de Novo Ambiguous Restraints for Iterative Assignment¶
A pipeline for automated de novo contact map assignment
ariaec is a Python library that provides de novo structure prediction based on ARIA pipeline and evolutionary restraints inferred from co-evolution.
The package add a new command line interface aside the usual ARIA commands in order to convert data, setup an ARIA project with evolutionary restraints, analyze contact maps or protein structures and generate statistics from a culled list of PDB files.
Quick Start¶
Be sure to check if the following packages are correctly installed with your python installation or virtual environment.
- pip (>= 18.0)
- git (>= 2.0)
- cns-solve (1.21)
- ccpnmr analysis (optional)
- ccpn data model (optional)
Then the easiest solution is to call the pip command below :
pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec
Warning
This package contains patches for CNS-solve which needs to be compiled
after the installation. Please follow post installation instruction
before using aria2
pipeline.
For more information about installation and usage, please refer to the ARIAEC documentation.
Contributing¶
Please read guidelines for contributing for any suggestions or bug report.
License¶
ARIA
Ambiguous Restraints for Iterative Assignment
A software for automated NOE assignment
Version 2.3
- 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.
- Core package
- aria.core.Analyser module
- aria.core.AriaPeak module
- aria.core.AriaXML module
- aria.core.Assignment module
- aria.core.AssignmentFilter module
- aria.core.Atom module
- aria.core.Calibrator module
- aria.core.Chain module
- aria.core.ChemicalShiftFilter module
- aria.core.ChemicalShiftList module
- aria.core.Cluster module
- aria.core.Contribution module
- aria.core.ContributionAssigner module
- aria.core.ConversionTable module
- aria.core.CovalentDistances module
- aria.core.CrossPeak module
- aria.core.CrossPeakFilter module
- aria.core.DataContainer module
- aria.core.Datum module
- aria.core.Experiment module
- aria.core.Factory module
- aria.core.FloatFile module
- aria.core.Infrastructure module
- aria.core.Iteration module
- aria.core.JobManager module
- aria.core.Merger module
- aria.core.MolMol module
- aria.core.Molecule module
- aria.core.Molprobity module
- aria.core.NOEModel module
- aria.core.NOESYSpectrum module
- aria.core.NOESYSpectrumFilter module
- aria.core.Network module
- aria.core.OrderedDict module
- aria.core.PDBReader module
- aria.core.PeakAssigner module
- aria.core.Project module
- aria.core.Protocol module
- aria.core.Relaxation module
- aria.core.Report module
- aria.core.Residue module
- aria.core.RmsReport module
- aria.core.Settings module
- aria.core.ShiftAssignment module
- aria.core.ShiftAssignmentFilter module
- aria.core.Singleton module
- aria.core.SpinPair module
- aria.core.StructureEnsemble module
- aria.core.SuperImposer module
- aria.core.Topology module
- aria.core.TypeChecking module
- aria.core.ViolationAnalyser module
- aria.core.WhatifProfile module
- aria.core.ariabase module
- aria.core.ccpn_conversion module
- aria.core.cns module
- aria.core.conversion module
- aria.core.mathutils module
- aria.core.tools module
- aria.core.xmlparser module
- aria.core.xmlutils module
- aria.core.gui package
- aria.core.legacy package
- aria.core.legacy.AminoAcid module
- aria.core.legacy.Comparisons module
- aria.core.legacy.DeleteCnsComments module
- aria.core.legacy.DeleteComments module
- aria.core.legacy.DictWithDefault module
- aria.core.legacy.FortranFormat module
- aria.core.legacy.HeteronucleusPlusProton module
- aria.core.legacy.NoeList module
- aria.core.legacy.Nomenclature module
- aria.core.legacy.PpmList module
- aria.core.legacy.PseudoAtom module
- aria.core.legacy.ReadXeasy module
- aria.core.legacy.SequenceList module
- aria.core.legacy.Talos2Aria module
- aria.core.legacy.TextFile module
- aria.core.legacy.QualityChecks package
- aria.core.legacy.QualityChecks.DelTrailingSlash module
- aria.core.legacy.QualityChecks.Descriptive module
- aria.core.legacy.QualityChecks.QualityChecks module
- aria.core.legacy.QualityChecks.ReadCheckDB module
- aria.core.legacy.QualityChecks.RunProcheck module
- aria.core.legacy.QualityChecks.RunProsa module
- aria.core.legacy.QualityChecks.RunWhatif module
- aria.core.scientific package
- Conbox package
- aria.conbox.analysis module
- aria.conbox.commands module
- aria.conbox.common module
- aria.conbox.converter module
- aria.conbox.maplot module
- aria.conbox.ndconv module
- aria.conbox.pdbdist module
- aria.conbox.pdbqual module
- aria.conbox.pdbstat module
- aria.conbox.protein module
- aria.conbox.protmap module
- aria.conbox.reader module
- aria.conbox.settings module
- aria.conbox.setup module