Author: bugman
Date: Mon Oct 12 00:30:47 2009
New Revision: 9744
URL: http://svn.gna.org/viewcvs/relax?rev=9744&view=rev
Log:
Created the bmrb.citation() user function.
Modified:
branches/bmrb/generic_fns/exp_info.py
branches/bmrb/prompt/bmrb.py
Modified: branches/bmrb/generic_fns/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/exp_info.py?rev=9744&r1=9743&r2=9744&view=diff
==============================================================================
--- branches/bmrb/generic_fns/exp_info.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Mon Oct 12 00:30:47 2009
@@ -73,6 +73,47 @@
raise RelaxError("relax cannot be the only program used in the
analysis - spectral analysis programs, etc. must also have been used. Please
use the relevant BMRB user functions to specify these.")
+def citation(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.
+
+ @keyword authors: The list of authors. Each author element is
a list of four elements: the first name, last name, first initial, and middle
initials.
+ @type authors: list of lists of str
+ @keyword doi: The DOI number, e.g. "10.1000/182".
+ @type doi: None or str
+ @keyword pubmed_id: The identification code assigned to the
publication by PubMed.
+ @type pubmed_id: None or int
+ @keyword full_citation: 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.
+ @type full_citation: str
+ @keyword title: The title of the publication.
+ @type title: str
+ @keyword status: The publication status. Can be one of in
"preparation", "in press", "published", "retracted", or "submitted".
+ @type status: str
+ @keyword type: The publication type. Can be one of
"abstract", "BMRB only", "book", "book chapter", "internet", "journal",
"personal communication", or "thesis".
+ @type type: str
+ @keyword journal_abbrev: 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.
+ @type journal_abbrev: str
+ @keyword journal_full: The full journal name.
+ @type journal_full: str
+ @keyword volume: The volume number.
+ @type volume: int
+ @keyword issue: The issue number.
+ @type issue: int
+ @keyword page_first: The first page number.
+ @type page_first: int
+ @keyword page_last: The last page number.
+ @type page_last: int
+ @keyword year: The publication year.
+ @type year: int
+ """
+
+ # Set up the experimental info data container, if needed.
+ if not hasattr(cdp, 'exp_info'):
+ cdp.exp_info = ExpInfo()
+
+ # Place the data in the container.
+ cdp.exp_info.add_citation(authors=authors, doi=doi, pubmed_id=pubmed_id,
full_citation=full_citation, title=title, status=status, type=type,
journal_abbrev=journal_abbrev, journal_full=journal_full, volume=volume,
issue=issue, page_first=page_first, page_last=page_last, year=year)
+
+
def software(name=None, version=None, url=None, vendor_name=None, cite=None,
tasks=None):
"""Select by name the software used in the analysis.
Modified: branches/bmrb/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/bmrb.py?rev=9744&r1=9743&r2=9744&view=diff
==============================================================================
--- branches/bmrb/prompt/bmrb.py (original)
+++ branches/bmrb/prompt/bmrb.py Mon Oct 12 00:30:47 2009
@@ -36,6 +36,130 @@
class BMRB(User_fn_class):
"""Class for interfacing with the BMRB (http://www.bmrb.wisc.edu/)."""
+
+ def citation(self, authors=None, doi=None, pubmed_id=None,
full_citation=None, title=None, status='published', type='journal',
journal_abbrev=None, journal_full=None, volume=None, issue=None,
page_first=None, page_last=None, year=None):
+ """Specify a citation to be added the BMRB data file.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ 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.
+
+ 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)
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "bmrb.citation("
+ text = text + "authors=" + repr(authors)
+ text = text + ", doi=" + repr(doi)
+ text = text + ", pubmed_id=" + repr(pubmed_id)
+ text = text + ", full_citation=" + repr(full_citation)
+ text = text + ", title=" + repr(title)
+ text = text + ", status=" + repr(status)
+ text = text + ", type=" + repr(type)
+ text = text + ", journal_abbrev=" + repr(journal_abbrev)
+ text = text + ", journal_full=" + repr(journal_full)
+ text = text + ", volume=" + repr(volume)
+ text = text + ", issue=" + repr(issue)
+ text = text + ", page_first=" + repr(page_first)
+ text = text + ", page_last=" + repr(page_last)
+ text = text + ", year=" + repr(year) + ")"
+ print(text)
+
+ # The argument checks.
+ check.is_str_list(authors, 'authors', list_of_lists=True)
+ check.is_str(doi, 'DOI number', can_be_none=True)
+ check.is_str(pubmed_id, 'Pubmed ID number', can_be_none=True)
+ check.is_str(full_citation, 'full citation')
+ check.is_str(title, 'title')
+ check.is_str(status, 'status')
+ check.is_str(type, 'type')
+ check.is_str(journal_abbrev, 'journal abbreviation',
can_be_none=True)
+ check.is_str(journal_full, 'full journal name', can_be_none=True)
+ check.is_int(volume, 'volume', can_be_none=True)
+ check.is_int(issue, 'issue', can_be_none=True)
+ check.is_int(page_first, 'first page number', can_be_none=True)
+ check.is_int(page_last, 'last page number', can_be_none=True)
+ check.is_int(year, 'publication year')
+
+ # Execute the functional code.
+ exp_info.citation(authors=authors, doi=doi, pubmed_id=pubmed_id,
full_citation=full_citation, title=title, status=status, type=type,
journal_abbrev=journal_abbrev, journal_full=journal_full, volume=volume,
issue=issue, page_first=page_first, page_last=page_last, year=year)
+
def display(self, version='3.1'):
"""Display the BMRB data in NMR-STAR format."""
r9744 - in /branches/bmrb: generic_fns/exp_info.py prompt/bmrb.py