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Class for interfacing with the BMRB (http://www.bmrb.wisc.edu/).
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Specify a citation to be added the BMRB data file.
Keyword Arguments
~~~~~~~~~~~~~~~~~
cite_id: The citation ID string.
authors: The list of authors. Each author element is a list of four elements (the first name, last
name, first initial, and middle initials).
doi: The DOI number, e.g. '10.1000/182'.
pubmed_id: The identification code assigned to the publication by PubMed.
full_citation: The full citation as given in a reference list.
title: The title of the publication.
status: The publication status.
type: The type of publication.
journal_abbrev: The standard journal abbreviation.
journal_full: The full journal name.
volume: The volume number.
issue: The issue number.
page_first: The first page number.
page_last: The last page number.
year: The publication year.
Description
~~~~~~~~~~~
The full_citation should be in a format similar to that used in a journal article by either cutting
and pasting from another document or by typing. Please include author names, title, journal, page
numbers, and year or equivalent information for the type of publication given.
The journal status can only be one of:
"preparation",
"in press",
"published",
"retracted",
"submitted".
The citation type can only be one of:
"abstract",
"BMRB only",
"book",
"book chapter",
"internet",
"journal",
"personal communication",
"thesis".
The standard journal abbreviation is that defined by the Chemical Abstract Services for the journal
where the data are or will be published. If the data in the deposition are related to a J. Biomol.
NMR paper, the value must be 'J. Biomol. NMR' to alert the BMRB annotators so that the deposition is
properly processed. If the depositor truly does not know the journal, a value of 'not known' or
'na' is acceptable.
Examples
~~~~~~~~
To add the citation "d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of the
model-free problem and the diffusion seeded model-free paradigm. Mol. Biosyst., 3(7),
483-494.", type:
relax> bmrb.citation(authors=[["Edward", "d'Auvergne", "E.", "J."], ["Paul", "Gooley", "P.",
"R."]], doi="10.1039/b702202f", pubmed_id="17579774",
full_citation="d'Auvergne E. J., Gooley P. R. (2007). Set theory
formulation of the model-free problem and the diffusion seeded
model-free paradigm. Mol. Biosyst., 3(7), 483-494.", title="Set theory
formulation of the model-free problem and the diffusion seeded
model-free paradigm.", status="published", type="journal",
journal_abbrev="Mol. Biosyst.", journal_full="Molecular Biosystems",
volume=3, issue=7, page_first=483, page_last=498, year=2007)
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Read BMRB files in the NMR-STAR format. Keyword Arguments ~~~~~~~~~~~~~~~~~ file: The name of the BMRB STAR formatted file. dir: The directory where the file is located. version: For the reading to use the given NMR-STAR version. sample_conditions: The sample conditions label in the NMR-STAR file to restrict loading to. Description ~~~~~~~~~~~ To search for the results file in the current working directory, set dir to None. Note that only one sample condition can be read per relax data pipe. Therefore if sample_conditions is not given and multiple conditions exist in the NMR-STAR file, a RelaxError will be raised. |
Specify the scripts used in the analysis.
Keyword Arguments
~~~~~~~~~~~~~~~~~
file: The script file name.
dir: The directory name.
analysis_type: The type of analysis performed.
model_selection: The model selection technique used, if relevant.
engine: The software engine used in the analysis.
model_elim: A model-free specific flag specifying if model elimination was performed.
universal_solution: A model-free specific flag specifying if the universal solution was sought
after.
Description
~~~~~~~~~~~
This user function allows scripts used in the analysis to be included in the BMRB deposition. The
following addition information may need to be specified with the script.
The analysis_type must be set. Allowable values include all the data pipe types used in relax, ie:
'frame order': The Frame Order theories,
'jw': Reduced spectral density mapping,
'mf': Model-free analysis,
'N-state': N-state model of domain motions,
'noe': Steady state NOE calculation,
'relax_fit': Relaxation curve fitting,
The model_selection argument only needs to be set if the script selects between different
mathematical models. This can be anything, but the following are recommended:
'AIC': Akaike's Information Criteria.
'AICc': Small sample size corrected AIC.
'BIC': Bayesian or Schwarz Information Criteria.
'Bootstrap': Bootstrap model selection.
'CV': Single-item-out cross-validation.
'Expect': The expected overall discrepancy (the true values of the parameters are required).
'Farrow': Old model-free method by Farrow et al., 1994.
'Palmer': Old model-free method by Mandel et al., 1995.
'Overall': The realised overall discrepancy (the true values of the parameters are required).
The engine is the software used in the calculation, optimisation, etc. This can be anything, but
those recognised by relax (automatic program info, citations, etc. added) include:
'relax': hence relax was used for the full analysis.
'modelfree4': Art Palmer's Modelfree4 program was used for optimising the model-free parameter
values.
'dasha': The Dasha program was used for optimising the model-free parameter values.
'curvefit': Art Palmer's curvefit program was used to determine the R1 or R2 values.
The model_elim flag is model-free specific and should be set if the methods from "d'Auvergne, E. J.
and Gooley, P. R. (2006). Model-free model elimination: A new step in the model-free dynamic
analysis of NMR relaxation data. J. Biomol. NMR, 35(2), 117-135." were used. This should be set to
True for the full_analysis.py script.
The universal_solution flag is model-free specific and should be set if the methods from "d'Auvergne
E. J., Gooley P. R. (2007). Set theory formulation of the model-free problem and the diffusion
seeded model-free paradigm. Mol. Biosyst., 3(7), 483-494." were used. This should be set to True
for the full_analysis.py script.
Examples
~~~~~~~~
For BMRB deposition, to specify that the full_analysis.py script was used, type one of:
relax> bmrb.script('full_analysis.py', 'model-free', 'AIC', 'relax', True, True)
relax> bmrb.script(file='full_analysis.py', dir=None, analysis_type='model-free',
model_selection='AIC', engine='relax', model_elim=True,
universal_solution=True)
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Specify the software used in the analysis.
Keyword Arguments
~~~~~~~~~~~~~~~~~
name: The name of the software program utilised.
version: The version of the software, if applicable.
url: The web address of the software.
vendor_name: The name of the company or person behind the program.
cite_ids: A list of the citation ID numbers.
tasks: A list of all the tasks performed by the software.
Description
~~~~~~~~~~~
This user function allows the software used in the analysis to be specified in full detail.
For the tasks list, this should be a python list of strings (eg. ['spectral processing']). Although
not restricted to these, the values suggested by the BMRB are:
'chemical shift assignment',
'chemical shift calculation',
'collection',
'data analysis',
'geometry optimization',
'peak picking',
'processing',
'refinement',
'structure solution'
Examples
~~~~~~~~
For BMRB deposition, to say that Sparky was used in the analysis, type:
relax> cite_id = bmrb.citation(authors=[['Tom', 'Goddard', 'T.', 'D.'], ['D', 'Kneller',
'D.', 'G.']], title=""Goddard, T. D. and Kneller, D. G., SPARKY 3, University of
California, San Francisco."
relax> bmrb.software('Sparky', version='3.110', url="http://www.cgl.ucsf.edu/home/sparky/",
vendor_name="Goddard, T. D.", cite_ids=[cite_id], tasks=["spectral analysis"])
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Select the software used in the analysis.
Keyword Arguments
~~~~~~~~~~~~~~~~~
name: The name of the software program utilised.
version: The version of the software, if applicable.
Description
~~~~~~~~~~~
Rather than specifying all the information directly, this user function allows the software packaged
used in the analysis to be selected by name. The programs currently supported are:
'NMRPipe' - http://spin.niddk.nih.gov/NMRPipe/
'Sparky' - http://www.cgl.ucsf.edu/home/sparky/
More can be added if all relevant information (program name, description, website, original
citation, purpose, etc.) is emailed to relax-users@gna.org.
Note that relax is automatically added to the BMRB file.
Examples
~~~~~~~~
For BMRB deposition, to say that both NMRPipe and Sparky were used prior to relax, type:
relax> bmrb.software_select('NMRPipe')
relax> bmrb.software_select('Sparky', version='3.113')
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Select the thiol state of the system.
Keyword Arguments
~~~~~~~~~~~~~~~~~
state: The thiol state.
Description
~~~~~~~~~~~
The thiol state can be any text, thought the BMRB suggests the following:
'all disulfide bound',
'all free',
'all other bound',
'disulfide and other bound',
'free and disulfide bound',
'free and other bound',
'free disulfide and other bound',
'not available',
'not present',
'not reported',
'unknown'.
Alternatively the pure states 'reduced' or 'oxidised' could be specified.
Examples
~~~~~~~~
For BMRB deposition, to say that the protein studied is in the oxidised state, tyype one of:
relax> bmrb.thiol_state('oxidised')
relax> bmrb.thiol_state(state='oxidised')
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BMRB file writing. Keyword Arguments ~~~~~~~~~~~~~~~~~ file: The name of the BMRB file to output results to. Optionally this can be a file object, or any object with a write() method. dir: The directory name. version: The NMR-STAR dictionary format version to use. force: A flag which if True will cause the any pre-existing file to be overwritten. Description ~~~~~~~~~~~ To place the BMRB file in the current working directory, set dir to None. If dir is set to the special name 'pipe_name', then the results file will be placed into a directory with the same name as the current data pipe. |
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