longrange_hb |
bool |
False |
use long range hbond restraints. If there is no hbond map given, use the naive method from METAPSICOV (Take the top nf_longrange_hb * seq length predicted contacts from the contactlist and set those who are in a beta sheet as hb |
nf_longrange_hb |
float |
0.1 |
Number hbond generated = nf * seq length |
longrange_hbtype |
{main, all} |
main |
Consider short range hbond only as main chain hydrogen bond or for all donor/acceptor |
hb_dminus |
float |
0.0 |
distance lower bound in tbl hbond restraints |
hb_dplus |
float |
0.5 |
distance upper bound in tbl hbond restraints |
native_reliable |
bool |
False |
Define native contact map as reliable in aria iterative protocol. Those contacts will not be filtered |
evfold_weight |
bool |
False |
use EVFold weight -> 10/i (i:contact rank) for contact map derived distance restraints in aria protocol |
neighborhood_contact |
bool |
False |
Generate restraints for neighbors foreach contact in the contact map |
atom_groups |
{all, heavy, min} |
min |
use all, heavy atms or from a minimizedlist (CA, CB, SC) for contribution list for each distance restraint |
contributions_type |
{same, allvsall, onevsall} |
same |
By default contributions list will be a simple list between atoms of the same type (CA-CA, CB-CB, …). Otherwise, compute pairwise product between contribution lists of the 2 residues (onevsall and allvsall). In the case of ADR, onevsall will generate one ADR for all contribution pairs between an atom of the first residue against all the other atoms in the second residue. |
distance_type |
{fixed, pdbstat, distfile} |
fixed |
Define distance use for target distance. By default the target distance is fixed by parameters listed below. Otherwise a distance map derived from pdb distance distribution or given by the user can be used. |
groupby_method |
{mean, min, deff} |
min |
If a distance map is used for setting distance target, define if we use min, mean or deff distance on all the possible values. |
deffpow |
int |
6 |
|
pdbdistance_level |
{ss, res} |
ss |
|
ambiguous_distance_restraint |
bool |
False |
Generate Ambiguous Distance Restraints. Otherwise, each distance restraints will have only one contribution (unambiguous distance restraints) |
restraint_distance |
float |
2.5 |
|
lower_bound |
float |
1.0 |
|
def_upper_bound |
float |
5.0 |
|
ca_upper_bound |
float |
7.0 |
|
cb_upper_bound |
float |
7.0 |
|
n_factor |
float |
1.0 |
Factor used for selection of contacts according to their score (n * factor with n as sequence length) |
contactfilter |
all or combination of pos, cons, cys, ssclash separated by + character |
all |
If empty, use only position filter (avoid short range restraints) |
conservation_treshold |
int |
95 |
Remove contact with highly conservated residues |
position_treshold |
int |
5 |
Remove short range contacts |
seed |
int |
89764443 |
If no scoremap to select top n contacts, choose a subset with random.sample method. For reproductibility, the seed used for the sampling is provided here |
net_deconv |
bool |
False |
use network deconvolution to filter contact map |
nd_beta |
float |
0.99 |
eigenvalue scaling parameter for network deconvolution. Corresponding to propagation of indirect effects over longer indirect paths. |
nd_alpha |
float |
1.0 |
Network density parameter corresponding to the use of the full mutual information and direct information matrices |
runid |
int |
1 |
|
cpus |
int |
100 |
|
host_command |
str |
“sbatch -t 02:00:00” |
|
host_executable |
path |
|
|
temp_root |
path |
examples/tmp |
|
parameter_definition |
{} |
automatic |
|
ss_dist_format |
{} |
tbl |
|
ss_dist_enabled |
{yes, no} |
yes |
|
ss_dist_add_to_network |
{yes, no} |
no |
|
ss_dist_calibrate |
{yes, no} |
no |
|
ss_dist_run_network_anchoring |
{yes, no} |
no |
|
ss_dist_filter_contributions |
{yes, no} |
no |
|
dist_format |
{} |
xml |
|
dist_enabled |
{yes, no} |
yes |
|
dist_add_to_network |
{yes, no} |
no |
|
dist_calibrate |
{yes, no} |
no |
|
dist_run_network_anchoring |
{yes, no} |
no |
|
dist_filter_contributions |
{yes, no} |
yes |
|
dist_avg_exponent |
int |
6 |
|
cns_executable |
path |
|
|
cns_keep_output |
{yes, no} |
no |
|
unambiguous_restraints_k_cool1_initial |
float |
10.0 |
|
unambiguous_restraints_k_cool1_final |
float |
50.0 |
|
unambiguous_restraints_k_cool2 |
float |
50.0 |
|
hbond_restraints_k_cool1_initial |
float |
10.0 |
|
hbond_restraints_k_cool1_final |
float |
50.0 |
|
hbond_restraints_k_cool2 |
float |
50.0 |
|
dihedral_restraints_k_cool1 |
float |
25.0 |
|
dihedral_restraints_k_cool2 |
float |
200.0 |
|
logharmonic_potential_enabled |
{yes, no} |
no |
|
logharmonic_potential_use_auto_weight |
{yes, no} |
no |
|
logharmonic_potential_weight_unambig |
float |
25.0 |
|
logharmonic_potential_weight_ambig |
float |
10.0 |
|
logharmonic_potential_weight_hbond |
float |
25.0 |
|
rama_potential_enabled |
{yes, no} |
yes |
|
hbdb_potential_enabled |
{yes, no} |
no |
|
scoring_method |
{} |
standard |
|
md_parameters_random_seed |
int |
89764443 |
|
md_parameters_steps_high |
int |
10000 |
|
md_parameters_steps_cool1 |
int |
5000 |
|
md_parameters_steps_cool2 |
int |
4000 |
|
water_refinement_solvent |
{} |
water |
|
water_refinement_n_structures |
int |
10 |
|
water_refinement_enabled |
{yes, no} |
no |
|
water_refinement_write_solvent_molecules |
{yes, no} |
no |
|
procheck_executable |
path |
|
|
procheck_enabled |
{yes, no} |
yes |
|
prosa_executable |
path |
|
|
prosa_enabled |
{yes, no} |
yes |
|
whatif_executable |
path |
|
|
whatif_enabled |
{yes, no} |
yes |
|
clashlist_executable |
path |
|
|
clahlist_enabled |
{yes, no} |
no |
|
pickle_output |
{yes, no} |
no |
|
iterations |
int |
8 |
|
iteration_n_structures |
int |
100 |
|
iteration_sort_criterion |
{} |
total_energy |
|
iteration_n_best_structures |
int |
15 |
|
iteration_n_kept_structures |
int |
0 |
|
merging_method |
{} |
standard |
|
calib_relaxation_matrix |
{yes, no} |
no |
|
calib_distance_cutoff |
float |
6.0 |
|
calib_estimator |
{} |
ratio_of_averages |
|
calib_error_estimator |
{} |
distance |
|
viol_violation_tolerance |
list of float |
1000.0,5.0,3.0,1.0,1.0,1.0,0.1,0.1,0.1 |
|
viol_violation_threshold |
float |
0.5 |
|
viol_sigma_mode |
{} |
fix |
|
partassign_weight_threshold |
list of float |
1.0,0.9999,0.999,0.99,0.98,0.96,0.93,0.9,0.8 |
|
partassign_max_contributions |
int |
1000 |
|
partassign_exponent |
int |
6 |
|
netanch_high_residue_threshold |
float |
4.0 |
|
netanch_enabled |
{yes, no} |
no |
|
netanch_min_residue_threshold |
float |
1.0 |
|
netanch_min_atom_threshold |
float |
0.25 |
|
clustering_enabled |
{yes, no} |
no |
Clustering step group generated structures into clusters. Cluster ensemble with the lowest energy will then be selected at the end of each iteration |
clustering_mask |
{CA, CB} |
CA |
Atom coordinate mask |
clustering_nclusters |
int |
2 |
Number of clusters |
clustering_method |
{kmeans, hclust, hdbscan} |
kmeans |
|