Package lib

The relax-lib package - a collection of functions, objects, and methods for the study of dynamics.

Submodules

• 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.checks
• lib.chemical_shift: The relax-lib NMR package - a library of functions for chemical shifts.
• lib.compat: Temporary module for allowing relax to support both Python 2 and 3.
• 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.b14: The Baldwin (2014) 2-site exact solution model for all time scales B14.
  • 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.matrix_exponential: Module for the calculation of the matrix exponential, for higher dimensional data.
  • lib.dispersion.matrix_power: Module for the calculation of the matrix power, for higher dimensional data.
  • 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.dispersion.variables: Variables for the relaxation dispersion specific analysis.
• 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.conversions: Functions for creating or calculating the rotor axis for the frame order models.
  • lib.frame_order.double_rotor: Module for the double rotor frame order model.
  • 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.frame_order.simulation: Module for simulating the frame order motions.
  • lib.frame_order.variables: Variables for the frame order analysis.
• lib.geometry: The relax-lib geometry package - a library of functions for studies of geometry.
  • lib.geometry.angles: Module for the manipulation of angular information.
  • 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.plotting: The relax library plotting package - a library of functions for plotting data via different software packages.
  • lib.plotting.api: The relax library plotting API.
  • lib.plotting.gnuplot: Module for data plotting using gnuplot.
  • lib.plotting.grace: Module for interfacing with Grace (also known as Xmgrace, Xmgr, and ace).
  • lib.plotting.text: Module for data plotting in plain text format.
  • lib.plotting.veusz: Module for data plotting using veusz.
• lib.regex: Module implementing relax regular expression.
• lib.selection
• lib.sequence
• lib.sequence_alignment: The relax-lib sequence alignment package - a library of functions for aligning proteins, DNA, RNA or other molecules.
  • lib.sequence_alignment.align_protein: General sequence alignment functions.
  • lib.sequence_alignment.msa: Multiple sequence alignment (MSA) algorithms.
  • lib.sequence_alignment.needleman_wunsch: Functions for implementing the Needleman-Wunsch sequence alignment algorithm.
  • lib.sequence_alignment.substitution_matrices: Substitution matrices for use in sequence alignment.
• 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.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.angles
  • lib.structure.cones: Module containing all the different cone type classes.
  • lib.structure.conversion
  • lib.structure.files: Module for handling different structural file formats.
  • lib.structure.geometric
  • lib.structure.internal: The relax-lib structure.internal package - the internal structural object.
    • lib.structure.internal.coordinates: Module for handling atomic coordinate information.
    • 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.internal.selection: Module containing the fast structural selection object.
  • lib.structure.mass
  • lib.structure.pca: Module for performing a principle component analysis (PCA).
  • 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.progress: Text based progress meters.
  • 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.timing: Module for various timing purposes.
• lib.warnings
• lib.xml: Module containing generic functions for creation and parsing of XML representations of Python objects.

Variables

__package__ = None
hash(x)