Package bmrblib

Package for interfacing with the BioMagResBank.

This file is part of the BMRB library.

The Biological Magnetic Resonance Data Bank, or BioMagResBank and BMRB for short, is a repository for data from NMR spectroscopy on proteins, peptides, nucleic acids, and other biomolecules. This bmrblib library handles the NMR-STAR formatted files, the base format of all BMRB data. It can both read and write NMR-STAR files.

Version: trunk

Submodules

• 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.

Functions

class instance create_nmr_star(title, file_path, version=None)
Initialise the NMR-STAR object.

str determine_version(file_path)
Determine the version of the given NMR-STAR file.

Variables

__package__ = 'bmrblib'

Imports: pystarlib, F_OK, NMR_STAR_v2_1, NMR_STAR_v3_1, NMR_parameters, Star_version, access, assembly_supercategory, citations, experimental_details, kinetics, search, structure, sys, thermodynamics, version

Function Details

create_nmr_star(title, file_path, version=None)

Initialise the NMR-STAR object.

Parameters:

• title (str) - The title of the NMR-STAR data.
• file_path (str) - The full file path.
• version (str) - The NMR-STAR version to use.

Returns: class instance

The NMR-STAR python object.

determine_version(file_path)

Determine the version of the given NMR-STAR file.

Parameters:

• file_path (str) - The full file path.

Returns: str

The NMR-STAR version number.