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--- a/README.md
+++ b/README.md
@@ -21,976 +21,4 @@ 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
-
-===============================================================================
-
-Copyright (C) Benjamin Bardiaux, Michael Habeck, Therese Malliavin,
- Wolfgang Rieping, and Michael Nilges
-
-All rights reserved.
-
-NO WARRANTY. This software package is provided 'as is' without warranty of
-any kind, expressed or implied, including, but not limited to the implied
-warranties of merchantability and fitness for a particular purpose or
-a warranty of non-infringement.
-
-Distribution of substantively modified versions of this module is
-prohibited without the explicit permission of the copyright holders.
-
-
-===============================================================================
-
-Contents:
-
-1. What's new in version 2.4 ?
-
- 1.1 Potential of Mean Forces for dihedral angles () and H-bonds ()
- 1.2 Clustering step during the iterative process
- 1.3 Extended scoring function including PMF, coulombic and full Lennard Jones functions
- 1.4 Restraints generation from evolutionary couplings and secondary structure prediction
-
-2. Installation
-
- 2.1 Python
- 2.2 Python Numpy extension
- 2.3 Tix graphics library
- 2.4 Tcl/Tk libraries
- 2.5 Python matplotlib extension
-
-3. Running ARIA
-
- 3.1 Data conversion and XML format
- 3.2 The project file
- 3.3 Project setup
- 3.4 Running ARIA
- 3.5 Example
-
-4. Miscellaneous topics
-
- 4.1 Non-standard atom and residue definitions
- 4.2 Atom naming convention
- 4.3 The project directory tree
-
-===============================================================================
-
-
-1. What's new in version 2.3?
-----------------------------------
-
-- bug fixes
-
-- support of CCPN version 2 (instead of CCPN v1)
-
-- extension of symmetric oligomers support (C3, C5 and D2)
- (in the GUI, go to "Data > Symmetry")
-
-- introduction of the log-harmonic potential for distance restraints (Nilges et al. Structure, 2008)
- (go to "Structure Generation > CNS > Annealing Parameters > Log-Hamonic potential")
-
-- import of CCPN Models/Structure ensembles as initial structure for the minimization protocol or
- as template structures for the initial assignment/calibration step.
-
-- addition of Zinc ions coordination (through covalent bonds)
- (go to "Add > Zinc Coordination")
-
-- Automated Molprobilty (clashlist) analysis
- (go to "Analyses > Molprobity Clashlist")
-
-- addition of old aria1.x features (keep_structures, only fully assigned peaks)
-
-
-2. Installation:
-----------------
-
-Un-Tar the ARIA distribution using the following command:
-
- gunzip aria2.3.2.tar.gz
- tar xvf aria2.3.2.tar
-
-This creates a new directory ./aria2.3
-
-The directory structure of the distribution is as follows:
-
- ./cns
- ./cns/protocols
- ./cns/protocols/analysis
- ./cns/src
- ./cns/toppar
- ./src
- ./src/py
- ./src/py/data
- ./src/py/aria
- ./src/py/aria/gui
- ./src/py/aria/legacy
- ./src/xml
- ./examples
- ./examples/ccpn
-
-- You find the source code of ARIA in the directory ./src of the distribution,
- Python modules are located in ./src/py/aria and /src/py/aria/gui,
- XML DTDs can be found in ./src/xml.
-
-- The CNS protocols implementing, e.g., the simulated annealing protocol used
- to calculate a structure, are stored in ./cns/protocols. CNS analysis
- protocols can be found in the sub-directory, ./cns/protocols/analysis.
-
-- The only piece of Fortran code that needs to be compiled together with your
- CNS sources can be found in ./cns/src; only the code for floating
- chirality assignment is being used. The installation procedure has not
- changed since ARIA version 1.2:
-
- a) Academic users can obtain a free version of CNS from the CNS web site:
-
- http://cns.csb.yale.edu
-
- Commercial users need to purchase a CNX license from Accelrys (MSI).
-
- b) The ARIA fortran sources are located in the subdirectory ./cns/src of
- the distribution. Please copy all the files to the directory
- cns_solve_1.2/source of the unpacked cns_solve distribution (this will
- overwrite some files which is okay).
-
- c) Edit the file "cns_solve_env" in the directory cns_solve_1.2 to define the
- location of the CNSsolve directory.
-
- d) Go to directory cns_solve_1.2 and type "make install". This should start
- the compilation process.
-
-ARIA 2 is written in Python and requires the following packages which are
-not bundled to the main distribution:
-
- 1) Python 2.4 or later
-
- 2) Numpy version 1.0 or later
-
- 3) Tcl/Tk 8.3 or later for Tkinter support (part of Python standard package)
-
- 4) Tix8.1.4 or later
-
-In order to use the CCPN data model for import/export or data conversion, you
-also need to install the
-
- 5) CCPN data model, and the
-
- 6) CCPNMR Analysis software in case you want to export into CCPN the
- restraint lists and analyses of your structures that ARIA performs
- after a calculation, e.g. the result of the violation analysis.
-
- 7) Matplotlib plotting library
-
-In many popular LINUX distributions, Python is part of the default
-installation. If Python is already installed on your system, you can check
-whether your installation meets all of the requirements above by executing
-the script "check.py" which is located in the root directory of the
-ARIA distribution:
-
- python <aria-installation-path>/check.py
-
-The script checks the Python version, whether the Numeric package and
-Tkinter/Tix is installed. Please note, that the script cannot check whether
-Tcl/Tk/Tix is working properly.
-
-2.1 Python
-----------
-
-The latest version of Python can be downloaded from the Python homepage at
-
- http://www.python.org.
-
-Go to the "download" section and download the source tar-ball.
-The installation is straight forward for most UNIX systems (LINUX in
-particular). Follow the installation notes of the Python distribution and
-make sure that Tkinter support is enabled.
-
-Note: In order to install Python with Tcl/Tk (i.e. Tkinter) support,
- please make sure that both libraries are installed on your system.
- If any of the libraries is missing, please check and install the
- missing components prior to the installtion of Python.
-
-After Python has been installed sucessfully, you can run "check.py" to check
-whether the Tkinter module has been installed correctly.
-
-2.2 Python Numpy extension
------------------------------
-
-ARIA 2.3 now supports only the new Numpy package.
-If you already have Numpy installed, there is no need to install Numpy.
-
-Numpy:
-
-The Python Numpy extension is obtainable from SourceForge at:
-
- http://numpy.scipy.org/
-
-Download the package "Numpy" version 1.0 or later.
-For installation, please follow installation instructions provided by the
-
-2.3 Tix graphics library
-------------------------
-
-The Tix (Tk Interface eXtension) graphics library provides high-level
-widgets, extending the standard capabilities of Tk widgets. The latest Tix
-library can be obtained from SourceForge at
-
- http://tix.sourceforge.net
-
-Installing Tix also requires the sources of Tcl/Tk. Make sure that the
-Tcl/Tk version used during Tix installation matches the version installed on
-your system (if Python with Tkinter support is already installed, you can
-check the Tk version linked with Python by using the script "check.py"). Please
-consult the installation notes for further instructions.
-
-
-2.4 Tcl/Tk libraries
---------------------
-
-Both libraries are obtainable from http://www.tcl.tk
-
-2.5 CCPN distribution
----------------------
-
-In order to use the CCPN data model for import/export or data conversion, you
-also need to install the CCPN data model, and the CCPNMR Analysis software in
-case you want to export restraint lists, NOE assignments, and analyses of the
-generated structures, e.g. the result of the violation analysis. The complete
-CCPN distribution including the API, the FormatConverter, and CCPNMR Analysis
-can be obtained at
-
- http://www.ccpn.ac.uk/ccpn/software/downloads-v2/
-
-The CCPN distribution provides scripts which guide you through the
-installation process.
-
-2.6 Python Matplotlib extensions
------------------------------
-
-The plotting library Matplotlib can be downloaded from
- http://matplotlib.sourceforge.net/
-
-
-3. Running ARIA
----------------
-
-For convenience we suggest to add the following lines to your login script:
-
-- csh; edit ".cshrc"
-
- setenv ARIA2 <aria-installation-path>
- alias aria2 <Python-executable> -O $ARIA2/aria2.py
-
-- bash; edit ".bashrc"
-
- export ARIA2=<aria-installation-path>
- alias=aria2 "<Python-executable> -O $ARIA2/aria2.py"
-
-
-- zsh; edit ".zshrc"
-
- export ARIA2=<aria-installation-path>
- alias aria2="<Python-executable> -O $ARIA2/aria2.py"
-
-
-For running ARIA, please enter "aria2" or "aria2 --help" for help.
-
-Creating, setting-up and running an ARIA project,
-requires the following steps:
-
-3.1 Converting your data into ARIA XML format
----------------------------------------------
-
-ARIA provides routines for converting your data in the following way:
-all data sources need to be specified in a simple XML file, "conversion.xml",
-say. To create an empty conversion template XML file use the following command:
-
- aria2 --convert -t conversion.xml
-
-Here, "-t" means "template". This command creates a new text file,
-"conversion.xml", formatted in XML. It contains several input fields that
-need to be filled-in in order to start the conversion process. For example,
-format or your peak lists (ANSIG, NMRVIEW, XEASY etc.), proton / hetero
-dimensions etc.
-
-Once your completed "conversion.xml" file has been stored, run ARIA again
-to perform the conversion:
-
- aria2 --convert conversion.xml
-
-This command first loads and parses the conversion file. It then reads in
-your data files (i.e peak lists, shift lists, sequence file), converts them
-into XML and stores them at the specified locations. The newly created XML
-files can then be edited using a XML or text editor.
-
-3.2 The project file
-------------------------
-
-The complete definition of an ARIA project, i.e. type and location of the data
-sources (the XML files containing your peak and shift lists etc.), parameters
-for the minimization protocol, or parameters for other ARIA sub-modules such as
-the violation analysis etc., is encapsulated in the project's XML file
-("project-xml").
-
-In your conversion XML file, you can specify the filename of a project file,
-"new_project.xml", say, if you want ARIA to create a new project file. This
-project file will already reference the converted data.
-
-Alternatively, you can create an (empty) project template XML file by
-invoking the command
-
- aria --project_template new_project.xml
-
-To complete the project template file, you need to fill in the fields
-referencing your data by hand. For further instructions, please have a
-look at a conversion file.
-
-In order to setup an ARIA project, it is necessary to provide some additional
-information:
-
- - working directory The root directory of your project.
-
- - file_root The 'nickname' of your project.
- For instance, the file_root serves as
- basename for all PDB-files: e.g. if
- file_root is set to "bpti", PDB-files
- will be called bpti_1.pdb ... .
-
- - temporary path
-
- - list of available machines In particular if want to run the
- structure calculation on several
- machines simultaniously, you need
- to specify a list of those machines.
-
- If the list is empty, ARIA uses the
- local host.
-
- - Path of the CNS executable.
-
-Generally, you may use ARIAs graphical user interface (GUI), an XML editor or
-a text editor to display and edit your project. However, ARIA's GUI is
-intended to streamline the project setup and further provides brief
-descriptions / help for most of the parameter settings. For launching the GUI
-with the project "new_project.xml" use the command
-
- aria2 --gui new_project.xml or
-
- aria2 -g new_project.xml
-
-If the project file is omitted, the GUI starts without loading a project.
-
-3.3 Project setup
------------------
-
-Once the project XML file "new_project.xml" has been completed,
-run ARIA to setup the project:
-
- aria2 -s new_project.xml
-
-This command reads-in the project file and performs some validity checks.
-If the project could be loaded successfully, the following actions
-are performed:
-
- a) Creating of the directory tree: it creates the full directory tree
- needed by ARIA and CNS
-
- b) Data setup: copies all (XML) data files from its source locations to
- the local directory "data".
-
- c) Copy CNS specific files (such as protocols): all CNS specific files
- are copied from their source location (ARIAs installation path) to the
- local directory "cns/...".
-
-Details on the directory tree can be found in section 4.3.
-
-If the project has already been set-up, a re-setup skips all existing files.
-To enforce overwriting of existing files, use the option -f:
-
- aria2 -sf new_project.xml
-
-Forced setup overwrites/updates the following files:
-
- a) Data files in the local directory "data",
- b) CNS specific files.
-
-3.4 Running ARIA
-----------------
-
-After your project has been setup, start ARIA by invoking the command:
-
- aria2 new_project.xml
-
-Use the GUI to modify protocol- and/or parameters of the minimisation
-protocol. It is only necessary to re-setup you project, if your data files
-or the CNS protocols have been modified.
-
-3.5 Example
------------
-
-Predefined XML files for peak and shift lists of the HRDC domain can be found
-in the directory "examples/werner/". For further instructions of how to
-use the example, please have a look in the file "examples/werner/README".
-
-The same directory also provides a CCPN project which contains the same data.
-Instructions for how launch a calculation from a CCPN project are given in
-examples/werner/README.
-
-4. Miscellaneous topics
------------------------
-
-4.1 Non-standard atom or residue definitions
---------------------------------------------
-
-In order to work with non-standard atoms and residues like ions or
-ligands the one needs to modify several CNS protocols and parameter
-files. By default, the CNS script "generate.inp" is executed in order
-to generate a PSF file. The PSF file needs to be patched manually and
-copied to the cns/protocols directory of the run's local directory
-tree if one wants to setup the PSF file in the ARIA run.
-
-If you want to use your own tempalte PDB file and PSF file, you can
-either modify the CNS script "generate.inp", or you just copy your PSF
-and "xxxx_template" PDB file to the directory "cns/begin". Please
-disable the automatic generation of these files (in the GUI see node
-"CNS" in branch "Structure Generation").
-
-Additionally, you need to modify the CNS topology, parameter and linkage
-files. Please make sure that you introduce the right bonds if you want to use
-torsion angle dynamics in the structure generation. User-specific files can be
-set via the GUI in the panel "Sequence".
-
-The HIC-Up server may assist you in creating the necessary patches and
-modifications in the definition files (http://xray.bmc.uu.se/hicup/).
-
-
-4.2 Atom names
---------------
-
-ARIA 2 follows the IUPAC standard for naming atoms, standard amino
-acids and nucleotides. In case of non-standard atoms and residues the
-user can choose his own naming convention in the sequence XML
-file. Because CNS relies on its own naming convention, please note
-that the calculated structures will have CNS atom and residue names.
-
-The IUPAC atom names used by ARIA can be found in the XML file
-"atomnames.xml" located in the directory "src/py/data" of the
-distribution. During data conversion, atom names in your data are
-translated according to the specifications made in the converion XML file.
-
-4.3 The project directory tree
-------------------------------
-
-The directory tree for an ARIA run is setup by using "aria2 -s
-<project-xml>". It copies the data XML files from its source locations
-(as specified in the project file) to the local directory "data".
-When running ARIA, all data files are read from the *local*
-directory. In other words, only modifications of the data stored in
-the *local* directory are considered when re-running a project.
-
-All CNS specific files (protocols, topology/parameters files etc) are
-copied from their source location (ARIA's installation path) into the local
-directory "cns/xxx".
-
-The directory tree for a typical ARIA run (run's nickname is "1" in example
-below) of nine iterations has the following structure:
-
- run1/data/........................ local copies of the data files,
- run1/data/begin/.................. for storing the starting structure,
- run1/data/sequence/............... copy of the sequence XML file,
- run1/data/spectra/................ copies of the chemical shift and peak
- lists as XML files, reports on the
- seed assignment and filtering,
- run1/data/templates/.............. for storing an initial structure ensemble,
- run1/data/hbonds/................. H-bond ".tbl" files
- .
- .
- run1/structures/.................. structure calculation results,
- iteration reports, analysis results,
- CNS output, etc.
- run1/structures/it0/.............. PDB-, ".float"-, and restraint files for
- the first iteration
- run1/structures/it1/
- .
- .
- run1/structures/it8/.............. last iteration in this example,
- run1/structures/it8/analysis/..... results of CNS analyses,
- run1/structures/it8/analysis/cns/. output of the CNS analysis scripts
- run1/structures/refine/........... directory containing water/DMSO refined
- structures,
- run1/cns/......................... for storing CNS specific files,
- run1/cns/data/.................... data file in CNS format, created in
- each run,
- run1/cns/data/sequence/........... sequence in PDB format using CNS atom
- names created from the sequence
- XML file,
- run1/cns/data/hbonds/............. copies of the H-bond .tbl files to
- files with fixed names, i.e.,
- "hbonds.tbl", "hbonds_talos.tbl", ...
- run1/cns/data/jcouplings/......... copies of the J-coupling ".tbl" files,
- . files belonging the same class are
- . concatenated and stored in "c1.tbl",
- . "c2.tbl", etc.,
- run1/cns/protocols/............... refinement protocols, etc.,
- run1/cns/protocols/analysis/...... analysis protocols,
- run1/cns/toppar/.................. topology, linkage and parameter files,
- run1/cns/begin.................... PSF file, "_template" PDB file, etc.,
- run1/cache........................ cache file to speed-up re-runs.
-
-The data specified in the project XML file are always copied to their
-respective subdirectories in the directory run1/data. If you want to
-modify the data (after the project has been setup) please edit the
-files located in run1/data/... . The directory run1/cns/data is only
-used internally for structure calculation and should not be altered.
-
-
-
-
-
-
-
-
-# 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
-
-```
+structure calculation. Bioinformatics 23:381-382
\ No newline at end of file