Module Hierarchy

• auto_analyses: Package for all of the automatic analyses, hard coded protocols to be used as a black box.
  • auto_analyses.dauvergne_protocol: Automatic analysis for black-box model-free results.
  • auto_analyses.frame_order: The full frame order analysis.
  • auto_analyses.noe: The automatic relaxation curve fitting protocol.
  • auto_analyses.relax_disp: The automatic relaxation dispersion protocol.
  • auto_analyses.relax_fit: The automatic relaxation curve fitting protocol.
  • auto_analyses.stereochem_analysis: Determination of relative stereochemistry in organic molecules.
• bmrblib: Package for interfacing with the BioMagResBank.
  • bmrblib.NMR_parameters: Supergroup 5 - NMR parameters.
    • bmrblib.NMR_parameters.chem_shift_anisotropy: The chemical shift anisotropy data saveframe category.
    • bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1: The v3.1 chemical shift anisotropy data saveframe category.
  • bmrblib.assembly_supercategory: Supergroup 3 - Molecular assembly.
    • bmrblib.assembly_supercategory.entity: The entity saveframe category.
    • bmrblib.assembly_supercategory.entity_v2_1: The v2.1 entity saveframe category.
    • bmrblib.assembly_supercategory.entity_v3_1: The v3.1 entity saveframe category.
  • bmrblib.base_classes: The BMRB library base classes.
  • bmrblib.citations: Supergroup 2 - Citations.
    • bmrblib.citations.citations: The citations saveframe category.
    • bmrblib.citations.citations_v3_1: The citations saveframe category.
  • bmrblib.entry_information: Supergroup 1 - Entry information.
  • bmrblib.experimental_details: Supergroup 4 - Experimental descriptions.
    • bmrblib.experimental_details.experiment: The model_free saveframe category (used to be called order_parameters).
    • bmrblib.experimental_details.experiment_v3_1: The model_free saveframe category (used to be called order_parameters).
    • bmrblib.experimental_details.method: The method saveframe category.
    • bmrblib.experimental_details.method_v3_1: The method saveframe category.
    • bmrblib.experimental_details.nmr_spectrometer: The method saveframe category.
    • bmrblib.experimental_details.nmr_spectrometer_v3_1: The method saveframe category.
    • bmrblib.experimental_details.sample_conditions: The model_free saveframe category (used to be called order_parameters).
    • bmrblib.experimental_details.sample_conditions_v2_1: The model_free saveframe category (used to be called order_parameters).
    • bmrblib.experimental_details.sample_conditions_v3_1: The model_free saveframe category (used to be called order_parameters).
    • bmrblib.experimental_details.software: The software saveframe category.
    • bmrblib.experimental_details.software_v3_1: The software saveframe category.
  • bmrblib.kinetics: Supergroup 6 - Kinetic data.
    • bmrblib.kinetics.auto_relaxation: The Auto relaxation data saveframe category.
    • bmrblib.kinetics.auto_relaxation_v3_1: The v3.1 Auto relaxation data saveframe category.
    • bmrblib.kinetics.heteronucl_NOEs: The Heteronuclear NOE data saveframe category.
    • bmrblib.kinetics.heteronucl_NOEs_v2_1: The v2.1 Heteronuclear NOE data saveframe category.
    • bmrblib.kinetics.heteronucl_NOEs_v3_1: The v3.1 Heteronuclear NOE data saveframe category.
    • bmrblib.kinetics.heteronucl_T1_relaxation: The Heteronuclear T1 data saveframe category.
    • bmrblib.kinetics.heteronucl_T1_relaxation_v2_1: The v2.1 Heteronuclear T1 data saveframe category.
    • bmrblib.kinetics.heteronucl_T1_relaxation_v3_1: The v3.1 Heteronuclear T1 data saveframe category.
    • bmrblib.kinetics.heteronucl_T2_relaxation: The Heteronuclear T2 data saveframe category.
    • bmrblib.kinetics.heteronucl_T2_relaxation_v2_1: The v2.1 Heteronuclear T2 data saveframe category.
    • bmrblib.kinetics.heteronucl_T2_relaxation_v3_1: The v3.1 Heteronuclear T2 data saveframe category.
    • bmrblib.kinetics.relaxation: The relaxation data BMRB API interface.
  • bmrblib.misc: Functions for manipulating NMR-STAR dictionary data.
  • bmrblib.nmr_star_dict: The base classes for the NMR-STAR dictionary support within relax.
  • bmrblib.nmr_star_dict_v2_1: The base classes for the NMR-STAR dictionary support within relax.
  • bmrblib.nmr_star_dict_v3_1: The NMR-STAR dictionary API for version 3.1.
  • bmrblib.pystarlib
    • bmrblib.pystarlib.File: Classes for dealing with STAR syntax
    • bmrblib.pystarlib.FileTest: Unit test
    • bmrblib.pystarlib.SaveFrame: Classes for dealing with STAR syntax
    • bmrblib.pystarlib.SaveFrameTest: Unit test for SaveFrameTest.py Setup taken from "Dive Into Python"
    • bmrblib.pystarlib.TagTable: Classes for dealing with STAR syntax
    • bmrblib.pystarlib.TagTableTest
    • bmrblib.pystarlib.Text: Classes for dealing with STAR syntax
    • bmrblib.pystarlib.TextTest
    • bmrblib.pystarlib.Utils: Just a few utilities that can be of more general use.
    • bmrblib.pystarlib.UtilsTest
    • bmrblib.pystarlib.testAll
  • bmrblib.structure: Supergroup 8 - Structure determination.
    • bmrblib.structure.tensor: The tensor saveframe category.
  • bmrblib.thermodynamics: Supergroup 7 - Thermodynamic data.
    • bmrblib.thermodynamics.model_free: The model_free saveframe category (used to be called order_parameters).
    • bmrblib.thermodynamics.model_free_v3_1: The v3.1 Heteronuclear NOE data saveframe category.
  • bmrblib.version: The NMR-STAR version singleton object.
• colour: Module for colour manipulation.
• compat: Temporary module for allowing relax to support both Python 2 and 3.
• data_store: Package containing the relax data storage object.
  • data_store.align_tensor: The alignment tensor objects of the relax data store.
  • data_store.data_classes: Basic objects used to build the relax data store.
  • data_store.diff_tensor: The diffusion tensor objects of the relax data store.
  • data_store.exp_info: The experimental information data container of the relax data store.
  • data_store.gui: The GUI data objects of the relax data store.
  • data_store.interatomic: The interatomic data containers of the relax data store.
  • data_store.mol_res_spin: The molecule-residue-spin containers of the relax data store.
  • data_store.pipe_container: The data pipe objects of the relax data store.
  • data_store.prototype: Module containing the Prototype base class for the molecule-residue-spin containers.
  • data_store.relax_xml: Module containing generic functions for creation and parsing of XML representations of Python objects.
• dep_check: Module for checking relax dependencies.
• docs: Directory containing all of relax's documentation.
  • docs.latex: The directory of LaTeX files for building the relax manual.
    • docs.latex.fetch_docstrings: User function definition conversion to LaTeX for the relax manual.
• gui: Package for the Bieri GUI interface for relax.
  • gui.about
  • gui.analyses: Package for the automatic and custom analysis GUI elements.
    • gui.analyses.auto_model_free: Module for the automatic model-free protocol frame.
    • gui.analyses.auto_noe: Module containing the base class for the automatic NOE analysis frames.
    • gui.analyses.auto_r1: Module for the automatic R1 analysis frame.
    • gui.analyses.auto_r2: Module for the automatic R2 analysis frame.
    • gui.analyses.auto_relax_disp: Module for the automatic relaxation dispersion analysis.
    • gui.analyses.auto_rx_base: Module containing the base class for the automatic R1 and R2 analysis frames.
    • gui.analyses.base: Module containing the base class for all frames.
    • gui.analyses.elements: Package of GUI elements specific for the analysis frames.
      • gui.analyses.elements.bool_element: Module containing the base class for all frames.
      • gui.analyses.elements.float_element: Module containing the base class for all frames.
      • gui.analyses.elements.model_list: Auto-analysis GUI element for the control of lists of models.
      • gui.analyses.elements.spin_element: Module containing the base class for all frames.
      • gui.analyses.elements.text_element: Module containing the base class for all frames.
    • gui.analyses.execute: Module containing the class for threaded and non-threaded analysis execution.
    • gui.analyses.results_analysis
    • gui.analyses.wizard: Module for the analysis selection wizard.
  • gui.base_classes: Base classes used by the GUI.
  • gui.components: Package for the different GUI components for packing into sizer boxes.
    • gui.components.base_list: Module containing the base GUI element for listing things.
    • gui.components.citations: Module containing the citations GUI element for listing the citations relevant for the analysis.
    • gui.components.free_file_format
    • gui.components.grid: Module containing the classes for GUI components involving spectral data.
    • gui.components.menu: Module for the main relax menu bar.
    • gui.components.molecule: Module containing the classes for GUI components involving molecules.
    • gui.components.relax_data: Module containing the classes for GUI components involving relaxation data.
    • gui.components.relax_data_meta: Module containing the classes for GUI components involving relaxation data.
    • gui.components.scripts: Module containing the scripts GUI element for listing the scripts used in the analysis.
    • gui.components.software: Module containing the software GUI element for listing the software used in the analysis.
    • gui.components.spectrum: Module containing the classes for GUI components involving spectral data.
  • gui.controller: Log window of relax GUI controlling all calculations.
  • gui.errors: Module for handling errors in the GUI.
  • gui.export_bmrb: The BMRB export wizard.
  • gui.filedialog: relax specific file and directory dialogs.
  • gui.fonts: A standard set of font definitions for consistency throughout the GUI.
  • gui.icons: All of the icons for relax.
  • gui.input_elements: Package of the GUI elements used for user input of data.
    • gui.input_elements.bool: Module containing a set of special GUI elements to be used in the relax wizards.
    • gui.input_elements.combo_list: The combo list GUI element.
    • gui.input_elements.dir: Module containing a set of special GUI elements to be used in the relax wizards.
    • gui.input_elements.file: Module containing a set of special GUI elements to be used in the relax wizards.
    • gui.input_elements.sequence: Module containing a set of special GUI elements to be used in the relax wizards.
    • gui.input_elements.sequence_2D: Module containing a set of special GUI elements to be used in the relax wizards.
    • gui.input_elements.spin_id: GUI element for the user input of spin IDs.
    • gui.input_elements.value: GUI element for the user input of values.
  • gui.interpreter: A threaded version of the relax interpreter for use by the GUI.
  • gui.menu: The main relax menu bar.
  • gui.message
  • gui.misc: Miscellaneous functions used throughout the GUI.
  • gui.pipe_editor: The pipe editor GUI element.
  • gui.references: The relax related references window.
  • gui.relax_gui: Main module for the relax graphical user interface.
  • gui.relax_prompt: The relax prompt GUI element.
  • gui.results_viewer: Module containing the base class for the results frame.
  • gui.spin_viewer: Package for the spin viewer window.
    • gui.spin_viewer.containers: The molecule, residue, and spin containers for the spin viewer.
    • gui.spin_viewer.frame: The spin viewer frame.
    • gui.spin_viewer.splitter: The splitter window element to hold the tree view and containers.
    • gui.spin_viewer.tree: The molecule, residue, and spin tree view GUI elements.
  • gui.string_conv: Conversion functions for python objects to GUI strings and back.
  • gui.uf_objects: Module containing the special objects for auto-generating the GUI user functions and classes.
  • gui.wizards: Package for the relax wizards.
    • gui.wizards.peak_intensity: Module containing the base class for the automatic R1 and R2 analysis frames.
    • gui.wizards.wiz_objects: Base class module for the wizard GUI elements.
• info: Module containing the introductory text container.
• lib: The relax-lib package - a collection of functions, objects, and methods for the study of dynamics.
  • lib.alignment: The relax-lib NMR package - a library of functions for alignment-based NMR data.
    • lib.alignment.alignment_tensor: Module for the manipulation of alignment tensors.
    • lib.alignment.paramag_centre: Module for functions relating to the paramagnetic centre.
    • lib.alignment.pcs: Module for the calculation of pseudocontact shifts.
    • lib.alignment.rdc: Module for the calculation of RDCs.
  • lib.ansi: Module containing ANSI escape sequences and helper functions for colour terminal output.
  • lib.arg_check: Argument checking functions for the relax user functions.
  • lib.auto_relaxation: The relax-lib NMR package - a library of functions for auto-relaxation rates.
    • lib.auto_relaxation.ri
    • lib.auto_relaxation.ri_comps
    • lib.auto_relaxation.ri_prime
  • lib.check_types: Special module for checking types.
  • lib.chemical_shift: The relax-lib NMR package - a library of functions for chemical shifts.
  • lib.curve_fit: The relax-lib NMR package - a library of functions for various types of curve-fitting.
    • lib.curve_fit.exponential: Module for exponential curve-fitting.
  • lib.diffusion: The relax-lib NMR package - a library of functions for rotational diffusion.
    • lib.diffusion.correlation_time
    • lib.diffusion.direction_cosine
    • lib.diffusion.main: Module for the support of diffusion tensors.
    • lib.diffusion.weights
  • lib.dispersion: The relax-lib NMR package - a library of functions for relaxation dispersion.
    • lib.dispersion.cr72: The Carver and Richards (1972) 2-site all time scale exchange CR72 and CR72 full models.
    • lib.dispersion.dpl94: The Davis, Perlman and London (1994) 2-site fast exchange R1rho DPL94 model.
    • lib.dispersion.it99: The Ishima and Torchia (1999) 2-site all time scale exchange (with pA >> pB) IT99 model.
    • lib.dispersion.lm63: The Luz and Meiboom (1963) 2-site fast exchange LM63 model.
    • lib.dispersion.lm63_3site: The Luz and Meiboom (1963) 3-site fast exchange LM63 3-site model.
    • lib.dispersion.m61: The Meiboom (1961) 2-site fast exchange R1rho M61 model.
    • lib.dispersion.m61b: The Meiboom (1961) 2-site on-resonance skewed population R1rho M61 skew model.
    • lib.dispersion.mmq_cr72: The CR72 model extended for MMQ CPMG data, called the MMQ CR72 model.
    • lib.dispersion.mp05: The Miloushev and Palmer (2005) 2-site exchange R1rho MP05 model.
    • lib.dispersion.ns_cpmg_2site_3d: The numerical fit of 2-site Bloch-McConnell equations for CPMG-type experiments, the NS CPMG 2-site 3D and NS CPMG 2-site 3D full models.
    • lib.dispersion.ns_cpmg_2site_expanded: The numerical fit of 2-site Bloch-McConnell equations for CPMG-type experiments, the NS CPMG 2-site expanded model.
    • lib.dispersion.ns_cpmg_2site_star: The numerical fit of 2-site Bloch-McConnell equations for CPMG-type experiments, the NS CPMG 2-site star and NS CPMG 2-site star full models.
    • lib.dispersion.ns_matrices: A collection of functions for generating the relaxation matrices for the numerical solutions.
    • lib.dispersion.ns_mmq_2site: The numeric solution for the 2-site Bloch-McConnell equations for MMQ CPMG data, the NS MMQ 2-site model.
    • lib.dispersion.ns_mmq_3site: The numeric solution for the 3-site Bloch-McConnell equations for MMQ CPMG data, the NS MMQ 3-site linear and NS MMQ 3-site models.
    • lib.dispersion.ns_r1rho_2site: The numerical solution for the 2-site Bloch-McConnell equations for R1rho-type data, the NS R1rho 2-site model.
    • lib.dispersion.ns_r1rho_3site: The numerical solution for the 3-site Bloch-McConnell equations for R1rho-type data, the NS R1rho 3-site linear and NS R1rho 3-site model.
    • lib.dispersion.tap03: The Trott, Abergel and Palmer (2003) off-resonance 2-site exchange R1rho TAP03 model.
    • lib.dispersion.tp02: The Trott and Palmer (2002) 2-site exchange R1rho TP02 model.
    • lib.dispersion.tsmfk01: The Tollinger et al (2001) 2-site very-slow exchange TSMFK01 model.
    • lib.dispersion.two_point: The relaxation dispersion equations.
  • lib.errors: Module containing all of the RelaxError objects.
  • lib.float: ieeefloat a set of functions for dealing with IEEE-754 float objects.
  • lib.frame_order: The relax-lib NMR package - a library of functions for the frame order theories.
    • lib.frame_order.format: Module containing functions related to the Frame Order theories.
    • lib.frame_order.free_rotor: Module for the handling of Frame Order.
    • lib.frame_order.iso_cone: Module for the handling of Frame Order.
    • lib.frame_order.iso_cone_free_rotor: Module for the handling of Frame Order.
    • lib.frame_order.iso_cone_torsionless: Module for the handling of Frame Order.
    • lib.frame_order.matrix_ops: Module for the handling of Frame Order.
    • lib.frame_order.pseudo_ellipse: Module for the pseudo-ellipse frame order model.
    • lib.frame_order.pseudo_ellipse_free_rotor: Module for the handling of Frame Order.
    • lib.frame_order.pseudo_ellipse_torsionless: Module for the handling of Frame Order.
    • lib.frame_order.rotor: Module for the handling of Frame Order.
  • lib.geometry: The relax-lib geometry package - a library of functions for studies of geometry.
    • lib.geometry.coord_transform: Module for transforming between different coordinate systems.
    • lib.geometry.lines: Functions relating to line geometry.
    • lib.geometry.pec: Module for the pseudo-elliptical functions.
    • lib.geometry.rotations
    • lib.geometry.vectors: Collection of functions for vector operations.
  • lib.io
  • lib.linear_algebra: The relax-lib NMR package - a library of functions for advanced linear algebra not present in numpy.
    • lib.linear_algebra.kronecker_product: Module for the calculation of the Kronecker product.
    • lib.linear_algebra.matrix_exponential: Module for the calculation of the matrix exponential.
    • lib.linear_algebra.matrix_power: Module for matrix power operations.
  • lib.list: Module for handling Python lists.
  • lib.mathematics: Module for basic mathematical operations.
  • lib.model_selection: Module for the statistical concept of model selection.
  • lib.nmr: Module containing functions related to basic NMR concepts.
  • lib.order: The relax-lib NMR package - a library of functions for order and entropy.
    • lib.order.order_parameters: Module for the conversion of order parameters to specific model parameters and vice versa.
  • lib.periodic_table: Module containing a Python object representation of the period table.
  • lib.physical_constants: Module containing all physical constants used in relax, as well as all associated functions.
  • lib.regex: Module implementing relax regular expression.
  • lib.selection
  • lib.software: The relax-lib NMR package - a library of functions for creating input, reading output and control of external software.
    • lib.software.bruker_dc: Module for the reading of Bruker Dynamics Centre (DC) files.
    • lib.software.grace: Module for interfacing with Grace (also known as Xmgrace, Xmgr, and ace).
    • lib.software.opendx: The relax-lib NMR package - a library of functions for interacting with the OpenDX software.
      • lib.software.opendx.execute: Module for executing OpenDX.
      • lib.software.opendx.files: Module for generating OpenDX files.
    • lib.software.xplor: Module containing functions for the parsing and creation of Xplor formatted files.
  • lib.spectral_densities: The relax-lib NMR package - a library of functions for power spectral density functions.
    • lib.spectral_densities.model_free
    • lib.spectral_densities.model_free_components
  • lib.spectrum: The relax-lib NMR package - a library of functions for spectral data.
    • lib.spectrum.nmrpipe: Module containing functions for handling NMRPipe SeriesTab files.
    • lib.spectrum.nmrview: Module containing functions for handling NMRView files.
    • lib.spectrum.objects: Module containing objects used to handle peak list data.
    • lib.spectrum.peak_list: Module containing functions for the handling of peak intensities.
    • lib.spectrum.sparky: Module containing functions for handling Sparky files.
    • lib.spectrum.xeasy: Module containing functions for handling XEasy files.
  • lib.statistics: Module for calculating simple statistics.
  • lib.structure: The relax-lib structure package - a library of functions handling structural information.
    • lib.structure.cones: Module containing all the different cone type classes.
    • lib.structure.internal: The relax-lib structure.internal package - the internal structural object.
      • lib.structure.internal.displacements: The objects representing displacement information in the internal structural object.
      • lib.structure.internal.models
      • lib.structure.internal.molecules: The objects representing molecules in the internal structural object.
      • lib.structure.internal.object: Module containing the internal relax structural object.
    • lib.structure.mass
    • lib.structure.pdb_read: Module for parsing PDB records.
    • lib.structure.pdb_write: Module for creating PDB records.
    • lib.structure.represent: The relax-lib structure.represent package - creation of structures representing abstract ideas.
      • lib.structure.represent.cone
      • lib.structure.represent.diffusion_tensor
      • lib.structure.represent.rotor: Representations of a mechanical rotor.
    • lib.structure.statistics: Module for handling all types of structural statistics.
    • lib.structure.superimpose: Module for handling all types of structural superimpositions.
  • lib.text: The relax-lib text package - a library of functions for text manipulation.
    • lib.text.gui: Module defining a number of text elements for use in the GUI.
    • lib.text.sectioning: Functions for the formatting of titles, subtitles and other sectioning.
    • lib.text.string: Module for building documentation.
    • lib.text.table: Functions for the text formatting of tables.
  • lib.warnings
• minfx: This is the minfx optimisation library.
  • minfx.base_classes: Bases classes for the minfx optimisation library.
  • minfx.bfgs: Quasi-Newton Broyden-Fletcher-Goldfarb-Shanno (BFGS) nonlinear optimization.
  • minfx.cauchy_point: Cauchy Point trust region nonlinear optimization.
  • minfx.constraint_linear: Linear inequality constraint functions and gradients.
  • minfx.coordinate_descent: Back-and-forth coordinate descent (CD) optimization.
  • minfx.dogleg: Dogleg trust region optimization.
  • minfx.errors: Module containing all of the MinfxError objects.
  • minfx.exact_trust_region: Exact trust region optimization.
  • minfx.fletcher_reeves_cg: Fletcher-Reeves conjugate gradient optimization.
  • minfx.generic: Generic minimisation function for easy access to all of the optimization algorithms.
  • minfx.grid: The grid search algorithm.
  • minfx.hessian_mods: The Hessian modification package.
    • minfx.hessian_mods.cholesky_mod: Cholesky Hessian modification with added multiple of the identity.
    • minfx.hessian_mods.eigenvalue: Eigenvalue Hessian modification.
    • minfx.hessian_mods.gmw81: The Gill, Murray, and Wright (GMW) modified Cholesky Hessian modification algorithm.
    • minfx.hessian_mods.gmw81_old: The Gill, Murray, and Wright (GMW) modified Cholesky Hessian modification algorithm.
    • minfx.hessian_mods.se99: The Schnabel and Eskow (SE) revised modified Cholesky factorisation Hessian modification algorithm.
  • minfx.hestenes_stiefel_cg: Hestenes-Stiefel conjugate gradient optimization.
  • minfx.levenberg_marquardt: Levenberg-Marquardt optimization.
  • minfx.line_search: The line search algorithm package.
    • minfx.line_search.backtrack: Backtracking line search algorithm.
    • minfx.line_search.interpolate: Quadratic and cubic interpolation method.
    • minfx.line_search.more_thuente: A line search algorithm from More and Thuente.
    • minfx.line_search.nocedal_wright_interpol: A line search algorithm based on interpolation.
    • minfx.line_search.nocedal_wright_wolfe: A line search algorithm implemented using the strong Wolfe conditions.
    • minfx.line_search.test_functions: Testing functions.
  • minfx.log_barrier_function: Logarithmic barrier function optimization constraint algorithm.
  • minfx.method_of_multipliers: Method of multipliers or augmented Lagrangian method optimization constraint algorithm.
  • minfx.ncg: Line search Newton conjugate gradient optimization.
  • minfx.newton: Newton (or Newton-Raphson - NR) optimization.
  • minfx.polak_ribiere_cg: Polak-Ribiere conjugate gradient optimization.
  • minfx.polak_ribiere_plus_cg: Polak-Ribiere + conjugate gradient optimization.
  • minfx.simplex: Downhill simplex optimization.
  • minfx.steepest_descent: Steepest descent (SD) optimization.
  • minfx.steihaug_cg: Steihaug conjugate-gradient trust region optimization.
• multi: The multi-processor package.
  • multi.memo: The module containing the Memo classes.
  • multi.misc: The non-public module for storing the API functions and classes of the multi-processor package.
  • multi.mpi4py_processor: The MPI processor fabric via the mpi4py Python implementation.
  • multi.multi_processor_base: Module containing a Processor base class to be used by any multi-processor fabric.
  • multi.processor: The processor class is the central class in the multi python multiprocessor framework.
  • multi.processor_io: Module containing classes for IO stream capture on slave processors.
  • multi.result_commands: Module containing command objects sent from the slaves back to the master.
  • multi.result_queue: Module containing the results queue objects.
  • multi.slave_commands: Module containing command objects sent from the master to the slaves.
  • multi.uni_processor: The uni-processor fabric for running on a single CPU.
• pipe_control: Package of analysis independent code.
  • pipe_control.align_tensor: Module containing functions for the handling of alignment tensors.
  • pipe_control.angles: Module for the manipulation of angular information.
  • pipe_control.bmrb: Module containing functions for BMRB support.
  • pipe_control.bruker: Module for the reading of Bruker Dynamics Centre (DC) files.
  • pipe_control.chemical_shift: Module containing functions for the handling of chemical shifts.
  • pipe_control.dasha: Module for interfacing with Dasha.
  • pipe_control.diffusion_tensor: Module for the support of diffusion tensors.
  • pipe_control.domain: Module containing the structural domain related functions.
  • pipe_control.eliminate: Module implementing the mathematical modelling step of model elimination.
  • pipe_control.exp_info: Module containing functions for specifying the experimental details.
  • pipe_control.fix: Module for holding certain model components fixed during optimisation.
  • pipe_control.grace: Module for interfacing with Grace (also known as Xmgrace, Xmgr, and ace).
  • pipe_control.interatomic: Module for the manipulation of the interatomic data structures in the relax data store.
  • pipe_control.j_coupling: Module for the manipulation of J coupling data.
  • pipe_control.minimise: Module for model minimisation/optimisation.
  • pipe_control.model_selection: Module for selecting the best model.
  • pipe_control.mol_res_spin: Module for the manipulation of the molecule-residue-spin data structures in the relax data store.
  • pipe_control.molmol: Module for interfacing with Molmol.
  • pipe_control.monte_carlo: Module for performing Monte Carlo simulations for error analysis.
  • pipe_control.noesy: Module for NOESY related operations.
  • pipe_control.opendx: Module containing the base class for the OpenDX space mapping classes.
  • pipe_control.palmer: Module for interfacing with Art Palmer's Modelfree 4 program.
  • pipe_control.paramag: Module for the manipulation of paramagnetic data.
  • pipe_control.pcs: Module for the manipulation of pseudo-contact shift data.
  • pipe_control.pipes: Module for manipulating data pipes.
  • pipe_control.plotting: Module for the plotting of data.
  • pipe_control.pymol_control: Module for interfacing with PyMOL.
  • pipe_control.rdc: Module for the manipulation of RDC data.
  • pipe_control.relax_data: Module for the manipulation of relaxation data.
  • pipe_control.reset
  • pipe_control.result_files: Module for handling result files.
  • pipe_control.results: Module for reading/writing/displaying the results in a data pipe.
  • pipe_control.script: Functions for executing relax scripts.
  • pipe_control.selection: Module for selecting and deselecting spins.
  • pipe_control.sequence: Module for handling the molecule, residue, and spin sequence.
  • pipe_control.spectrometer: Module for manipulating the spectrometer experimental information.
  • pipe_control.spectrum: Module containing functions for the handling of peak intensities.
  • pipe_control.state: Module for reading and writing the relax program state.
  • pipe_control.structure: This package consists of modules used reading, writing, creating, structural information.
    • pipe_control.structure.geometric
    • pipe_control.structure.main
    • pipe_control.structure.mass
  • pipe_control.value: Module for the manipulation of parameter and constant values.
  • pipe_control.vmd: Module for interfacing with VMD.
• prompt: Package for the prompt based interface.
  • prompt.command
  • prompt.doc_string: Module containing various shared docstrings.
  • prompt.help: The prompt UI help system.
  • prompt.interpreter: The prompt based relax user interface (UI).
  • prompt.tab_completion
  • prompt.uf_docstring: The base class for all the user function classes.
  • prompt.uf_objects: The special auto-generated user function and class objects.
• relax: The main module for relax execution.
• scons: SCons build target package.
  • scons.distrib: SCons targets for building the relax distribution packages.
  • scons.install: SCons targets for installing relax.
  • scons.manuals: SCons targets for building the relax manuals.
• relax (script)
• sconstruct (script)
• setup: This script is used to build relax as an application on certain platforms.
• specific_analyses: Package of analysis specific code.
  • specific_analyses.api_base: The module defining the analysis specific API.
  • specific_analyses.api_common: Common API methods for use in different specific analyses.
  • specific_analyses.api_objects: A module of special objects used within the analysis specific API.
  • specific_analyses.consistency_tests: The consistency testing analysis of multi-field relaxation data.
  • specific_analyses.frame_order: The Frame Order analysis of domain dynamics.
  • specific_analyses.hybrid: Analysis specific code for the hybridisation of different data pipes.
  • specific_analyses.jw_mapping: The reduced spectral density mapping analysis.
  • specific_analyses.model_free: Analysis specific code for the Lipari-Szabo model-free analysis.
    • specific_analyses.model_free.bmrb: The BMRB methods of the specific API for model-free analysis.
    • specific_analyses.model_free.macro_base: The Molmol and Pymol base macro methods of the specific API for model-free analysis.
    • specific_analyses.model_free.main: The main methods of the specific API for model-free analysis.
    • specific_analyses.model_free.mf_minimise: The optimisation methods of the specific API for model-free analysis.
    • specific_analyses.model_free.molmol: The Molmol macro methods of the specific API for model-free analysis.
    • specific_analyses.model_free.multi_processor_commands: Module for the multi-processor command system.
    • specific_analyses.model_free.pymol: The Pymol macro methods of the specific API for model-free analysis.
    • specific_analyses.model_free.results: The result creation and processing methods of the specific API for model-free analysis.
  • specific_analyses.n_state_model: The N-state model or structural ensemble analysis.
    • specific_analyses.n_state_model.data: Module for handling base data of the N-state model or structural ensemble analysis.
    • specific_analyses.n_state_model.parameters: Module for handling the parameters of the N-state model or structural ensemble analysis.
  • specific_analyses.noe: The steady-state heteronuclear NOE analysis.
    • specific_analyses.noe.main: The main methods of the analysis specific API for the steady-state heteronuclear NOE calculation.
  • specific_analyses.relax_disp: The relaxation dispersion analysis.
    • specific_analyses.relax_disp.api: The relaxation dispersion API object.
    • specific_analyses.relax_disp.catia: Functions for interfacing with Flemming Hansen's CATIA program.
    • specific_analyses.relax_disp.checks: Module for functions for checking different aspects of the dispersion setup.
    • specific_analyses.relax_disp.cpmgfit: Functions for interfacing with Art Palmer's CPMGFit program.
    • specific_analyses.relax_disp.disp_data: Module for handling relaxation dispersion data within the relax data store.
    • specific_analyses.relax_disp.nessy: Functions for interfacing with Michael Bieri's NESSY program.
    • specific_analyses.relax_disp.optimisation: Module for the optimisation of the relaxation dispersion models.
    • specific_analyses.relax_disp.parameters: Functions relating to the parameters of the relaxation dispersion models.
    • specific_analyses.relax_disp.sherekhan: Functions for interfacing with Adam Mazur's ShereKhan program.
    • specific_analyses.relax_disp.variables: Variables for the relaxation dispersion specific analysis.
  • specific_analyses.relax_fit: The R1 and R2 exponential relaxation curve fitting analysis.
  • specific_analyses.setup: Module for handling the setup of the specific analyses.
• status: Module containing the status singleton object.
• target_functions: Package containing all of relax's number crunching code.
  • target_functions.chi2: Module containing functions for calculating the chi-squared value, gradient, and Hessian.
  • target_functions.consistency_tests
  • target_functions.ens_pivot_finder: Module for the target function for handling all types of structural superimpositions.
  • target_functions.frame_order: Module containing the target functions of the Frame Order theories.
  • target_functions.jw_mapping
  • target_functions.mf
  • target_functions.n_state_model
  • target_functions.potential: Functions for calculating various optimisation potentials.
  • target_functions.relax_disp: Target functions for relaxation dispersion.
  • target_functions.relax_fit
• test_suite: The relax test-suite.
  • test_suite.clean_up: Module of functions for cleaning up after the tests.
  • test_suite.formatting
  • test_suite.gui_tests: The relax GUI tests.
    • test_suite.gui_tests.base_classes: Base classes for the GUI tests.
    • test_suite.gui_tests.bmrb: GUI tests for the BMRB related activities.
    • test_suite.gui_tests.bruker: GUI tests for the Bruker Dynamics Center support.
    • test_suite.gui_tests.consistency_tests: GUI tests for the relaxation data consistency testing related activities.
    • test_suite.gui_tests.dead_uf_pages: GUI tests for catching dead user function pages.
    • test_suite.gui_tests.frame_order: GUI tests for the frame order related activities.
    • test_suite.gui_tests.general: Generic GUI tests.
    • test_suite.gui_tests.interatomic
    • test_suite.gui_tests.jw_mapping: GUI tests for the J(w) mapping related activities.
    • test_suite.gui_tests.model_free
    • test_suite.gui_tests.n_state_model: GUI tests for the N-state model related activities.
    • test_suite.gui_tests.noe
    • test_suite.gui_tests.pipes: GUI tests for pipe related activities.
    • test_suite.gui_tests.relax_disp: GUI tests for the relaxation dispersion analyses.
    • test_suite.gui_tests.rx
    • test_suite.gui_tests.state
    • test_suite.gui_tests.test_user_functions: Module for testing the special features of the user function GUI windows.
  • test_suite.relax_test_loader: Replacement unittest.TestLoader class.
  • test_suite.relax_test_runner
  • test_suite.system_tests: The relax system/functional tests.
    • test_suite.system_tests.align_tensor
    • test_suite.system_tests.angles
    • test_suite.system_tests.base_classes: Base classes for the system tests.
    • test_suite.system_tests.bmrb
    • test_suite.system_tests.bruker
    • test_suite.system_tests.chemical_shift: The module for the system tests for chemical shift support in relax.
    • test_suite.system_tests.consistency_tests
    • test_suite.system_tests.dasha
    • test_suite.system_tests.diffusion_tensor
    • test_suite.system_tests.frame_order
    • test_suite.system_tests.generic
    • test_suite.system_tests.grace
    • test_suite.system_tests.interatomic: System tests of the interatomic data container operations.
    • test_suite.system_tests.jw_mapping
    • test_suite.system_tests.load_spins
    • test_suite.system_tests.model_elimination
    • test_suite.system_tests.model_free
    • test_suite.system_tests.model_selection
    • test_suite.system_tests.mol_res_spin: System tests of the molecule, residue, and spin sequence operators.
    • test_suite.system_tests.n_state_model
    • test_suite.system_tests.noe
    • test_suite.system_tests.noe_restraints
    • test_suite.system_tests.palmer
    • test_suite.system_tests.pcs: PCS-based system tests.
    • test_suite.system_tests.peak_lists
    • test_suite.system_tests.pipes
    • test_suite.system_tests.rdc: RDC-based system tests.
    • test_suite.system_tests.relax_data
    • test_suite.system_tests.relax_disp
    • test_suite.system_tests.relax_fit
    • test_suite.system_tests.results
    • test_suite.system_tests.selection: System tests for testing the select and deselect user functions.
    • test_suite.system_tests.sequence
    • test_suite.system_tests.state
    • test_suite.system_tests.structure
    • test_suite.system_tests.unit_vectors
    • test_suite.system_tests.value
  • test_suite.test_suite_runner
  • test_suite.unit_tests: The relax unit tests.
    • test_suite.unit_tests._auto_analyses
      • test_suite.unit_tests._auto_analyses.test___init__
    • test_suite.unit_tests._data_store
      • test_suite.unit_tests._data_store.test___init__
      • test_suite.unit_tests._data_store.test_align_tensor
      • test_suite.unit_tests._data_store.test_diff_tensor
      • test_suite.unit_tests._data_store.test_mol_res_spin
      • test_suite.unit_tests._data_store.test_pipe_container
    • test_suite.unit_tests._lib
      • test_suite.unit_tests._lib._alignment
        • test_suite.unit_tests._lib._alignment.test___init__
      • test_suite.unit_tests._lib._auto_relaxation
        • test_suite.unit_tests._lib._auto_relaxation.test___init__
      • test_suite.unit_tests._lib._chemical_shift
        • test_suite.unit_tests._lib._chemical_shift.test___init__
      • test_suite.unit_tests._lib._curve_fit
        • test_suite.unit_tests._lib._curve_fit.test___init__
      • test_suite.unit_tests._lib._diffusion
        • test_suite.unit_tests._lib._diffusion.test___init__
      • test_suite.unit_tests._lib._dispersion
        • test_suite.unit_tests._lib._dispersion.test___init__
      • test_suite.unit_tests._lib._frame_order
        • test_suite.unit_tests._lib._frame_order.test___init__
        • test_suite.unit_tests._lib._frame_order.test_matrix_ops
      • test_suite.unit_tests._lib._geometry
        • test_suite.unit_tests._lib._geometry.test___init__
        • test_suite.unit_tests._lib._geometry.test_lines
        • test_suite.unit_tests._lib._geometry.test_pec
        • test_suite.unit_tests._lib._geometry.test_rotations
      • test_suite.unit_tests._lib._linear_algebra
        • test_suite.unit_tests._lib._linear_algebra.test___init__
        • test_suite.unit_tests._lib._linear_algebra.test_kronecker_product
        • test_suite.unit_tests._lib._linear_algebra.test_matrix_exponential
      • test_suite.unit_tests._lib._order
        • test_suite.unit_tests._lib._order.test___init__
      • test_suite.unit_tests._lib._software
        • test_suite.unit_tests._lib._software._opendx
          • test_suite.unit_tests._lib._software._opendx.test___init__
        • test_suite.unit_tests._lib._software.test___init__
      • test_suite.unit_tests._lib._spectral_densities
        • test_suite.unit_tests._lib._spectral_densities.test___init__
      • test_suite.unit_tests._lib._spectrum
        • test_suite.unit_tests._lib._spectrum.test_sparky
      • test_suite.unit_tests._lib._structure
        • test_suite.unit_tests._lib._structure._internal
          • test_suite.unit_tests._lib._structure._internal.test___init__
        • test_suite.unit_tests._lib._structure._represent
          • test_suite.unit_tests._lib._structure._represent.test___init__
        • test_suite.unit_tests._lib._structure.test___init__
        • test_suite.unit_tests._lib._structure.test_pdb_read
        • test_suite.unit_tests._lib._structure.test_pdb_write
      • test_suite.unit_tests._lib._text
        • test_suite.unit_tests._lib._text.test___init__
        • test_suite.unit_tests._lib._text.test_sectioning
        • test_suite.unit_tests._lib._text.test_table
      • test_suite.unit_tests._lib.test___init__
      • test_suite.unit_tests._lib.test_float
      • test_suite.unit_tests._lib.test_io
      • test_suite.unit_tests._lib.test_mathematics: Unit tests of the lib.mathematics module.
      • test_suite.unit_tests._lib.test_regex
      • test_suite.unit_tests._lib.test_selection
    • test_suite.unit_tests._multi
      • test_suite.unit_tests._multi.test___init__
    • test_suite.unit_tests._pipe_control
      • test_suite.unit_tests._pipe_control._structure
        • test_suite.unit_tests._pipe_control._structure.test___init__
        • test_suite.unit_tests._pipe_control._structure.test_internal
      • test_suite.unit_tests._pipe_control.molecule: Dummy molecule module used for renaming the pipe_control.mol_res_spin fns.
      • test_suite.unit_tests._pipe_control.residue: Dummy residue module used for renaming the pipe_control.mol_res_spin fns.
      • test_suite.unit_tests._pipe_control.spin: Dummy spin module used for renaming the pipe_control.mol_res_spin fns.
      • test_suite.unit_tests._pipe_control.test___init__
      • test_suite.unit_tests._pipe_control.test_align_tensor
      • test_suite.unit_tests._pipe_control.test_diffusion_tensor
      • test_suite.unit_tests._pipe_control.test_mol_res_spin
      • test_suite.unit_tests._pipe_control.test_molecule
      • test_suite.unit_tests._pipe_control.test_pipes
      • test_suite.unit_tests._pipe_control.test_relax_data
      • test_suite.unit_tests._pipe_control.test_residue
      • test_suite.unit_tests._pipe_control.test_selection
      • test_suite.unit_tests._pipe_control.test_sequence
      • test_suite.unit_tests._pipe_control.test_spin
      • test_suite.unit_tests._pipe_control.test_state
      • test_suite.unit_tests._pipe_control.test_value
    • test_suite.unit_tests._prompt
      • test_suite.unit_tests._prompt.container
      • test_suite.unit_tests._prompt.data_types
      • test_suite.unit_tests._prompt.test___init__
      • test_suite.unit_tests._prompt.test_align_tensor
      • test_suite.unit_tests._prompt.test_dasha
      • test_suite.unit_tests._prompt.test_deselect
      • test_suite.unit_tests._prompt.test_diffusion_tensor
      • test_suite.unit_tests._prompt.test_eliminate
      • test_suite.unit_tests._prompt.test_minimisation
      • test_suite.unit_tests._prompt.test_model_free
      • test_suite.unit_tests._prompt.test_molecule
      • test_suite.unit_tests._prompt.test_molmol
      • test_suite.unit_tests._prompt.test_n_state_model
      • test_suite.unit_tests._prompt.test_noe
      • test_suite.unit_tests._prompt.test_pymol
      • test_suite.unit_tests._prompt.test_relax_data
      • test_suite.unit_tests._prompt.test_relax_disp
      • test_suite.unit_tests._prompt.test_relax_fit
      • test_suite.unit_tests._prompt.test_residue
      • test_suite.unit_tests._prompt.test_select
      • test_suite.unit_tests._prompt.test_sequence
      • test_suite.unit_tests._prompt.test_spectrum
      • test_suite.unit_tests._prompt.test_spin
      • test_suite.unit_tests._prompt.test_state
      • test_suite.unit_tests._prompt.test_structure
      • test_suite.unit_tests._prompt.test_uf_objects: Unit test module for the prompt.uf_objects module.
      • test_suite.unit_tests._prompt.test_value
    • test_suite.unit_tests._scons
    • test_suite.unit_tests._specific_analyses
      • test_suite.unit_tests._specific_analyses._model_free
        • test_suite.unit_tests._specific_analyses._model_free.test___init__
        • test_suite.unit_tests._specific_analyses._model_free.test_main
      • test_suite.unit_tests._specific_analyses._relax_disp
        • test_suite.unit_tests._specific_analyses._relax_disp.test___init__
        • test_suite.unit_tests._specific_analyses._relax_disp.test_disp_data
      • test_suite.unit_tests._specific_analyses.test___init__
      • test_suite.unit_tests._specific_analyses.test_api
      • test_suite.unit_tests._specific_analyses.test_n_state_model
    • test_suite.unit_tests._target_functions
      • test_suite.unit_tests._target_functions.test___init__
      • test_suite.unit_tests._target_functions.test_chi2
      • test_suite.unit_tests._target_functions.test_n_state_model
    • test_suite.unit_tests._user_functions
      • test_suite.unit_tests._user_functions.test___init__
    • test_suite.unit_tests.align_tensor_testing_base
    • test_suite.unit_tests.base_classes: Base classes for the system tests.
    • test_suite.unit_tests.diffusion_tensor_testing_base
    • test_suite.unit_tests.minimisation_testing_base
    • test_suite.unit_tests.model_free_testing_base
    • test_suite.unit_tests.molecule_testing_base
    • test_suite.unit_tests.n_state_model_testing_base
    • test_suite.unit_tests.package_checking
    • test_suite.unit_tests.relax_data_testing_base
    • test_suite.unit_tests.residue_testing_base
    • test_suite.unit_tests.sequence_testing_base
    • test_suite.unit_tests.spin_testing_base
    • test_suite.unit_tests.state_testing_base
    • test_suite.unit_tests.structure_testing_base
    • test_suite.unit_tests.unit_test_runner: Utilities for unit test running from the command line or within the relax testing frame work.
    • test_suite.unit_tests.value_testing_base
• user_functions: Package containing all of the user function details.
  • user_functions.align_tensor: The align_tensor user function definitions.
  • user_functions.angles: The angles user function definitions.
  • user_functions.bmrb: The bmrb user function definitions.
  • user_functions.bruker: The bruker user function definitions for interfacing with the Bruker Dynamics Center.
  • user_functions.chemical_shift: The chemical_shift user function definitions.
  • user_functions.consistency_tests: The consistency_tests user function definitions.
  • user_functions.dasha: The dasha user function definitions for controlling the Dasha model-free software.
  • user_functions.data: Module containing the user function data singleton which stores all of the data.
  • user_functions.deselect: The deselect user function definitions.
  • user_functions.diffusion_tensor: The diffusion_tensor user function definitions.
  • user_functions.domain: The domain user function definitions.
  • user_functions.dx: The dx user function definitions for controlling the OpenDX visualisation software.
  • user_functions.eliminate: The eliminate user function definitions for removing failed models.
  • user_functions.fix: The fix user function definitions.
  • user_functions.frame_order: The frame_order user function definitions.
  • user_functions.grace: The grace user function definitions for controlling the Grace data viewing software.
  • user_functions.interatom: The interatom user function definitions.
  • user_functions.j_coupling: The j_coupling user function definitions.
  • user_functions.jw_mapping: The jw_mapping user function definitions for Reduced Spectral Density Mapping.
  • user_functions.minimisation: The minimisation user function definitions.
  • user_functions.model_free: The model_free user function definitions for model-free analysis.
  • user_functions.model_selection: The model_selection user function definitions.
  • user_functions.molecule: The molecule user function definitions.
  • user_functions.molmol: The molmol user function definitions for interacting with Molmol.
  • user_functions.monte_carlo: The monte_carlo user function definitions for Monte Carlo simulations.
  • user_functions.n_state_model: The n_state_model user function definitions.
  • user_functions.noe: The noe user function definitions.
  • user_functions.objects: The module of all the objects used to hold the user function details.
  • user_functions.palmer: The palmer user function definitions for controlling the Modelfree4 software.
  • user_functions.paramag: The paramag user function definitions for paramagnetic related functions.
  • user_functions.pcs: The pcs user function definitions.
  • user_functions.pipe: The pipe user function definitions.
  • user_functions.pymol_control: The pymol user function definitions for interacting with PyMOL.
  • user_functions.rdc: The rdc user function definitions.
  • user_functions.relax_data: The relax_data user function definitions.
  • user_functions.relax_disp: The relax_disp user function definitions.
  • user_functions.relax_fit: The relax_fit user function definitions.
  • user_functions.reset: The reset user function definitions.
  • user_functions.residue: The residue user function definitions.
  • user_functions.results: The results user function definitions.
  • user_functions.script: The script user function definitions.
  • user_functions.select: The select user function definitions.
  • user_functions.sequence: The sequence user function definitions.
  • user_functions.spectrometer: The spectrometer user function definitions for loading spectrometer information.
  • user_functions.spectrum: The spectrum user function definitions.
  • user_functions.spin: The spin user function definitions.
  • user_functions.state: The state user function definitions.
  • user_functions.structure: The structure user function definitions.
  • user_functions.sys_info: The sys_info user function definitions.
  • user_functions.value: The value user function definitions.
  • user_functions.vmd: The vmd user function definitions for controlling VMD.
• version: Module for relax version information.