc
set_of_protein :
mod_array_protein::array_protein_type
size_array :
mod_record::trajectory
size_x :
mod_grid::type_grid
sizebox :
mod_geometry::box
start_position :
mod_geometry::geometry
state :
mod_record::nodecomplexe
stoke_radius :
mod_analytic::analytic
,
mod_setofgrid::sogrid
sum_square_energy :
mod_onecomplexe::one_complexe
sumtime :
mod_rate_calculation::association_rate
surface :
mod_protein::protein
surface_id :
mod_force_energy::type_force_energy
symetric :
mod_force_energy
- t -
t_calc :
mod_input_parameter::param_list
time_next_flex :
mod_flexibility::flexible
total_conf :
mod_flexibility::list_flex_type
,
mod_input_parameter::param_list
trajectory_enum :
mod_record
transform_escape :
mod_rate_calculation::association_rate
type :
mod_analytic::analytic
,
mod_geometry::geometry
type_calc_str :
mod_type_calc::type_calculation
type_reaction :
mod_reactioncriteria::react_criter
type_record :
mod_record::record
- v -
variable :
com_sda::parameter_timestep
version :
mod_record::record
version_number :
mod_record::record
visited_conf :
mod_flexibility::flexible
- w -
which_atom_surface :
mod_setofgrid::sogrid
win0 :
mod_input_parameter::param_list
window :
mod_rate_calculation::association_rate
- x -
x_min :
mod_geometry::box
x_origin :
mod_residencetime::residence_time
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