Package generic_fns :: Module bmrb
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Module bmrb

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Module containing functions for BMRB support.

Functions [hide private]
 
display(version='3.1')
Display the results in the BMRB NMR-STAR format.
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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.
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list of str
list_sample_conditions(star)
Get a listing of all the sample conditions.
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list of str
molecule_names(data, N=0)
Generate the molecule names list.
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int
num_spins(data)
Determine the number of spins in the given data.
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read(file=None, directory=None, version=None, sample_conditions=None)
Read the contents of a BMRB NMR-STAR formatted file.
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write(file=None, directory=None, version='3.1', force=False)
Create a BMRB NMR-STAR formatted file.
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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)

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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)

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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)

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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)

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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.
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