Module Hierarchy

• ansi: Module containing ANSI escape sequences and helper functions for colour terminal output.
• arg_check: Argument checking functions for the relax user functions.
• 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.noe: The automatic relaxation curve fitting 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.
• data: Package containing the relax data storage object.
  • data.align_tensor
  • data.data_classes: Basic objects used to build the relax data store.
  • data.diff_tensor
  • data.exp_info: Module holding the experimental information data container.
  • data.gui: Data store objects for holding all the GUI specific variables.
  • data.mol_res_spin: The molecule-residue-spin containers.
  • data.pipe_container
  • data.prototype: Module containing the Prototype base class for the molecule-residue-spin containers.
  • data.relax_xml: Module containing generic fns for creation and parsing of XML representations of python objects.
• dep_check: Module for checking relax dependencies.
• doc_builder: Module for building documentation.
• docs: Directory containing all of relax's documentation.
  • docs.latex
    • docs.latex.fetch_docstrings
• float: ieeefloat a set of functions for dealing with IEEE-754 float objects.
• generic_fns
  • generic_fns.align_tensor: Module containing functions for the handling of alignment tensors.
  • generic_fns.angles: Module for the manipulation of angular information.
  • generic_fns.bmrb: Module containing functions for BMRB support.
  • generic_fns.bruker: Module for the reading of Bruker Dynamics Centre (DC) files.
  • generic_fns.dasha: Module for interfacing with Dasha.
  • generic_fns.diffusion_tensor: Module for the support of diffusion tensors.
  • generic_fns.eliminate: Module implementing the mathematical modelling step of model elimination.
  • generic_fns.exp_info: Module containing functions for specifying the experimental details.
  • generic_fns.fix: Module for holding certain model components fixed during optimisation.
  • generic_fns.frame_order: Module containing functions related to the Frame Order theories.
  • generic_fns.frq: Module for manipulating the spectrometer frequency of experiments.
  • generic_fns.grace: Module for interfacing with Grace (also known as Xmgrace, Xmgr, and ace).
  • generic_fns.minimise: Module for model minimisation/optimisation.
  • generic_fns.model_selection: Module for selecting the best model.
  • generic_fns.mol_res_spin: Module for the manipulation of the molecule-residue-spin data structures in the relax data store.
  • generic_fns.molmol: Module for interfacing with Molmol.
  • generic_fns.monte_carlo: Module for performing Monte Carlo simulations for error analysis.
  • generic_fns.noesy: Module for NOESY related operations.
  • generic_fns.palmer: Module for interfacing with Art Palmer's Modelfree 4 program.
  • generic_fns.paramag: Module for the manipulation of paramagnetic data.
  • generic_fns.pcs: Module for the manipulation of pseudocontact shift data.
  • generic_fns.pipes: Module for manipulating data pipes.
  • generic_fns.pymol_control: Module for interfacing with PyMOL.
  • generic_fns.rdc: Module for the manipulation of RDC data.
  • generic_fns.relax_data: Module for the manipulation of relaxation data.
  • generic_fns.relax_re: Module implementing relax regular expression.
  • generic_fns.reset
  • generic_fns.results: Module for reading/writing/displaying the results in a data pipe.
  • generic_fns.selection: Module for selecting and deselecting spins.
  • generic_fns.sequence: Module for handling the molecule, residue, and spin sequence.
  • generic_fns.spectrum: Module containing functions for the handling of peak intensities.
  • generic_fns.state: Module for reading and writing the relax program state.
  • generic_fns.structure: This package consists of modules used reading, writing, creating, structural information.
    • generic_fns.structure.api_base: The API for accessing, creating, and modifying structural information.
    • generic_fns.structure.cones: Module containing all the different cone type classes.
    • generic_fns.structure.geometric
    • generic_fns.structure.internal: Module containing the internal relax structural object.
    • generic_fns.structure.main
    • generic_fns.structure.mass
    • generic_fns.structure.scientific: Module containing the Scientific Python PDB specific structural object class.
    • generic_fns.structure.superimpose: Module for handling all types of structural superimpositions.
  • generic_fns.sys_info: Module for displaying system information.
  • generic_fns.temperature: Module for setting the experimental temperature.
  • generic_fns.value: Module for the manipulation of parameter and constant values.
  • generic_fns.vmd: Module for interfacing with VMD.
  • generic_fns.xplor: Module containing functions for the parsing and creation of Xplor formatted files.
• 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_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: 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.combo_list: The combo list GUI element.
    • gui.components.conversion: Package for the different conversion tools used to bring together the GUI and API of relax.
    • 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.relax_data: Module containing the classes for GUI components involving relaxation data.
    • 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.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.interpreter: A threaded version of the relax interpreter for use by the GUI.
  • gui.menu: Module for the main relax menu bar.
  • gui.message
  • gui.misc: Miscellaneous functions used throughout the GUI.
  • gui.paths: Collection of all the image and icon paths.
  • 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.settings
  • 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.user_functions: User function GUI elements.
    • gui.user_functions.base: Base class module for the user function GUI elements.
    • gui.user_functions.bmrb: The BMRB user function GUI elements.
    • gui.user_functions.bruker: The Bruker Dynamics Center user function GUI elements.
    • gui.user_functions.deselect: The deselect user function GUI elements.
    • gui.user_functions.gpl: The gpl user function.
    • gui.user_functions.grace: The value user function GUI elements.
    • gui.user_functions.mol_res_spin: The molecule, residue, spin base classes.
    • gui.user_functions.molecule: The molecule user function GUI elements.
    • gui.user_functions.molmol: The molmol user function GUI elements.
    • gui.user_functions.noe: The noe user function GUI elements.
    • gui.user_functions.pipe: The pipe user function GUI elements.
    • gui.user_functions.pymol: The pymol user function GUI elements.
    • gui.user_functions.relax_data: The relaxation data user function GUI elements.
    • gui.user_functions.relax_fit: The relaxation data user function GUI elements.
    • gui.user_functions.residue: The residue user function GUI elements.
    • gui.user_functions.results: The results user function GUI elements.
    • gui.user_functions.script: The script user functions.
    • gui.user_functions.select: The select user function GUI elements.
    • gui.user_functions.sequence: The sequence user function GUI elements.
    • gui.user_functions.spectrum: The spectrum user function GUI elements.
    • gui.user_functions.spin: The spin user function GUI elements.
    • gui.user_functions.structure: The structure user function GUI elements.
    • gui.user_functions.sys_info: The structure user function GUI elements.
    • gui.user_functions.value: The value user function GUI elements.
  • gui.wizard: Base class module for the wizard GUI elements.
  • gui.wizard_elements: Module containing a set of special GUI elements to be used in the relax wizards.
• info: Module containing the introductory text container.
• maths_fns: Package containing all of relax's number crunching code.
  • maths_fns.alignment_tensor: Module for the manipulation of alignment tensors.
  • maths_fns.chi2: Module containing functions for calculating the chi-squared value, gradient, and Hessian.
  • maths_fns.consistency_tests
  • maths_fns.coord_transform: Module for transforming between different coordinate systems.
  • maths_fns.correlation_time
  • maths_fns.direction_cosine
  • maths_fns.frame_order: Module containing the target functions of the Frame Order theories.
  • maths_fns.frame_order_matrix_ops: Module for the handling of Frame Order.
  • maths_fns.jw_mapping
  • maths_fns.jw_mf
  • maths_fns.jw_mf_comps
  • maths_fns.kronecker_product: Module for the calculation of the Kronecker product.
  • maths_fns.mf
  • maths_fns.n_state_model
  • maths_fns.order_parameters: Module for the conversion of order parameters to specific model parameters and vice versa.
  • maths_fns.paramag_centre: Module for functions relating to the paramagnetic centre.
  • maths_fns.pcs: Module for the calculation of pseudocontact shifts.
  • maths_fns.potential: Functions for calculating various optimisation potentials.
  • maths_fns.pseudo_ellipse: Module for the pseudo-elliptical functions.
  • maths_fns.rdc: Module for the calculation of RDCs.
  • maths_fns.ri
  • maths_fns.ri_comps
  • maths_fns.ri_prime
  • maths_fns.rotation_matrix
  • maths_fns.weights
• 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.
• opendx: Package relating to the OpenDX data visualisation program.
  • opendx.base_map: Module containing the base class for the OpenDX space mapping classes.
  • opendx.isosurface_3D: Module containing the OpenDX 3D space isosurface mapping class.
  • opendx.main: Module containing the functions which interface relax with OpenDX.
• physical_constants: Module containing all physical constants used in relax, as well as all associated functions.
• prompt: Package for the prompt based interface.
  • prompt.align_tensor: Module containing the 'align_tensor' user function class.
  • prompt.angles: Module containing the 'angles' user function class.
  • prompt.base_class: The base class for all the user function classes.
  • prompt.bmrb: Module containing the BMRB user function class.
  • prompt.bruker: Module containing the Bruker Dynamics Center user function class.
  • prompt.command
  • prompt.consistency_tests: Module containing the 'consistency_tests' user function class.
  • prompt.dasha: Module containing the 'dasha' user function class for controlling the Dasha model-free software.
  • prompt.deselect: Module containing the 'deselect' user function class.
  • prompt.diffusion_tensor: Module containing the 'diffusion_tensor' user function class.
  • prompt.doc_string: Module containing various shared docstrings.
  • prompt.dx: Module containing the 'dx' user function class for controlling the OpenDX visualisation software.
  • prompt.eliminate: Module containing the 'eliminate' user function for removing failed models.
  • prompt.fix: Module containing the 'fix' user function class.
  • prompt.frame_order: Module containing the user function class of the Frame Order theories.
  • prompt.frq: Module containing the 'frq' user function class for manipulating spectrometer frequencies.
  • prompt.gpl: Module containing the 'gpl' user function for displaying licence information.
  • prompt.grace: Module containing the 'grace' user function class for controlling the Grace data viewing software.
  • prompt.help: The prompt UI help system.
  • prompt.interpreter: The prompt based relax user interface (UI).
  • prompt.jw_mapping: Module containing the Reduced Spectral Density Mapping 'jw_mapping' user function class.
  • prompt.minimisation: Module containing the 'minimisation' user function class.
  • prompt.model_free: Module containing the model-free analysis 'model_free' user function class.
  • prompt.model_selection: Module containing the 'model_selection' user function class.
  • prompt.molecule: Module containing the 'molecule' user function class.
  • prompt.molmol: Module containing the 'molmol' user function class for interacting with MOLMOL.
  • prompt.monte_carlo: Module containing the Monte Carlo simulation 'monte_carlo' user function class.
  • prompt.n_state_model: Module containing the 'n_state_model' user function class.
  • prompt.noe: Module containing the 'noe' user function class.
  • prompt.palmer: Module containing the 'palmer' user function class for controlling the Modelfree4 software.
  • prompt.paramag: Module containing the user function class for paramagnetic related functions.
  • prompt.pcs: Module containing the 'pcs' pseudocontact shift user function class.
  • prompt.pipe: Module containing the 'pipe' user function class.
  • prompt.pymol_control: Module containing the 'pymol' user function class for interacting with PyMOL.
  • prompt.rdc: Module containing the 'rdc' user function class.
  • prompt.relax_data: Module containing the 'relax_data' user function class.
  • prompt.relax_fit: Module containing the 'relax_fit' user function class.
  • prompt.reset
  • prompt.residue: Module containing the 'residue' user function class.
  • prompt.results: Module containing the 'results' user function class.
  • prompt.select: Module containing the 'select' user function class.
  • prompt.sequence: Module containing the 'sequence' user function class.
  • prompt.spectrum: Module containing the 'spectrum' user function class.
  • prompt.spin: Module containing the 'spin' user function class.
  • prompt.state: Module containing the 'state' user function class.
  • prompt.structure: Module containing the 'structure' user function class.
  • prompt.sys_info: Module containing the 'sys_info' user function class.
  • prompt.tab_completion
  • prompt.temperature: Module containing the 'temperature' user function class.
  • prompt.value: Module containing the 'value' user function class.
  • prompt.view: Module containing molecular viewing 'view()' user function.
  • prompt.vmd: Module containing the 'vmd' user function class for controlling VMD.
• relax
• relax_errors: Module containing all of the RelaxError objects.
• relax_io: Module containing advanced IO functions for relax.
• relax_warnings: Module containing all of the RelaxWarning objects.
• scons
  • scons.distrib
  • scons.install
  • 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_fns: This package consists of modules which are specific to the type of the data pipe.
  • specific_fns.api_base
  • specific_fns.api_common: API methods in common between different analysis types.
  • specific_fns.api_objects: A module of special objects used within the specific function API.
  • specific_fns.consistency_tests
  • specific_fns.frame_order: Module for the specific methods of the Frame Order theories.
  • specific_fns.hybrid
  • specific_fns.jw_mapping
  • specific_fns.model_free: The model-free specific code.
    • specific_fns.model_free.bmrb
    • specific_fns.model_free.macro_base: The module containing the base class for the model-free macros.
    • specific_fns.model_free.main
    • specific_fns.model_free.mf_minimise
    • specific_fns.model_free.molmol: The model-free Molmol macro module.
    • specific_fns.model_free.multi_processor_commands: Module for the multi-processor command system.
    • specific_fns.model_free.pymol: The model-free PyMOL macro module.
    • specific_fns.model_free.results: Module for the creation and processing of model-free results files.
  • specific_fns.n_state_model: Module for the specific analysis of the N-state dynamic model.
  • specific_fns.noe: The NOE specific code.
    • specific_fns.noe.main
  • specific_fns.relax_fit: The relaxation curve fitting specific code.
  • specific_fns.setup
• status: Module containing the status singleton object.
• test_suite: The relax test-suite.
  • 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.model_free
    • test_suite.gui_tests.noe
    • test_suite.gui_tests.rx
    • test_suite.gui_tests.state
  • test_suite.relax_test_loader: Replacement unittest.TestLoader class.
  • test_suite.relax_test_runner
  • test_suite.shared_data: The relax test-suite shared data.
    • test_suite.shared_data.diffusion_tensor: The relax test-suite shared diffusion tensor data.
      • test_suite.shared_data.diffusion_tensor.generate_data: relax script for creating a PDB file and relaxation data.
  • 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.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.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.n_state_model
    • test_suite.system_tests.noe
    • test_suite.system_tests.noe_restraints
    • test_suite.system_tests.palmer
    • 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_fit
    • test_suite.system_tests.results
    • test_suite.system_tests.sequence
    • test_suite.system_tests.state
    • test_suite.system_tests.structure
    • test_suite.system_tests.unit_vectors
  • 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
      • test_suite.unit_tests._data.test___init__
      • test_suite.unit_tests._data.test_align_tensor
      • test_suite.unit_tests._data.test_diff_tensor
      • test_suite.unit_tests._data.test_mol_res_spin
      • test_suite.unit_tests._data.test_pipe_container
    • test_suite.unit_tests._generic_fns
      • test_suite.unit_tests._generic_fns._structure
        • test_suite.unit_tests._generic_fns._structure.test___init__
        • test_suite.unit_tests._generic_fns._structure.test_api_base
        • test_suite.unit_tests._generic_fns._structure.test_internal
        • test_suite.unit_tests._generic_fns._structure.test_scientific
      • test_suite.unit_tests._generic_fns.molecule: Dummy molecule module used for renaming the generic_fns.mol_res_spin fns.
      • test_suite.unit_tests._generic_fns.residue: Dummy residue module used for renaming the generic_fns.mol_res_spin fns.
      • test_suite.unit_tests._generic_fns.spin: Dummy spin module used for renaming the generic_fns.mol_res_spin fns.
      • test_suite.unit_tests._generic_fns.test___init__
      • test_suite.unit_tests._generic_fns.test_align_tensor
      • test_suite.unit_tests._generic_fns.test_diffusion_tensor
      • test_suite.unit_tests._generic_fns.test_mol_res_spin
      • test_suite.unit_tests._generic_fns.test_molecule
      • test_suite.unit_tests._generic_fns.test_pipes
      • test_suite.unit_tests._generic_fns.test_relax_data
      • test_suite.unit_tests._generic_fns.test_relax_re
      • test_suite.unit_tests._generic_fns.test_residue
      • test_suite.unit_tests._generic_fns.test_selection
      • test_suite.unit_tests._generic_fns.test_sequence
      • test_suite.unit_tests._generic_fns.test_spin
      • test_suite.unit_tests._generic_fns.test_state
      • test_suite.unit_tests._generic_fns.test_value
    • test_suite.unit_tests._maths_fns
      • test_suite.unit_tests._maths_fns.test___init__
      • test_suite.unit_tests._maths_fns.test_chi2
      • test_suite.unit_tests._maths_fns.test_frame_order_matrix_ops
      • test_suite.unit_tests._maths_fns.test_kronecker_product
      • test_suite.unit_tests._maths_fns.test_n_state_model
      • test_suite.unit_tests._maths_fns.test_pseudo_ellipse
      • test_suite.unit_tests._maths_fns.test_rotation_matrix
    • test_suite.unit_tests._multi
      • test_suite.unit_tests._multi.test___init__
    • test_suite.unit_tests._opendx
      • test_suite.unit_tests._opendx.test___init__
    • test_suite.unit_tests._prompt
      • 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_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_value
    • test_suite.unit_tests._scons
    • test_suite.unit_tests._specific_fns
      • test_suite.unit_tests._specific_fns._model_free
        • test_suite.unit_tests._specific_fns._model_free.test___init__
        • test_suite.unit_tests._specific_fns._model_free.test_main
      • test_suite.unit_tests._specific_fns.test___init__
      • test_suite.unit_tests._specific_fns.test_api
      • test_suite.unit_tests._specific_fns.test_n_state_model
    • 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.test_float
    • test_suite.unit_tests.test_relax_io
    • 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
• version: Module for relax version information.