Author: bugman
Date: Wed Feb 24 00:15:26 2010
New Revision: 10880
URL: http://svn.gna.org/viewcvs/relax?rev=10880&view=rev
Log:
Shifted to using the Info_box rather than the local CITE variable.
This is for the d'Auvergne and Gooley, 2003, 2006, and 2007 refs. The rest
will be converted later.
Modified:
branches/bmrb/generic_fns/exp_info.py
Modified: branches/bmrb/generic_fns/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/exp_info.py?rev=10880&r1=10879&r2=10880&view=diff
==============================================================================
--- branches/bmrb/generic_fns/exp_info.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Wed Feb 24 00:15:26 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008-2009 Edward d'Auvergne
#
+# Copyright (C) 2008-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -23,7 +23,11 @@
# Module docstring.
"""Module containing functions for specifying the experimental details."""
+# Python module imports.
+from string import split
+
# relax module imports.
+from info import Info_box
from data.exp_info import ExpInfo
from relax_errors import RelaxError
from relax_io import open_read_file
@@ -144,54 +148,6 @@
CITE['Sparky'].title = "Sparky."
CITE['Sparky'].status = "unpublished"
CITE['Sparky'].type = "internet"
-
-# Model-free model selection citation.
-CITE['Mf model selection'] = Cite_store()
-CITE['Mf model selection'].authors = [["Edward", "d'Auvergne",
"E.", "J."], ["Paul", "Gooley", "P.", "R."]]
-CITE['Mf model selection'].doi = "10.1023/A:1021902006114"
-CITE['Mf model selection'].pubmed_id = "12566997"
-CITE['Mf model selection'].full_citation = "d'Auvergne, E. J. and
Gooley, P. R. (2003). The use of model selection in the model-free analysis
of protein dynamics. J. Biomol. NMR, 25(1), 25-39."
-CITE['Mf model selection'].title = "The use of model selection
in the model-free analysis of protein dynamics."
-CITE['Mf model selection'].status = "published"
-CITE['Mf model selection'].type = "journal"
-CITE['Mf model selection'].journal_abbrev = "J. Biomol. NMR"
-CITE['Mf model selection'].journal_full = "Journal of Biomolecular NMR"
-CITE['Mf model selection'].volume = 25
-CITE['Mf model selection'].page_first = 25
-CITE['Mf model selection'].page_last = 39
-CITE['Mf model selection'].year = 2003
-
-# Model-free model elimination citation.
-CITE['Mf model elimination'] = Cite_store()
-CITE['Mf model elimination'].authors = [["Edward", "d'Auvergne",
"E.", "J."], ["Paul", "Gooley", "P.", "R."]]
-CITE['Mf model elimination'].doi = "10.1007/s10858-006-9007-z"
-CITE['Mf model elimination'].pubmed_id = "16791734"
-CITE['Mf model elimination'].full_citation = "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."
-CITE['Mf model elimination'].title = "Model-free model
elimination: A new step in the model-free dynamic analysis of NMR relaxation
data."
-CITE['Mf model elimination'].status = "published"
-CITE['Mf model elimination'].type = "journal"
-CITE['Mf model elimination'].journal_abbrev = "J. Biomol. NMR"
-CITE['Mf model elimination'].journal_full = "Journal of Biomolecular
NMR"
-CITE['Mf model elimination'].volume = 35
-CITE['Mf model elimination'].page_first = 117
-CITE['Mf model elimination'].page_last = 135
-CITE['Mf model elimination'].year = 2006
-
-# Model-free set theory citation.
-CITE['Set theory'] = Cite_store()
-CITE['Set theory'].authors = [["Edward", "d'Auvergne", "E.",
"J."], ["Paul", "Gooley", "P.", "R."]]
-CITE['Set theory'].doi = "10.1039/b702202f"
-CITE['Set theory'].pubmed_id = "17579774"
-CITE['Set theory'].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."
-CITE['Set theory'].title = "Set theory formulation of the
model-free problem and the diffusion seeded model-free paradigm."
-CITE['Set theory'].status = "published"
-CITE['Set theory'].type = "journal"
-CITE['Set theory'].journal_abbrev = "Mol. Biosyst."
-CITE['Set theory'].journal_full = "Molecular BioSystems"
-CITE['Set theory'].volume = 3
-CITE['Set theory'].page_first = 483
-CITE['Set theory'].page_last = 494
-CITE['Set theory'].year = 2007
@@ -354,21 +310,28 @@
# Model selection.
if model_selection in ['AIC', 'AICc', 'BIC', 'Bootstrap', 'CV',
'Expect', 'Overall']:
cite_id.append('model-free model selection')
- cite_key.append('Mf model selection')
+ cite_key.append('dAuvergneGooley03')
# Model-free model elimination.
if model_elim:
cite_id.append('model-free model elimination')
- cite_key.append('Mf model elimination')
+ cite_key.append('dAuvergneGooley06')
# Universal solution citation.
if universal_solution:
cite_id.append('model-free set theory')
- cite_key.append('Set theory')
-
- # Add the citations.
+ cite_key.append('dAuvergneGooley07')
+
+ # Get the info box.
+ info = Info_box()
+
+ # Loop over all citations.
for id, key in zip(cite_id, cite_key):
- cdp.exp_info.add_citation(cite_id=id, authors=CITE[key].authors,
doi=CITE[key].doi, pubmed_id=CITE[key].pubmed_id,
full_citation=CITE[key].full_citation, title=CITE[key].title,
status=CITE[key].status, type=CITE[key].type,
journal_abbrev=CITE[key].journal_abbrev, journal_full=CITE[key].journal_full,
volume=CITE[key].volume, page_first=CITE[key].page_first,
page_last=CITE[key].page_last, year=CITE[key].year)
+ # Alias the bib entry.
+ bib = info.bib[key]
+
+ # Add the citation.
+ cdp.exp_info.add_citation(cite_id=id, authors=bib.author2,
doi=bib.doi, pubmed_id=bib.pubmed_id, full_citation=bib.cite_short(),
title=bib.title, status=bib.status, type=bib.type,
journal_abbrev=bib.journal, journal_full=bib.journal_full, volume=bib.volume,
page_first=split(bib.pages, '-')[0], page_last=split(bib.pages, '-')[1],
year=bib.year)
# Place the data in the container.
cdp.exp_info.setup_script(file=file, dir=dir, text=text,
cite_ids=cite_id, analysis_type=analysis_type,
model_selection=model_selection, engine=engine, model_elim=model_elim,
universal_solution=universal_solution)
r10880 - /branches/bmrb/generic_fns/exp_info.py