Module bmrb
source code
Module containing functions for BMRB support.
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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,
isotopes=None,
elements=None)
Generate the sequence data from the BRMB information. |
source code
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list of str
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list of str
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int
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read(file=None,
dir=None,
version=None,
sample_conditions=None)
Read the contents of a BMRB NMR-STAR formatted file. |
source code
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write(file=None,
dir=None,
version=' 3.1 ' ,
force=False)
Create a BMRB NMR-STAR formatted file. |
source code
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ds = The relax data storage obje...
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status = Status()
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__package__ = ' pipe_control '
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Imports:
F_OK,
access,
sys,
Relax_data_store,
dep_check,
Info_box,
RelaxError,
RelaxFileError,
RelaxFileOverwriteError,
RelaxNoModuleInstallError,
RelaxNoPipeError,
get_file_path,
mkdir_nofail,
exp_info,
create_spin,
generate_spin_id,
metadata_cleanup,
return_spin,
set_spin_element,
set_spin_isotope,
cdp_name,
add_result_file,
return_api,
Status,
version_full
Display the results in the BMRB NMR-STAR format.
- Parameters:
version (str) - The NMR-STAR version to create. This can be either '2.1', '3.0',
or '3.1'.
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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,
isotopes=None,
elements=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.
isotopes (list of str or None) - The optional list of isotope types.
elements (list of str or None) - The optional list of element types.
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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.
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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.
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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.
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read(file=None,
dir=None,
version=None,
sample_conditions=None)
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Read the contents of a BMRB NMR-STAR formatted file.
- Parameters:
file (str) - The name of the BMRB STAR formatted file.
dir (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.
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write(file=None,
dir=None,
version=' 3.1 ' ,
force=False)
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Create a BMRB NMR-STAR formatted file.
- Parameters:
file (str or file object) - The name of the file to create or a file object.
dir (str or None) - The optional directory to place the file into. If set to
'pipe_name', then it will be placed in a directory with the same
name as the current data pipe.
version (str) - The NMR-STAR version to create. This can be either '2.1', '3.0',
or '3.1'.
force (bool) - A flag which if True will allow a currently existing file to be
overwritten.
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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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