Author: bugman
Date: Thu Oct 29 17:54:26 2009
New Revision: 9857
URL: http://svn.gna.org/viewcvs/relax?rev=9857&view=rev
Log:
Added the model-free model selection and elimination and set theory papers as
citations.
These are also placed into the BMRB file.
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=9857&r1=9856&r2=9857&view=diff
==============================================================================
--- branches/bmrb/generic_fns/exp_info.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Thu Oct 29 17:54:26 2009
@@ -69,13 +69,14 @@
CITE = {}
SOFTWARE = {}
-# relax.
+# relax software.
SOFTWARE['relax'] = Software_store()
SOFTWARE['relax'].name = "relax"
SOFTWARE['relax'].authors = "The relax development team"
SOFTWARE['relax'].url = "http://nmr-relax.com";
SOFTWARE['relax'].tasks = ["data processing"]
+# relax citation 1.
CITE['relax 1'] = Cite_store()
CITE['relax 1'].authors = [["Edward", "d'Auvergne", "E.", "J."], ["Paul",
"Gooley", "P.", "R."]]
CITE['relax 1'].doi = "10.1007/s10858-007-9214-2"
@@ -92,6 +93,7 @@
CITE['relax 1'].page_last = 119
CITE['relax 1'].year = 2008
+# relax citation 2.
CITE['relax 2'] = Cite_store()
CITE['relax 2'].authors = [["Edward", "d'Auvergne", "E.", "J."], ["Paul",
"Gooley", "P.", "R."]]
CITE['relax 2'].doi = "10.1007/s10858-007-9213-3"
@@ -108,13 +110,12 @@
CITE['relax 2'].page_last = 133
CITE['relax 2'].year = 2008
-# NMRPipe citation.
+# NMRPipe software and citation.
SOFTWARE['NMRPipe'] = Software_store()
SOFTWARE['NMRPipe'].name = "NMRPipe"
SOFTWARE['NMRPipe'].authors = "Delaglio, F., Grzesiek, S., Vuister, G. W.,
Zhu, G., Pfeifer, J., and Bax, A"
SOFTWARE['NMRPipe'].url = "http://spin.niddk.nih.gov/NMRPipe/";
SOFTWARE['NMRPipe'].tasks = ["processing"]
-
CITE['NMRPipe'] = Cite_store()
CITE['NMRPipe'].authors = [["Frank", "Delaglio", "F.", None], ["Stephan",
"Grzesiek", "S.", None], ["Geerten", "Vuister", "G.", "W."], ["Guang", "Zhu",
"G.", None], ["John", "Pfeifer", "J.", None], ["Ad", "Bax", "A.", None]]
CITE['NMRPipe'].doi = "10.1007/BF00197809"
@@ -130,14 +131,13 @@
CITE['NMRPipe'].page_last = 293
CITE['NMRPipe'].year = 1995
-# Sparky citation.
+# Sparky software and citation.
SOFTWARE['Sparky'] = Software_store()
SOFTWARE['Sparky'].name = "Sparky"
SOFTWARE['Sparky'].authors = "Goddard, T. D. and Kneller, D. G."
SOFTWARE['Sparky'].ref = "Goddard, T. D. and Kneller, D. G., SPARKY 3,
University of California, San Francisco."
SOFTWARE['Sparky'].url = "http://www.cgl.ucsf.edu/home/sparky/";
SOFTWARE['Sparky'].tasks = ["spectral analysis"]
-
CITE['Sparky'] = Cite_store()
CITE['Sparky'].authors = [["Tom", "Goddard", "T.", "D."], ["Donald",
"Kneller", "D.", "G."]]
CITE['Sparky'].full_citation = "Goddard, T. D. and Kneller, D. G., SPARKY 3,
University of California, San Francisco."
@@ -145,6 +145,53 @@
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
@@ -300,6 +347,29 @@
text = f.read()
f.close()
+ # Init the citation structures.
+ cite_id = []
+ cite_key = []
+
+ # 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')
+
+ # Model-free model elimination.
+ if model_elim:
+ cite_id.append('model-free model elimination')
+ cite_key.append('Mf model elimination')
+
+ # Universal solution citation.
+ if universal_solution:
+ cite_id.append('model-free set theory')
+ cite_key.append('Set theory')
+
+ # Add the 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)
+
# Place the data in the container.
cdp.exp_info.setup_script(file=file, dir=dir, text=text,
analysis_type=analysis_type, model_selection=model_selection, engine=engine,
model_elim=model_elim, universal_solution=universal_solution)
r9857 - /branches/bmrb/generic_fns/exp_info.py