Configuration

The following tables list the available parameters with the corresponding sections. In order to change default parameters, the tool can accept a configuration file with the -c option in the Command Line Interface. This configuration file should follow the INI format. The default file can be downloaded here.

Note

There is no need to give all the parameters in a configuration file. If a field is not in the file, the CLI will take the value in the default file.

Example:

[section]
; comment
parameter: value

main

contactdef

Contact definition section used to define maplot from pdb file. More specific contact definitions can be added by following atomname_atomname syntax (e.g. ca_ca, cb_cb, …) or sc_sc if we want to use a single treshold for side chain contacts defined in scsc_min_file.

Name Type Default Description
default_cutoff float 8.0 Default cutoff used for all type of contact. Decrease this threshold if using other cutoff (e.g. 5.0)
atm1_atm2 (ca_ca, cb_cb, …) float None Specific treshold for a contact defined between atoms of two residues
sc_sc float None Default side chain atom treshold

setup

All the configuration parameters related to the setup command.

Name Type Default Description
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  

maplot

Name Type Default Description
n_factors list of float 0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.5,2.0 Number of EC tested: n * n_factor (n: sequence length)
save_fig bool True  
heatmap_linewidths float 0.0  
size_fig int 10  
plot_ext {} pdf  
plot_dpi int 200  
alpha float 1.0  

bbconv

Name Type Default Description
couplingmatrix      
start      
end      
outputprefix      
PSIPREDfile      
diversityvalue      
L      

pdbqual

Name Type Default Description
trash_directory path /tmp  
prosa bool False  
skip_prefix str fitted  
csh_executable path    

pdbdist

Name Type Default Description
contact_cutoff float 4.5 Cutoff used to search neighbor atoms
dssp_exec path /c6/shared/bin/dssp Path of DSSP executable
download_pdbs bool True  
obsolete_directory path /tmp/obsolete  
remove_pdbs bool False  
pair_list {} min  

pdbstat

Name Type Default Description
mode {simple} simple Extract minimal distance, mean of minimal mode, maximal distance from distance distribution to define bounds in serialized dictionaries
groups {ss,res,atm} ss+atm+res Group levels in serialized dictionaries
sample_minsize int 20  

analysis

Name Type Default Description
atmask {CA, CB} CA  
violation_treshold float 0.5  
nbest_structures int 15  
sort_criterion {} total_energy