Author: bugman
Date: Tue Oct 13 18:24:23 2009
New Revision: 9756
URL: http://svn.gna.org/viewcvs/relax?rev=9756&view=rev
Log:
The relax citations are now placed into the BMRB file.
Modified:
branches/bmrb/data/exp_info.py
branches/bmrb/generic_fns/exp_info.py
Modified: branches/bmrb/data/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/data/exp_info.py?rev=9756&r1=9755&r2=9756&view=diff
==============================================================================
--- branches/bmrb/data/exp_info.py (original)
+++ branches/bmrb/data/exp_info.py Tue Oct 13 18:24:23 2009
@@ -115,6 +115,9 @@
# Append the container.
self.citations.append(cite)
+ # Return the index of this citation.
+ return len(self.citations) - 1
+
def software_setup(self, name, version=None, url=None, vendor_name=None,
cite=None, tasks=None):
"""Set up the software information.
Modified: branches/bmrb/generic_fns/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/exp_info.py?rev=9756&r1=9755&r2=9756&view=diff
==============================================================================
--- branches/bmrb/generic_fns/exp_info.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Tue Oct 13 18:24:23 2009
@@ -32,9 +32,37 @@
# relax fixed info.
RELAX_NAME = "relax"
RELAX_AUTHORS = "The relax development team"
-RELAX_REF = "d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of
NMR dynamic models I. Minimisation algorithms and their performance within
the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR,
40(2), 107-119; d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of
NMR dynamic models II. A new methodology for the dual optimisation of the
model-free parameters and the Brownian rotational diffusion tensor. J.
Biomol. NMR, 40(2), 121-133."
RELAX_URL = "http://nmr-relax.com";
RELAX_TASKS = ["data processing"]
+RELAX_CITE1_AUTHORS=[["Edward", "d'Auvergne", "E.", "J."], ["Paul",
"Gooley", "P.", "R."]]
+RELAX_CITE1_DOI="10.1007/s10858-007-9214-2"
+RELAX_CITE1_PUBMED_ID="18085410"
+RELAX_CITE1_FULL_CITATION="d'Auvergne, E. J. and Gooley, P. R. (2008).
Optimisation of NMR dynamic models I. Minimisation algorithms and their
performance within the model-free and Brownian rotational diffusion spaces.
J. Biomol. NMR, 40(2), 107-119."
+RELAX_CITE1_TITLE="Optimisation of NMR dynamic models I. Minimisation
algorithms and their performance within the model-free and Brownian
rotational diffusion spaces."
+RELAX_CITE1_STATUS="published"
+RELAX_CITE1_TYPE="journal"
+RELAX_CITE1_JOURNAL_ABBREV="J. Biomol. NMR"
+RELAX_CITE1_JOURNAL_FULL="Journal of Biomolecular NMR"
+RELAX_CITE1_VOLUME=40
+RELAX_CITE1_ISSUE=2
+RELAX_CITE1_PAGE_FIRST=107
+RELAX_CITE1_PAGE_LAST=119
+RELAX_CITE1_YEAR=2008
+RELAX_CITE2_AUTHORS=[["Edward", "d'Auvergne", "E.", "J."], ["Paul",
"Gooley", "P.", "R."]]
+RELAX_CITE2_DOI="10.1007/s10858-007-9213-3"
+RELAX_CITE2_PUBMED_ID="18085411"
+RELAX_CITE2_FULL_CITATION="d'Auvergne, E. J. and Gooley, P. R. (2008).
Optimisation of NMR dynamic models II. A new methodology for the dual
optimisation of the model-free parameters and the Brownian rotational
diffusion tensor. J. Biomol. NMR, 40(2), 121-133."
+RELAX_CITE2_TITLE="Optimisation of NMR dynamic models II. A new methodology
for the dual optimisation of the model-free parameters and the Brownian
rotational diffusion tensor."
+RELAX_CITE2_STATUS="published"
+RELAX_CITE2_TYPE="journal"
+RELAX_CITE2_JOURNAL_ABBREV="J. Biomol. NMR"
+RELAX_CITE2_JOURNAL_FULL="Journal of Biomolecular NMR"
+RELAX_CITE2_VOLUME=40
+RELAX_CITE2_ISSUE=2
+RELAX_CITE2_PAGE_FIRST=121
+RELAX_CITE2_PAGE_LAST=133
+RELAX_CITE2_YEAR=2008
+
# NMRPipe fixed info.
NMRPIPE_NAME = "NMRPipe"
@@ -59,6 +87,10 @@
@type star: NMR_STAR instance
"""
+ # First add relax.
+ cite1 = cdp.exp_info.add_citation(authors=RELAX_CITE1_AUTHORS,
doi=RELAX_CITE1_DOI, pubmed_id=RELAX_CITE1_PUBMED_ID,
full_citation=RELAX_CITE1_FULL_CITATION, title=RELAX_CITE1_TITLE,
status=RELAX_CITE1_STATUS, type=RELAX_CITE1_TYPE,
journal_abbrev=RELAX_CITE1_JOURNAL_ABBREV,
journal_full=RELAX_CITE1_JOURNAL_FULL, volume=RELAX_CITE1_VOLUME,
issue=RELAX_CITE1_ISSUE, page_first=RELAX_CITE1_PAGE_FIRST,
page_last=RELAX_CITE1_PAGE_LAST, year=RELAX_CITE1_YEAR)
+ cite2 = cdp.exp_info.add_citation(authors=RELAX_CITE2_AUTHORS,
doi=RELAX_CITE2_DOI, pubmed_id=RELAX_CITE2_PUBMED_ID,
full_citation=RELAX_CITE2_FULL_CITATION, title=RELAX_CITE2_TITLE,
status=RELAX_CITE2_STATUS, type=RELAX_CITE2_TYPE,
journal_abbrev=RELAX_CITE2_JOURNAL_ABBREV,
journal_full=RELAX_CITE2_JOURNAL_FULL, volume=RELAX_CITE2_VOLUME,
issue=RELAX_CITE2_ISSUE, page_first=RELAX_CITE2_PAGE_FIRST,
page_last=RELAX_CITE2_PAGE_LAST, year=RELAX_CITE2_YEAR)
+
# Loop over the citations.
if hasattr(cdp, 'exp_info') and hasattr(cdp.exp_info, 'citations'):
for citations in cdp.exp_info.citations:
@@ -172,11 +204,20 @@
# relax.
if name == 'relax':
- cdp.exp_info.software_setup(name=RELAX_NAME, version=version_full(),
vendor_name=RELAX_AUTHORS, url=RELAX_URL, cite=RELAX_REF, tasks=RELAX_TASKS)
+ # Add the citations.
+ cite1 = cdp.exp_info.add_citation(authors=RELAX_CITE1_AUTHORS,
doi=RELAX_CITE1_DOI, pubmed_id=RELAX_CITE1_PUBMED_ID,
full_citation=RELAX_CITE1_FULL_CITATION, title=RELAX_CITE1_TITLE,
status=RELAX_CITE1_STATUS, type=RELAX_CITE1_TYPE,
journal_abbrev=RELAX_CITE1_JOURNAL_ABBREV,
journal_full=RELAX_CITE1_JOURNAL_FULL, volume=RELAX_CITE1_VOLUME,
issue=RELAX_CITE1_ISSUE, page_first=RELAX_CITE1_PAGE_FIRST,
page_last=RELAX_CITE1_PAGE_LAST, year=RELAX_CITE1_YEAR)
+ cite2 = cdp.exp_info.add_citation(authors=RELAX_CITE2_AUTHORS,
doi=RELAX_CITE2_DOI, pubmed_id=RELAX_CITE2_PUBMED_ID,
full_citation=RELAX_CITE2_FULL_CITATION, title=RELAX_CITE2_TITLE,
status=RELAX_CITE2_STATUS, type=RELAX_CITE2_TYPE,
journal_abbrev=RELAX_CITE2_JOURNAL_ABBREV,
journal_full=RELAX_CITE2_JOURNAL_FULL, volume=RELAX_CITE2_VOLUME,
issue=RELAX_CITE2_ISSUE, page_first=RELAX_CITE2_PAGE_FIRST,
page_last=RELAX_CITE2_PAGE_LAST, year=RELAX_CITE2_YEAR)
+
+ # Add the software info.
+ cdp.exp_info.software_setup(name=RELAX_NAME, version=version_full(),
vendor_name=RELAX_AUTHORS, url=RELAX_URL, cite=[cite1, cite2],
tasks=RELAX_TASKS)
# NMRPipe.
if name == 'NMRPipe':
- cdp.exp_info.software_setup(name=NMRPIPE_NAME, version=version,
vendor_name=NMRPIPE_AUTHORS, url=NMRPIPE_URL, cite=NMRPIPE_REF,
tasks=NMRPIPE_TASKS)
+ # Add the citations.
+ #cite_index = cdp.exp_info.add_citation(authors=[["The relax
development team", None, None, None]])
+ cite_index = 1
+
+ cdp.exp_info.software_setup(name=NMRPIPE_NAME, version=version,
vendor_name=NMRPIPE_AUTHORS, url=NMRPIPE_URL, cite=cite_index,
tasks=NMRPIPE_TASKS)
# Sparky.
elif name == 'Sparky':
@@ -184,5 +225,9 @@
if not version:
raise RelaxError("The Sparky version number has not been
supplied.")
+ # Add the citations.
+ #cite_index = cdp.exp_info.add_citation(authors=[["The relax
development team", None, None, None]])
+ cite_index = 1
+
# Add the data.
- cdp.exp_info.software_setup(name=SPARKY_NAME, version=version,
vendor_name=SPARKY_AUTHORS, url=SPARKY_URL, cite=SPARKY_REF,
tasks=SPARKY_TASKS)
+ cdp.exp_info.software_setup(name=SPARKY_NAME, version=version,
vendor_name=SPARKY_AUTHORS, url=SPARKY_URL, cite=cite_index,
tasks=SPARKY_TASKS)
r9756 - in /branches/bmrb: data/exp_info.py generic_fns/exp_info.py