aria_ec.ini 6.95 KB
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[main]
; ------------------------- Main parameters ---------------------------------- #
; Leave these fields empty in order to use default files
ss_dist_file:
scsc_min_file:
ariaproject_template:

[contactdef]
; Contact definition section used to define contactmap from pdb file
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default_cutoff:                             7.0
ca_ca:                                      7.0
cb_cb:                                      7.0
sc_sc:                                      5.0
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; Add other contact cutoff below folowwing the syntax atm1_atm2

[setup]
; ------------------------------ TBL parameters ------------------------------ #
; longrange_hb                  : True, False [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               : N hbond generated = nf * seq length
; longrange_hbtype              : main, all; Consider short range hbond only
;                                 as main chain hydrogen bond or for all
;                                 donor/acceptor
; hb_dminus/dplus               : distance bounds in tbl restraints
longrange_hb:                               False
nf_longrange_hb:                            0.1
longrange_hbtype:                           main
hb_dminus:                                  0.0
hb_dplus:                                   0.5
; --------------------------- Contacts parameters ---------------------------- #
; evfold_weight                 : use EVFold weight -> 10/i (i:contact rank)
; neighborhood_contact          : add neighbors when writing restraint
; pair_list                     : all, min [min]; use all atom pairs or
;                                 minimized list (CA-CA, CB-CB, SC-SC)
; ambiguous_distance_restraint  : use Ambiguous Distance Restraints
; ambiguous_distance_type       : min, deff [min]; compute Deff from target
;                                 distance iif ADR
; distance_type                 : fixed, pdbstat, distfile [fixed]; fixed use
;                                 ca, cb and sc upper_bound
evfold_weight:                              False
neighborhood_contact:                       False
pair_list:                                  min
ambiguous_distance_restraint:               False
ambiguous_distance_type:                    min
deffpow:                                    6
; TODO: move groupby_method to contactdef section
groupby_method:                             min
distance_type:                              fixed
; TODO: move parameters below to contactdef section
; Parameters below used only when distance_type is set to "fixed"
restraint_distance:                         2.5
lower_bound:                                1.0
def_upper_bound:                            4.0
ca_upper_bound:                             7.0
cb_upper_bound:                             7.0
; ---------------------------- Filter parameters ----------------------------- #
; n_factor      : Number of EC selected: n * n_factor (n: sequence length)
; contactfilter : all or combinaison of pos, cons, cys, ssclash, nd
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;                 separated by "+" character [pos]. If empty, use only position
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;                 filter (avoid short range restraints)
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n_factor:                                   1.0
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contactfilter:                              pos
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conservation_treshold:                      95
position_treshold:                          5
nd_beta:                                    0.99
nd_alpha:                                   1.0
nd_control:                                 0
; --------------------------- ARIA XML parameters ---------------------------- #
runid:                                      1
cpus:                                       100
host_command:                               sbatch --cores-per-socket=10 -o /baycells/home/fallain/slurm.errors
working_directory:                          data/examples/out/aria_wd
temp_root:                                  data/examples/out/aria_tmp
parameter_definition:                       automatic
ss_dist_format:                             tbl
ss_dist_enabled:                            yes
ss_dist_add_to_network:                     no
ss_dist_calibrate:                          no
ss_dist_run_network_anchoring:              no
ss_dist_filter_contributions:               no
dist_format:                                xml
dist_enabled:                               yes
dist_add_to_network:                        no
dist_calibrate:                             no
dist_run_network_anchoring:                 no
dist_filter_contributions:                  yes
cns_executable:                             /Bis/home/bardiaux/bin/cns1.21.exe
cns_keep_output:                            no
unambiguous_restraints_k_cool1_initial:     10.0
unambiguous_restraints_k_cool1_final:       50.0
unambiguous_restraints_k_cool2:             50.0
hbond_restraints_k_cool1_initial:           10.0
hbond_restraints_k_cool1_final:             50.0
hbond_restraints_k_cool2:                   50.0
dihedral_restraints_k_cool1:                25.0
dihedral_restraints_k_cool2:                200.0
logharmonic_potential_enabled:              no
logharmonic_potential_use_auto_weight:      no
logharmonic_potential_weight_unambig:       25.0
logharmonic_potential_weight_ambig:         10.0
logharmonic_potential_weight_hbond:         25.0
rama_potential_enabled:                     no
md_parameters_random_seed:                  89764443
md_parameters_steps_high:                   10000
md_parameters_steps_cool1:                  5000
md_parameters_steps_cool2:                  4000
iteration_n_structures:                     100
iteration_n_best_structures:                15
iteration_n_kept_structures:                0
merging_method:                                standard
violation_analysis_violation_threshold:     0.5
water_refinement_solvent:                   water
water_refinement_n_structures:              10
water_refinement_enabled:                   no
water_refinement_write_solvent_molecules:   no
procheck_executable:                        procheck
prosa_executable:                           prosa
whatif_executable:                          whatif

[contactmap]
; -------------------------- Contactmap parameters --------------------------- #
; Plot settings
n_factor:                                   1.5
groupby_method:                             min
save_fig:                                   True
size_fig:                                   10
plot_ext:                                   pdf
plot_dpi:                                   200
alpha:                                      1.0

[bbconv]
; -------------------------- bbconverter parameters -------------------------- #
couplingmatrix:
start:
end:
outputprefix:
PSIPREDfile:
diversityvalue:
L: