diff --git a/README.md b/README.md
index 2db26663083bbfb852cba75674179bef801f85f1..0494e8eefb5e88c77f92f5e8e24a6714bb7dcb10 100644
--- a/README.md
+++ b/README.md
@@ -1,29 +1,446 @@
-# de Novo Ambiguous Restraints for Iterative Assignment
+# Description
-**A pipeline for automated de novo contact map assignment**
+ARIA version compatible with evolutionary restraints
-[](https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master)
-[](https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master)
-<!--[](https://doi.org/10.1093/bioinformatics/btl589)-->
+## Requirements
+Be sure to install these packages before running setup file
+* pip (>= 9.0)
+* setuptools (>= 18.0)
+* numpy (>= 1.11)
+* matplotlib
+* aria (>= 2.2)
-## Installation & usage
+## Installation
-Please refer to :
+```
+# Ariaec directory or in a virtualenv, call the following command:
+> pip install .
+```
-* [Main ARIA documentation](http://aria.pasteur.fr/documentation)
-* [NARIA documentation](http://bis-aria.pages.pasteur.fr/ariaec)
+# Command line
+The command line tool correspond to ariaec (or ec2aria for older versions)
+command in the terminal
+folder.
+```
+usage: ariaec [-h] -o OUTPUT_DIRECTORY [-c CONF_FILE] [--nolog] [-d]
+ {setup,bbconv,maplot,pdbqual,analysis,tbl2xml,pdbdist,pdbstat}
+ ...
+positional arguments:
+ {setup,bbconv,maplot,pdbqual,analysis,tbl2xml,pdbdist,pdbstat}
-## Contributing
+optional arguments:
+ -h, --help show this help message and exit
+ -o OUTPUT_DIRECTORY, --output OUTPUT_DIRECTORY
+ Output directory (default: None)
+ -c CONF_FILE, --conf CONF_FILE
+ configuration file (default: None)
+ --nolog Don't generate log files (default: False)
+ -d, --debug Increase output verbosity (default: False)
+```
-Please refer to the [guidelines for contributing](CONTRIBUTING.md) for any
-suggestions or bug report.
-<!--## Citation-->
+In order to change default parameters, the tool can accept a configuration file (.ini format). Default parameters are listed below:
-<!--If you use this software, please quote the following reference(s):-->
+```
+[main]
+; ------------------------- Main parameters ---------------------------------- #
+; Leave these fields empty in order to use default files
+; ariaproject_template : For backward compatibility with different
+; versions of ARIA since there is several
+; differences between aria templates.This package
+; can switch between 6 version actually:
+; - 2.3.0 with ramachandran potential tag
+; - 2.3.2 with exponent tag
+; - 2.3.3 with clustering tag
+; - 2.3.4 with scoring tag
+; - 2.3.5 with avg_exponent field in ambiguous
+; restraint tag
+; - 2.3.6 with method field in clustering tag
+ss_dist_file:
+scsc_min_file:
+interlowerbounds_pdbstat:
+intertarget_pdbstat:
+interupperbounds_pdbstat:
+intralowerbounds_pdbstat:
+intratarget_pdbstat:
+intraupperbounds_pdbstat:
+ariaproject_template: 2.3.6
+procheck_executable:
+prosa_executable:
+whatif_executable:
+clashlist_executable:
-<!--> Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,-->
-<!--Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR-->
-<!--structure calculation. Bioinformatics 23:381-382-->
\ No newline at end of file
+
+[contactdef]
+; Contact definition section used to define maplot from pdb file.
+; Decrease this threshold if using other cutoff (e.g. 5.0)
+default_cutoff: 8.0
+; Add contact cutoff folowwing the syntax atm1_atm2
+;ca_ca: 7.0
+;cb_cb: 7.0
+;sc_sc: 5.0
+
+[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 : 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/dplus : Float [0.0, 0.5]
+; distance bound in tbl restraints
+longrange_hb: False
+nf_longrange_hb: 0.1
+longrange_hbtype: main
+hb_dminus: 0.0
+hb_dplus: 0.5
+; ---------------------- Distance restraint parameters ----------------------- #
+; native_reliable : True, False [False]
+; Define native contact map as reliable in aria
+; iterative protocol. Those contacts will not be
+; filtered.
+; evfold_weight : True, False [False]
+; use EVFold weight -> 10/i (i:contact rank) for
+; contact map derived distance restraints in
+; aria protocol
+; neighborhood_contact : True, False [False]
+; Generate restraints for neighbors foreach
+; contact in the contact map
+; pair_list : all, heavy, min [min]
+; use all, heavy atms or from a minimized
+; list (CA, CB, SC) for contribution list for
+; each distance restraint
+; atoms_type : all, heavy, min [min]
+; use all, heavy atms or from a minimized
+; list (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
+; (not yet implemented) or given by the user can
+; be used.
+; pdbdistance_level : ss, res,
+; 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.
+; ambiguous_distance_restraint : True, False [False]
+; Generate Ambiguous Distance Restraints.
+; Otherwise, each distance restraints will have
+; only one contribution (unambiguous distance
+; restraints)
+native_reliable: False
+evfold_weight: False
+neighborhood_contact: False
+atoms_type: min
+contributions_type: same
+distance_type: fixed
+groupby_method: min
+deffpow: 6
+pdbdistance_level: ss
+ambiguous_distance_restraint: False
+; Parameters below used only when distance_type is set to "fixed"
+restraint_distance: 2.5
+lower_bound: 1.0
+def_upper_bound: 5.0
+; Specific tresholds only for unambig restraints
+ca_upper_bound: 7.0
+cb_upper_bound: 7.0
+; ---------------------------- Filter parameters ----------------------------- #
+; n_factor : float [1.0]
+; Factor used for selection of contacts according to their score
+; (n * n_factor with n as sequence length)
+; contactfilter : all or combination of pos, cons, cys, ssclash separated by "+"
+; character [pos]
+; If empty, use only position filter (avoid short range
+; restraints)
+n_factor: 1.0
+contactfilter: all
+; conservation_treshold : Float [95]
+; Remove contact with highly conservated residues
+; position_treshold : Int [5]
+; Remove short range contacts
+conservation_treshold: 95
+position_treshold: 5
+; seed : If no scoremap to select top n contacts, choose a subset wit
+; random.sample method. For reproductibility, the seed used for
+; the sampling is provided here
+seed: 89764443
+; net_deconv : use network deconvolution to filter contact map
+; 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
+nd_beta: 0.99
+nd_alpha: 1.0
+; --------------------------- ARIA XML parameters ---------------------------- #
+runid: 1
+cpus: 100
+host_command: "sbatch -t 02:00:00"
+host_executable: bin/cns1.21_aria_logn_linux_x86_64_intel.exe
+temp_root: examples/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
+dist_avg_exponent: 6
+cns_executable: 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: yes
+hbdb_potential_enabled: no
+scoring_method: standard
+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
+procheck_executable:
+procheck_enabled: yes
+prosa_executable:
+prosa_enabled: yes
+whatif_executable:
+whatif_enabled: yes
+clashlist_executable:
+clahlist_enabled: no
+pickle_output: no
+; --------------------------- Iteration parameters --------------------------- #
+; /!\ Parameters below can be formatted as a list if we want different values
+; foreach iteration. Actually, only 2 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
+viol_sigma_mode: fix
+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
+clustering_enabled: no
+clustering_mask: CA
+clustering_nclusters: 2
+clustering_method: kmeans
+
+[maplot]
+; -------------------------- Contactmap parameters --------------------------- #
+; Report settings
+; n_factors: Number of EC tested: n * n_factor (n: sequence length)
+n_factors: 0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.5,2.0
+; Plot settings
+save_fig: True
+heatmap_linewidths: 0.0
+size_fig: 10
+plot_ext: pdf
+plot_dpi: 200
+alpha: 1.0
+
+[bbconv]
+; -------------------------- bbconverter parameters -------------------------- #
+couplingmatrix:
+start:
+end:
+outputprefix:
+PSIPREDfile:
+diversityvalue:
+L:
+
+[pdbqual]
+trash_directory: /tmp
+prosa: False
+skip_prefix: fitted
+csh_executable: csh
+
+[pdbdist]
+; ----------------------- PDB distribution parameters ------------------------ #
+; contact_cutoff: float [4.5]
+; Cutoff used to search neighbor atoms
+; dssp_exec: path
+; Path of DSSP executable
+contact_cutoff: 4.5
+dssp_exec: /c6/shared/bin/dssp
+download_pdbs: True
+obsolete_directory: /tmp/obsolete
+remove_pdbs: False
+pair_list: min
+
+[pdbstat]
+; 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+res+atm]
+; Group levels in serialized dictionaries
+mode: simple
+groups: ss+atm+res
+sample_minsize: 20
+
+[analysis]
+atmask: CA
+violation_treshold: 0.5
+nbest_structures: 15
+sort_criterion: total_energy
+```
+
+
+## Setup
+Translate contact maps into distance restraints and setup ARIA infrastructure
+```
+usage: ariaec setup [-h] [-d DISTFILE] -t
+ {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}
+ [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
+ [-r REF] [--hb HB] [--ssidx] [--no-filter]
+ seq sspred infile [infile ...]
+
+optional arguments:
+ -h, --help show this help message and exit
+
+required arguments:
+ seq sequence file [FASTA]
+ sspred secondary structure prediction file
+ infile contact or pdb file(s) used to build aria distance
+ restraints
+ -d DISTFILE, --distfile DISTFILE
+ Pdb or distance matrix iif distance_type set to
+ distfile in conf file, use distances in the given file
+ as target distance to build distance restraints
+ -t {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...], --type {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
+ Infile(s) contact type(s)
+ -r REF, --ref REF Native pdb. Allow TP/FP detection.
+ --hb HB H-bonds contact file (eg: metapsicov.hb)
+ --ssidx Use secondary structure index
+ --no-filter Do not filter contact map.
+```
+
+## Contactmap
+Contactmap analysis and visualisation
+```
+usage: ariaec maplot [-h] -t
+ {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}
+ [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
+ [--merge {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]]
+ [--filter] [--onlyreport] [--ssidx]
+ [--prefix PREFIX [PREFIX ...]]
+ seq sspred infile [infile ...]
+
+positional arguments:
+ seq sequence file [FASTA]
+ sspred secondary structure prediction file
+ infile contact or pdb file(s) used to build aria distance
+ restraints
+
+optional arguments:
+ -h, --help show this help message and exit
+ -t {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...], --type {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
+ Infile(s) contact type(s)
+ --merge {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
+ Merge given contact types with other maps
+ --filter Use contact list filter and top n contacts selection
+ --onlyreport Generate only report file
+ --ssidx Use secondary structure index
+ --prefix PREFIX [PREFIX ...]
+ Contact map name
+
+```
+## Pdbqual
+Quality tool for pdb file(s)
+```
+usage: ariaec pdbqual [-h] infile [infile ...]
+
+positional arguments:
+ infile PDB file(s) used to run quality tools with aria API
+
+optional arguments:
+ -h, --help show this help message and exit
+```
+## Tbl2xml
+ARIA XML converter for tbl distance restraint
+```
+usage: ariaec tbl2xml [-h] molecule.xml list_name infile.tbl [infile.tbl ...]
+
+positional arguments:
+ molecule.xml ARIA XML molecule file
+ list_name Restraint list name in the tbl file
+ infile.tbl TBL distance restraint file(s)
+
+optional arguments:
+ -h, --help show this help message and exit
+
+```
+
+## Bbconv
+Convert contacts in bbcontact format
+```
+usage: ariaec bbconv [-h] -t
+ {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}
+ contactfile sspred seq [msa]
+
+positional arguments:
+ contactfile contacts file (pconsc, plm)
+ sspred psipred file
+ seq sequence file [FASTA]
+ msa MSA [FASTA] for diversityvalueused with bbcontacts
+
+optional arguments:
+ -h, --help show this help message and exit
+ -t {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}, --type {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}
+ Infile contact type
+
+```
diff --git a/README.new.md b/README.new.md
new file mode 100644
index 0000000000000000000000000000000000000000..2db26663083bbfb852cba75674179bef801f85f1
--- /dev/null
+++ b/README.new.md
@@ -0,0 +1,29 @@
+# de Novo Ambiguous Restraints for Iterative Assignment
+
+**A pipeline for automated de novo contact map assignment**
+
+[](https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master)
+[](https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master)
+<!--[](https://doi.org/10.1093/bioinformatics/btl589)-->
+
+
+## Installation & usage
+
+Please refer to :
+
+* [Main ARIA documentation](http://aria.pasteur.fr/documentation)
+* [NARIA documentation](http://bis-aria.pages.pasteur.fr/ariaec)
+
+
+## Contributing
+
+Please refer to the [guidelines for contributing](CONTRIBUTING.md) for any
+suggestions or bug report.
+
+<!--## Citation-->
+
+<!--If you use this software, please quote the following reference(s):-->
+
+<!--> Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,-->
+<!--Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR-->
+<!--structure calculation. Bioinformatics 23:381-382-->
\ No newline at end of file
diff --git a/README.old.md b/README.old.md
new file mode 100644
index 0000000000000000000000000000000000000000..0494e8eefb5e88c77f92f5e8e24a6714bb7dcb10
--- /dev/null
+++ b/README.old.md
@@ -0,0 +1,446 @@
+# Description
+
+ARIA version compatible with evolutionary restraints
+
+## Requirements
+
+Be sure to install these packages before running setup file
+* pip (>= 9.0)
+* setuptools (>= 18.0)
+* numpy (>= 1.11)
+* matplotlib
+* aria (>= 2.2)
+
+## Installation
+
+```
+# Ariaec directory or in a virtualenv, call the following command:
+> pip install .
+```
+
+# Command line
+
+The command line tool correspond to ariaec (or ec2aria for older versions)
+command in the terminal
+folder.
+```
+usage: ariaec [-h] -o OUTPUT_DIRECTORY [-c CONF_FILE] [--nolog] [-d]
+ {setup,bbconv,maplot,pdbqual,analysis,tbl2xml,pdbdist,pdbstat}
+ ...
+positional arguments:
+ {setup,bbconv,maplot,pdbqual,analysis,tbl2xml,pdbdist,pdbstat}
+
+optional arguments:
+ -h, --help show this help message and exit
+ -o OUTPUT_DIRECTORY, --output OUTPUT_DIRECTORY
+ Output directory (default: None)
+ -c CONF_FILE, --conf CONF_FILE
+ configuration file (default: None)
+ --nolog Don't generate log files (default: False)
+ -d, --debug Increase output verbosity (default: False)
+```
+
+
+In order to change default parameters, the tool can accept a configuration file (.ini format). Default parameters are listed below:
+
+```
+[main]
+; ------------------------- Main parameters ---------------------------------- #
+; Leave these fields empty in order to use default files
+; ariaproject_template : For backward compatibility with different
+; versions of ARIA since there is several
+; differences between aria templates.This package
+; can switch between 6 version actually:
+; - 2.3.0 with ramachandran potential tag
+; - 2.3.2 with exponent tag
+; - 2.3.3 with clustering tag
+; - 2.3.4 with scoring tag
+; - 2.3.5 with avg_exponent field in ambiguous
+; restraint tag
+; - 2.3.6 with method field in clustering tag
+ss_dist_file:
+scsc_min_file:
+interlowerbounds_pdbstat:
+intertarget_pdbstat:
+interupperbounds_pdbstat:
+intralowerbounds_pdbstat:
+intratarget_pdbstat:
+intraupperbounds_pdbstat:
+ariaproject_template: 2.3.6
+procheck_executable:
+prosa_executable:
+whatif_executable:
+clashlist_executable:
+
+
+[contactdef]
+; Contact definition section used to define maplot from pdb file.
+; Decrease this threshold if using other cutoff (e.g. 5.0)
+default_cutoff: 8.0
+; Add contact cutoff folowwing the syntax atm1_atm2
+;ca_ca: 7.0
+;cb_cb: 7.0
+;sc_sc: 5.0
+
+[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 : 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/dplus : Float [0.0, 0.5]
+; distance bound in tbl restraints
+longrange_hb: False
+nf_longrange_hb: 0.1
+longrange_hbtype: main
+hb_dminus: 0.0
+hb_dplus: 0.5
+; ---------------------- Distance restraint parameters ----------------------- #
+; native_reliable : True, False [False]
+; Define native contact map as reliable in aria
+; iterative protocol. Those contacts will not be
+; filtered.
+; evfold_weight : True, False [False]
+; use EVFold weight -> 10/i (i:contact rank) for
+; contact map derived distance restraints in
+; aria protocol
+; neighborhood_contact : True, False [False]
+; Generate restraints for neighbors foreach
+; contact in the contact map
+; pair_list : all, heavy, min [min]
+; use all, heavy atms or from a minimized
+; list (CA, CB, SC) for contribution list for
+; each distance restraint
+; atoms_type : all, heavy, min [min]
+; use all, heavy atms or from a minimized
+; list (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
+; (not yet implemented) or given by the user can
+; be used.
+; pdbdistance_level : ss, res,
+; 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.
+; ambiguous_distance_restraint : True, False [False]
+; Generate Ambiguous Distance Restraints.
+; Otherwise, each distance restraints will have
+; only one contribution (unambiguous distance
+; restraints)
+native_reliable: False
+evfold_weight: False
+neighborhood_contact: False
+atoms_type: min
+contributions_type: same
+distance_type: fixed
+groupby_method: min
+deffpow: 6
+pdbdistance_level: ss
+ambiguous_distance_restraint: False
+; Parameters below used only when distance_type is set to "fixed"
+restraint_distance: 2.5
+lower_bound: 1.0
+def_upper_bound: 5.0
+; Specific tresholds only for unambig restraints
+ca_upper_bound: 7.0
+cb_upper_bound: 7.0
+; ---------------------------- Filter parameters ----------------------------- #
+; n_factor : float [1.0]
+; Factor used for selection of contacts according to their score
+; (n * n_factor with n as sequence length)
+; contactfilter : all or combination of pos, cons, cys, ssclash separated by "+"
+; character [pos]
+; If empty, use only position filter (avoid short range
+; restraints)
+n_factor: 1.0
+contactfilter: all
+; conservation_treshold : Float [95]
+; Remove contact with highly conservated residues
+; position_treshold : Int [5]
+; Remove short range contacts
+conservation_treshold: 95
+position_treshold: 5
+; seed : If no scoremap to select top n contacts, choose a subset wit
+; random.sample method. For reproductibility, the seed used for
+; the sampling is provided here
+seed: 89764443
+; net_deconv : use network deconvolution to filter contact map
+; 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
+nd_beta: 0.99
+nd_alpha: 1.0
+; --------------------------- ARIA XML parameters ---------------------------- #
+runid: 1
+cpus: 100
+host_command: "sbatch -t 02:00:00"
+host_executable: bin/cns1.21_aria_logn_linux_x86_64_intel.exe
+temp_root: examples/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
+dist_avg_exponent: 6
+cns_executable: 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: yes
+hbdb_potential_enabled: no
+scoring_method: standard
+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
+procheck_executable:
+procheck_enabled: yes
+prosa_executable:
+prosa_enabled: yes
+whatif_executable:
+whatif_enabled: yes
+clashlist_executable:
+clahlist_enabled: no
+pickle_output: no
+; --------------------------- Iteration parameters --------------------------- #
+; /!\ Parameters below can be formatted as a list if we want different values
+; foreach iteration. Actually, only 2 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
+viol_sigma_mode: fix
+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
+clustering_enabled: no
+clustering_mask: CA
+clustering_nclusters: 2
+clustering_method: kmeans
+
+[maplot]
+; -------------------------- Contactmap parameters --------------------------- #
+; Report settings
+; n_factors: Number of EC tested: n * n_factor (n: sequence length)
+n_factors: 0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.5,2.0
+; Plot settings
+save_fig: True
+heatmap_linewidths: 0.0
+size_fig: 10
+plot_ext: pdf
+plot_dpi: 200
+alpha: 1.0
+
+[bbconv]
+; -------------------------- bbconverter parameters -------------------------- #
+couplingmatrix:
+start:
+end:
+outputprefix:
+PSIPREDfile:
+diversityvalue:
+L:
+
+[pdbqual]
+trash_directory: /tmp
+prosa: False
+skip_prefix: fitted
+csh_executable: csh
+
+[pdbdist]
+; ----------------------- PDB distribution parameters ------------------------ #
+; contact_cutoff: float [4.5]
+; Cutoff used to search neighbor atoms
+; dssp_exec: path
+; Path of DSSP executable
+contact_cutoff: 4.5
+dssp_exec: /c6/shared/bin/dssp
+download_pdbs: True
+obsolete_directory: /tmp/obsolete
+remove_pdbs: False
+pair_list: min
+
+[pdbstat]
+; 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+res+atm]
+; Group levels in serialized dictionaries
+mode: simple
+groups: ss+atm+res
+sample_minsize: 20
+
+[analysis]
+atmask: CA
+violation_treshold: 0.5
+nbest_structures: 15
+sort_criterion: total_energy
+```
+
+
+## Setup
+Translate contact maps into distance restraints and setup ARIA infrastructure
+```
+usage: ariaec setup [-h] [-d DISTFILE] -t
+ {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}
+ [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
+ [-r REF] [--hb HB] [--ssidx] [--no-filter]
+ seq sspred infile [infile ...]
+
+optional arguments:
+ -h, --help show this help message and exit
+
+required arguments:
+ seq sequence file [FASTA]
+ sspred secondary structure prediction file
+ infile contact or pdb file(s) used to build aria distance
+ restraints
+ -d DISTFILE, --distfile DISTFILE
+ Pdb or distance matrix iif distance_type set to
+ distfile in conf file, use distances in the given file
+ as target distance to build distance restraints
+ -t {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...], --type {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
+ Infile(s) contact type(s)
+ -r REF, --ref REF Native pdb. Allow TP/FP detection.
+ --hb HB H-bonds contact file (eg: metapsicov.hb)
+ --ssidx Use secondary structure index
+ --no-filter Do not filter contact map.
+```
+
+## Contactmap
+Contactmap analysis and visualisation
+```
+usage: ariaec maplot [-h] -t
+ {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}
+ [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
+ [--merge {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]]
+ [--filter] [--onlyreport] [--ssidx]
+ [--prefix PREFIX [PREFIX ...]]
+ seq sspred infile [infile ...]
+
+positional arguments:
+ seq sequence file [FASTA]
+ sspred secondary structure prediction file
+ infile contact or pdb file(s) used to build aria distance
+ restraints
+
+optional arguments:
+ -h, --help show this help message and exit
+ -t {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...], --type {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
+ Infile(s) contact type(s)
+ --merge {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
+ Merge given contact types with other maps
+ --filter Use contact list filter and top n contacts selection
+ --onlyreport Generate only report file
+ --ssidx Use secondary structure index
+ --prefix PREFIX [PREFIX ...]
+ Contact map name
+
+```
+## Pdbqual
+Quality tool for pdb file(s)
+```
+usage: ariaec pdbqual [-h] infile [infile ...]
+
+positional arguments:
+ infile PDB file(s) used to run quality tools with aria API
+
+optional arguments:
+ -h, --help show this help message and exit
+```
+## Tbl2xml
+ARIA XML converter for tbl distance restraint
+```
+usage: ariaec tbl2xml [-h] molecule.xml list_name infile.tbl [infile.tbl ...]
+
+positional arguments:
+ molecule.xml ARIA XML molecule file
+ list_name Restraint list name in the tbl file
+ infile.tbl TBL distance restraint file(s)
+
+optional arguments:
+ -h, --help show this help message and exit
+
+```
+
+## Bbconv
+Convert contacts in bbcontact format
+```
+usage: ariaec bbconv [-h] -t
+ {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}
+ contactfile sspred seq [msa]
+
+positional arguments:
+ contactfile contacts file (pconsc, plm)
+ sspred psipred file
+ seq sequence file [FASTA]
+ msa MSA [FASTA] for diversityvalueused with bbcontacts
+
+optional arguments:
+ -h, --help show this help message and exit
+ -t {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}, --type {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}
+ Infile contact type
+
+```