Package generic_fns :: Module bmrb

Module bmrb

Module containing functions for BMRB support.

Functions

display(version='3.1')
Display the results in the BMRB NMR-STAR format. source code

generate_sequence(N=0, spin_ids=None, spin_nums=None, spin_names=None, res_nums=None, res_names=None, mol_names=None)
Generate the sequence data from the BRMB information.

source code

list of str

list_sample_conditions(star)
Get a listing of all the sample conditions.

source code

list of str

molecule_names(data, N=0)
Generate the molecule names list.

source code

int

num_spins(data)
Determine the number of spins in the given data.

source code

read(file=None, directory=None, version=None, sample_conditions=None)
Read the contents of a BMRB NMR-STAR formatted file.

source code

write(file=None, directory=None, version='3.1', force=False)
Create a BMRB NMR-STAR formatted file. source code

Variables

[hide private]

ds = The relax data storage obje...

__package__ = 'generic_fns'

Imports: F_OK, access, sys, Relax_data_store, ExpInfo, dep_check, exp_info, create_spin, generate_spin_id, return_residue, return_spin, Info_box, RelaxError, RelaxFileError, RelaxFileOverwriteError, RelaxNoModuleInstallError, RelaxNoPipeError, get_file_path, mkdir_nofail, specific_fns, version_full

Function Details

[hide private]

generate_sequence(N=0, spin_ids=None, spin_nums=None, spin_names=None, res_nums=None, res_names=None, mol_names=None)

source code

Generate the sequence data from the BRMB information.

Parameters:

N (int) - The number of spins.
spin_ids (list of str) - The list of spin IDs.
spin_nums (list of int or None) - The list of spin numbers.
spin_names (list of str or None) - The list of spin names.
res_nums (list of int or None) - The list of residue numbers.
res_names (list of str or None) - The list of residue names.
mol_names (list of str or None) - The list of molecule names.

list_sample_conditions(star)

source code

Get a listing of all the sample conditions.

Parameters:

star (NMR_STAR instance) - The NMR-STAR dictionary object.

Returns: list of str

The list of sample condition names.

molecule_names(data, N=0)

source code

Generate the molecule names list.

Parameters:

data (dict) - An element of data from bmrblib.

Returns: list of str

The list of molecule names.

num_spins(data)

source code

Determine the number of spins in the given data.

Parameters:

data (dict) - An element of data from bmrblib.

Returns: int

The number of spins.

read(file=None, directory=None, version=None, sample_conditions=None)

source code

Read the contents of a BMRB NMR-STAR formatted file.

Parameters:

file (str) - The name of the BMRB STAR formatted file.
directory (None or str) - The directory where the file is located.
version (None or str) - The BMRB version to force the reading.
sample_conditions (None or str) - The sample condition label to read. Only one sample condition can be read per data pipe.

Variables Details

[hide private]

ds

Value:

The relax data storage object.

Data pipes:
  None

Data store objects:
  __dict__ <type 'dict'>: dict() -> new empty dictionary
  __doc__ <type 'str'>: The relax data storage object.
...