aria_ec.ini 8.88 KB
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[main]
; ------------------------- Main parameters ---------------------------------- #
; Leave these fields empty in order to use default files
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; ariaproject_template          : Since there is several differences between
;                                 aria version in template tags, this package
;                                 can switch between 2 version actually: 2.3.0
;                                 with ramachandran potential tag and 2.3.2 with
;                                 exponent tag
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ss_dist_file:
scsc_min_file:
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ariaproject_template:                       2.3.0
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[contactdef]
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; Contact definition section used to define contactmap from pdb file.
; Decrease this threshold if using other cutoff (ca_ca, ...)
default_cutoff:                             8.0
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; Add contact cutoff folowwing the syntax atm1_atm2
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;ca_ca:                                      7.0
;cb_cb:                                      7.0
;sc_sc:                                      5.0
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[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
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; pair_list                     : all, heavy, min [min]; use all atom pairs,
;                                 heavy atms or minimized list
;                                 (CA-CA, CB-CB, SC-SC)
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; 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
distance_type:                              fixed
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groupby_method:                             min
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; Parameters below used only when distance_type is set to "fixed"
restraint_distance:                         2.5
lower_bound:                                1.0
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def_upper_bound:                            5.0
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; Specific tresholds only for unambig restraints
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ca_upper_bound:                             7.0
cb_upper_bound:                             7.0
; ---------------------------- Filter parameters ----------------------------- #
; n_factor      : Number of EC selected: n * n_factor (n: sequence length)
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; contactfilter : all or combinaison of pos, cons, cys, ssclash
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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:                              all
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conservation_treshold:                      95
position_treshold:                          5
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; nd_beta       : eigenvalue scaling parameter for network deconvolution.
;                 Corresponding to propagation of indirect effects over
;                 longer indirect paths.
; nd_alpha      : Network density parameter corresponding to the use of the
;                 full mutual information and direct information matrices
net_deconv:                                 False
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nd_beta:                                    0.99
nd_alpha:                                   1.0
; --------------------------- ARIA XML parameters ---------------------------- #
runid:                                      1
cpus:                                       100
host_command:                               sbatch --cores-per-socket=10 -o /baycells/home/fallain/slurm.errors
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host_executable:                            /baycells/home/bardiaux/bin/cns1.21_aria_logn_linux_x86_64_intel.exe
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temp_root:                                  data/examples/out/setup
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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
water_refinement_solvent:                   water
water_refinement_n_structures:              10
water_refinement_enabled:                   no
water_refinement_write_solvent_molecules:   no
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procheck_executable:
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procheck_enabled:                           yes
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prosa_executable:
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prosa_enabled:                              yes
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whatif_executable:
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whatif_enabled:                             yes
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clashlist_executable:
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clahlist_enabled:                           no
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pickle_output:                              no
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; --------------------------- Iteration parameters --------------------------- #
; /!\ Parameters below can be formatted as a list if we want different values
; foreach iteration. Actually, only  parameters can be set with different
; values for each iterations (violation tolerance and partial assignment weight
; treshold)
iterations:                                 8
iteration_n_structures:                     100
iteration_sort_criterion:                   total_energy
iteration_n_best_structures:                15
iteration_n_kept_structures:                0
merging_method:                             standard
calib_relaxation_matrix:                    no
calib_distance_cutoff:                      6.0
calib_estimator:                            ratio_of_averages
calib_error_estimator:                      distance
viol_violation_tolerance:                   1000.0,5.0,3.0,1.0,1.0,1.0,0.1,0.1,0.1
viol_violation_threshold:                   0.5
partassign_weight_threshold:                1.0,0.9999,0.999,0.99,0.98,0.96,0.93,0.9,0.8
partassign_max_contributions:               1000
partassign_exponent:                        6
netanch_high_residue_threshold:             4.0
netanch_enabled:                            no
netanch_min_residue_threshold:              1.0
netanch_min_atom_threshold:                 0.25
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[contactmap]
; -------------------------- Contactmap parameters --------------------------- #
; Plot settings
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save_fig:                                   True
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size_fig:                                   10
plot_ext:                                   pdf
plot_dpi:                                   200
alpha:                                      1.0

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