Module exp_info

Module containing functions for specifying the experimental details.

Classes

Software_store
Software storage container.

Functions

bmrb_write_citations(star)
Generate the Citations saveframe records.

tuple of list of int and list of str bmrb_write_methods(star)
Generate the Software saveframe records.

tuple of list of int and list of str bmrb_write_software(star)
Generate the Software saveframe records.

citation(cite_id=None, authors=None, doi=None, pubmed_id=None, full_citation=None, title=None, status=None, type=None, journal_abbrev=None, journal_full=None, volume=None, issue=None, page_first=None, page_last=None, year=None)
Store a citation.

script(file=None, dir=None, analysis_type=None, model_selection=None, engine=None, model_elim=False, universal_solution=False)
Specify the scripts used in the analysis.

software(name=None, version=None, url=None, vendor_name=None, cite_ids=None, tasks=None)
Select by name the software used in the analysis.

software_select(name, version=None)
Select by name the software used in the analysis.

thiol_state(state=None)
Set the thiol state of the system.

Variables

SOFTWARE = {}

__package__ = 'generic_fns'

Imports: Info_box, ExpInfo, RelaxError, open_read_file, version_full

Function Details

bmrb_write_citations(star)

Generate the Citations saveframe records.

Parameters:

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

bmrb_write_methods(star)

Generate the Software saveframe records.

Parameters:

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

Returns: tuple of list of int and list of str

A list BMRB software IDs and a list of software labels.

bmrb_write_software(star)

Generate the Software saveframe records.

Parameters:

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

Returns: tuple of list of int and list of str

A list BMRB software IDs and a list of software labels.

citation(cite_id=None, authors=None, doi=None, pubmed_id=None, full_citation=None, title=None, status=None, type=None, journal_abbrev=None, journal_full=None, volume=None, issue=None, page_first=None, page_last=None, year=None)

Store a citation.

Parameters:

• cite_id (str) - The citation ID string.
• authors (list of lists of str) - The list of authors. Each author element is a list of four elements: the first name, last name, first initial, and middle initials.
• doi (None or str) - The DOI number, e.g. "10.1000/182".
• pubmed_id (None or int) - The identification code assigned to the publication by PubMed.
• full_citation (str) - A full citation 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.
• title (str) - The title of the publication.
• status (str) - The publication status. Can be one of in "preparation", "in press", "published", "retracted", or "submitted".
• type (str) - The publication type. Can be one of "abstract", "BMRB only", "book", "book chapter", "internet", "journal", "personal communication", or "thesis".
• journal_abbrev (str) - A standard journal abbreviation as 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.
• journal_full (str) - The full journal name.
• volume (int) - The volume number.
• issue (int) - The issue number.
• page_first (int) - The first page number.
• page_last (int) - The last page number.
• year (int) - The publication year.

script(file=None, dir=None, analysis_type=None, model_selection=None, engine=None, model_elim=False, universal_solution=False)

Specify the scripts used in the analysis.

Parameters:

• file (str) - The name of the file to open.
• dir (None or str) - The directory containing the file (defaults to the current directory if None).
• analysis_type (str) - The type of analysis performed.
• model_selection (None or str) - The model selection technique used, if relevant.
• engine (str) - The software engine used in the analysis.
• model_elim (bool) - A model-free specific flag specifying if model elimination was performed.
• universal_solution (bool) - A model-free specific flag specifying if the universal solution was sought after.

software(name=None, version=None, url=None, vendor_name=None, cite_ids=None, tasks=None)

Select by name the software used in the analysis.

Parameters:

• name (str) - The name of the software program.
• version (None or str) - The program version.
• url (None or str) - The program's URL.
• vendor_name (str) - The name of the company or person behind the program.
• cite_ids (None or str) - The citation ID numbers.
• tasks (list of str) - The tasks performed by the program.

software_select(name, version=None)

Select by name the software used in the analysis.

Parameters:

• name (str) - The name of the software program.
• version (None or str) - The program version.

thiol_state(state=None)

Set the thiol state of the system.

Parameters:

• state (str) - The thiol state of the molecule.