Author: bugman
Date: Thu Oct 29 17:26:35 2009
New Revision: 9855
URL: http://svn.gna.org/viewcvs/relax?rev=9855&view=rev
Log:
Separated the software info from CITE into the SOFTWARE dictionary.
Modified:
branches/bmrb/generic_fns/bmrb.py
branches/bmrb/generic_fns/exp_info.py
Modified: branches/bmrb/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/bmrb.py?rev=9855&r1=9854&r2=9855&view=diff
==============================================================================
--- branches/bmrb/generic_fns/bmrb.py (original)
+++ branches/bmrb/generic_fns/bmrb.py Thu Oct 29 17:26:35 2009
@@ -103,11 +103,11 @@
mkdir_nofail(directory, verbosity=0)
# Add the relax citations.
- cdp.exp_info.add_citation(cite_id='relax_ref1',
authors=exp_info.CITE['relax 1'].cite_authors, doi=exp_info.CITE['relax
1'].cite_doi, pubmed_id=exp_info.CITE['relax 1'].cite_pubmed_id,
full_citation=exp_info.CITE['relax 1'].cite_full_citation,
title=exp_info.CITE['relax 1'].cite_title, status=exp_info.CITE['relax
1'].cite_status, type=exp_info.CITE['relax 1'].cite_type,
journal_abbrev=exp_info.CITE['relax 1'].cite_journal_abbrev,
journal_full=exp_info.CITE['relax 1'].cite_journal_full,
volume=exp_info.CITE['relax 1'].cite_volume, issue=exp_info.CITE['relax
1'].cite_issue, page_first=exp_info.CITE['relax 1'].cite_page_first,
page_last=exp_info.CITE['relax 1'].cite_page_last, year=exp_info.CITE['relax
1'].cite_year)
- cdp.exp_info.add_citation(cite_id='relax_ref2',
authors=exp_info.CITE['relax 2'].cite_authors, doi=exp_info.CITE['relax
2'].cite_doi, pubmed_id=exp_info.CITE['relax 2'].cite_pubmed_id,
full_citation=exp_info.CITE['relax 2'].cite_full_citation,
title=exp_info.CITE['relax 2'].cite_title, status=exp_info.CITE['relax
2'].cite_status, type=exp_info.CITE['relax 2'].cite_type,
journal_abbrev=exp_info.CITE['relax 2'].cite_journal_abbrev,
journal_full=exp_info.CITE['relax 2'].cite_journal_full,
volume=exp_info.CITE['relax 2'].cite_volume, issue=exp_info.CITE['relax
2'].cite_issue, page_first=exp_info.CITE['relax 2'].cite_page_first,
page_last=exp_info.CITE['relax 2'].cite_page_last, year=exp_info.CITE['relax
2'].cite_year)
+ for id, key in zip(['relax_ref1', 'relax_ref2'], ['relax 1', 'relax 2']):
+ cdp.exp_info.add_citation(cite_id=id,
authors=exp_info.CITE[key].authors, doi=exp_info.CITE[key].doi,
pubmed_id=exp_info.CITE[key].pubmed_id,
full_citation=exp_info.CITE[key].full_citation,
title=exp_info.CITE[key].title, status=exp_info.CITE[key].status,
type=exp_info.CITE[key].type,
journal_abbrev=exp_info.CITE[key].journal_abbrev,
journal_full=exp_info.CITE[key].journal_full,
volume=exp_info.CITE[key].volume, issue=exp_info.CITE[key].issue,
page_first=exp_info.CITE[key].page_first,
page_last=exp_info.CITE[key].page_last, year=exp_info.CITE[key].year)
# Add the relax software package.
- cdp.exp_info.software_setup(name=exp_info.CITE['relax 1'].name,
version=version_full(), vendor_name=exp_info.CITE['relax 1'].authors,
url=exp_info.CITE['relax 1'].url, cite_ids=['relax_ref1', 'relax_ref2'],
tasks=exp_info.CITE['relax 1'].tasks)
+ cdp.exp_info.software_setup(name=exp_info.SOFTWARE['relax'].name,
version=version_full(), vendor_name=exp_info.SOFTWARE['relax'].authors,
url=exp_info.SOFTWARE['relax'].url, cite_ids=['relax_ref1', 'relax_ref2'],
tasks=exp_info.SOFTWARE['relax'].tasks)
# Execute the specific BMRB writing code.
write_function(file_path, version=version)
Modified: branches/bmrb/generic_fns/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/exp_info.py?rev=9855&r1=9854&r2=9855&view=diff
==============================================================================
--- branches/bmrb/generic_fns/exp_info.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Thu Oct 29 17:26:35 2009
@@ -30,9 +30,31 @@
from version import version_full
-# Storage container.
+# Storage containers.
class Cite_store:
"""Citation storage container."""
+
+ def __init__(self):
+ """Initialise all variables."""
+
+ self.authors = None
+ self.doi = None
+ self.pubmed_id = None
+ self.full_citation = None
+ self.title = None
+ self.status = None
+ self.type = None
+ self.journal_abbrev = None
+ self.journal_full = None
+ self.volume = None
+ self.issue = None
+ self.page_first = None
+ self.page_last = None
+ self.year = None
+
+
+class Software_store:
+ """Software storage container."""
def __init__(self):
"""Initialise all variables."""
@@ -41,98 +63,87 @@
self.authors = None
self.url = None
self.tasks = None
- self.cite_authors = None
- self.cite_doi = None
- self.cite_pubmed_id = None
- self.cite_full_citation = None
- self.cite_title = None
- self.cite_status = None
- self.cite_type = None
- self.cite_journal_abbrev = None
- self.cite_journal_full = None
- self.cite_volume = None
- self.cite_issue = None
- self.cite_page_first = None
- self.cite_page_last = None
- self.cite_year = None
-
-
-# Citation data structure.
+
+
+# Citation and software data structures.
CITE = {}
-
-# relax citations.
+SOFTWARE = {}
+
+# relax.
+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"]
+
CITE['relax 1'] = Cite_store()
-CITE['relax 1'].name = "relax"
-CITE['relax 1'].authors = "The relax development team"
-CITE['relax 1'].url = "http://nmr-relax.com";
-CITE['relax 1'].tasks = ["data processing"]
-CITE['relax 1'].cite_authors = [["Edward", "d'Auvergne", "E.", "J."],
["Paul", "Gooley", "P.", "R."]]
-CITE['relax 1'].cite_doi = "10.1007/s10858-007-9214-2"
-CITE['relax 1'].cite_pubmed_id = "18085410"
-CITE['relax 1'].cite_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."
-CITE['relax 1'].cite_title = "Optimisation of NMR dynamic models I.
Minimisation algorithms and their performance within the model-free and
Brownian rotational diffusion spaces."
-CITE['relax 1'].cite_status = "published"
-CITE['relax 1'].cite_type = "journal"
-CITE['relax 1'].cite_journal_abbrev = "J. Biomol. NMR"
-CITE['relax 1'].cite_journal_full = "Journal of Biomolecular NMR"
-CITE['relax 1'].cite_volume = 40
-CITE['relax 1'].cite_issue = 2
-CITE['relax 1'].cite_page_first = 107
-CITE['relax 1'].cite_page_last = 119
-CITE['relax 1'].cite_year = 2008
+CITE['relax 1'].authors = [["Edward", "d'Auvergne", "E.", "J."], ["Paul",
"Gooley", "P.", "R."]]
+CITE['relax 1'].doi = "10.1007/s10858-007-9214-2"
+CITE['relax 1'].pubmed_id = "18085410"
+CITE['relax 1'].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."
+CITE['relax 1'].title = "Optimisation of NMR dynamic models I. Minimisation
algorithms and their performance within the model-free and Brownian
rotational diffusion spaces."
+CITE['relax 1'].status = "published"
+CITE['relax 1'].type = "journal"
+CITE['relax 1'].journal_abbrev = "J. Biomol. NMR"
+CITE['relax 1'].journal_full = "Journal of Biomolecular NMR"
+CITE['relax 1'].volume = 40
+CITE['relax 1'].issue = 2
+CITE['relax 1'].page_first = 107
+CITE['relax 1'].page_last = 119
+CITE['relax 1'].year = 2008
CITE['relax 2'] = Cite_store()
-CITE['relax 1'].name = "relax"
-CITE['relax 1'].authors = "The relax development team"
-CITE['relax 1'].url = "http://nmr-relax.com";
-CITE['relax 1'].tasks = ["data processing"]
-CITE['relax 2'].cite_authors = [["Edward", "d'Auvergne", "E.", "J."],
["Paul", "Gooley", "P.", "R."]]
-CITE['relax 2'].cite_doi = "10.1007/s10858-007-9213-3"
-CITE['relax 2'].cite_pubmed_id = "18085411"
-CITE['relax 2'].cite_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."
-CITE['relax 2'].cite_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."
-CITE['relax 2'].cite_status = "published"
-CITE['relax 2'].cite_type = "journal"
-CITE['relax 2'].cite_journal_abbrev = "J. Biomol. NMR"
-CITE['relax 2'].cite_journal_full = "Journal of Biomolecular NMR"
-CITE['relax 2'].cite_volume = 40
-CITE['relax 2'].cite_issue = 2
-CITE['relax 2'].cite_page_first = 121
-CITE['relax 2'].cite_page_last = 133
-CITE['relax 2'].cite_year = 2008
+CITE['relax 2'].authors = [["Edward", "d'Auvergne", "E.", "J."], ["Paul",
"Gooley", "P.", "R."]]
+CITE['relax 2'].doi = "10.1007/s10858-007-9213-3"
+CITE['relax 2'].pubmed_id = "18085411"
+CITE['relax 2'].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."
+CITE['relax 2'].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."
+CITE['relax 2'].status = "published"
+CITE['relax 2'].type = "journal"
+CITE['relax 2'].journal_abbrev = "J. Biomol. NMR"
+CITE['relax 2'].journal_full = "Journal of Biomolecular NMR"
+CITE['relax 2'].volume = 40
+CITE['relax 2'].issue = 2
+CITE['relax 2'].page_first = 121
+CITE['relax 2'].page_last = 133
+CITE['relax 2'].year = 2008
# NMRPipe 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'].name = "NMRPipe"
-CITE['NMRPipe'].authors = "Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu,
G., Pfeifer, J., and Bax, A"
-CITE['NMRPipe'].url = "http://spin.niddk.nih.gov/NMRPipe/";
-CITE['NMRPipe'].tasks = ["processing"]
-CITE['NMRPipe'].cite_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'].cite_doi = "10.1007/BF00197809"
-CITE['NMRPipe'].cite_pubmed_id = "8520220"
-CITE['NMRPipe'].cite_full_citation = "Delaglio, F., Grzesiek, S., Vuister,
G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995). NMRPipe: a multidimensional
spectral processing system based on UNIX pipes. J. Biomol. NMR. 6, 277-293."
-CITE['NMRPipe'].cite_title = "NMRPipe: a multidimensional spectral
processing system based on UNIX pipes."
-CITE['NMRPipe'].cite_status = "published"
-CITE['NMRPipe'].cite_type = "journal"
-CITE['NMRPipe'].cite_journal_abbrev = "J. Biomol. NMR"
-CITE['NMRPipe'].cite_journal_full = "Journal of Biomolecular NMR"
-CITE['NMRPipe'].cite_volume = 6
-CITE['NMRPipe'].cite_page_first = 277
-CITE['NMRPipe'].cite_page_last = 293
-CITE['NMRPipe'].cite_year = 1995
+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"
+CITE['NMRPipe'].pubmed_id = "8520220"
+CITE['NMRPipe'].full_citation = "Delaglio, F., Grzesiek, S., Vuister, G. W.,
Zhu, G., Pfeifer, J., and Bax, A. (1995). NMRPipe: a multidimensional
spectral processing system based on UNIX pipes. J. Biomol. NMR. 6, 277-293."
+CITE['NMRPipe'].title = "NMRPipe: a multidimensional spectral processing
system based on UNIX pipes."
+CITE['NMRPipe'].status = "published"
+CITE['NMRPipe'].type = "journal"
+CITE['NMRPipe'].journal_abbrev = "J. Biomol. NMR"
+CITE['NMRPipe'].journal_full = "Journal of Biomolecular NMR"
+CITE['NMRPipe'].volume = 6
+CITE['NMRPipe'].page_first = 277
+CITE['NMRPipe'].page_last = 293
+CITE['NMRPipe'].year = 1995
# Sparky 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'].name = "Sparky"
-CITE['Sparky'].authors = "Goddard, T. D. and Kneller, D. G."
-CITE['Sparky'].ref = "Goddard, T. D. and Kneller, D. G., SPARKY 3,
University of California, San Francisco."
-CITE['Sparky'].url = "http://www.cgl.ucsf.edu/home/sparky/";
-CITE['Sparky'].tasks = ["spectral analysis"]
-CITE['Sparky'].cite_authors = [["Tom", "Goddard", "T.", "D."], ["Donald",
"Kneller", "D.", "G."]]
-CITE['Sparky'].cite_full_citation = "Goddard, T. D. and Kneller, D. G.,
SPARKY 3, University of California, San Francisco."
-CITE['Sparky'].cite_title = "Sparky."
-CITE['Sparky'].cite_status = "unpublished"
-CITE['Sparky'].cite_type = "internet"
+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."
+CITE['Sparky'].title = "Sparky."
+CITE['Sparky'].status = "unpublished"
+CITE['Sparky'].type = "internet"
@@ -338,13 +349,15 @@
# Init.
cite_ids = []
keys = []
+ software_keys = []
versions = []
# relax.
if name == 'relax':
# The info.
cite_ids.append(['relax_ref1', 'relax_ref2'])
- keys.append(['Relax 1', 'Relax 2'])
+ keys.append(['relax 1', 'relax 2'])
+ software_keys.append('relax')
versions.append(version_full())
# NMRPipe.
@@ -352,6 +365,7 @@
# The info.
cite_ids.append(['nmrpipe_ref'])
keys.append(['NMRPipe'])
+ software_keys.append('NMRPipe')
versions.append(version)
# Sparky.
@@ -363,16 +377,17 @@
# The info.
cite_ids.append(['sparky_ref'])
keys.append(['Sparky'])
+ software_keys.append('Sparky')
versions.append(version)
# Loop over the citations.
for i in range(len(cite_ids)):
for j in range(len(cite_ids[i])):
# Add the citations.
- cdp.exp_info.add_citation(cite_id=cite_ids[i][j],
authors=CITE[keys[i][j]].cite_authors, doi=CITE[keys[i][j]].cite_doi,
pubmed_id=CITE[keys[i][j]].cite_pubmed_id,
full_citation=CITE[keys[i][j]].cite_full_citation,
title=CITE[keys[i][j]].cite_title, status=CITE[keys[i][j]].cite_status,
type=CITE[keys[i][j]].cite_type,
journal_abbrev=CITE[keys[i][j]].cite_journal_abbrev,
journal_full=CITE[keys[i][j]].cite_journal_full,
volume=CITE[keys[i][j]].cite_volume,
page_first=CITE[keys[i][j]].cite_page_first,
page_last=CITE[keys[i][j]].cite_page_last, year=CITE[keys[i][j]].cite_year)
+ cdp.exp_info.add_citation(cite_id=cite_ids[i][j],
authors=CITE[keys[i][j]].authors, doi=CITE[keys[i][j]].doi,
pubmed_id=CITE[keys[i][j]].pubmed_id,
full_citation=CITE[keys[i][j]].full_citation, title=CITE[keys[i][j]].title,
status=CITE[keys[i][j]].status, type=CITE[keys[i][j]].type,
journal_abbrev=CITE[keys[i][j]].journal_abbrev,
journal_full=CITE[keys[i][j]].journal_full, volume=CITE[keys[i][j]].volume,
page_first=CITE[keys[i][j]].page_first, page_last=CITE[keys[i][j]].page_last,
year=CITE[keys[i][j]].year)
# Add the software info.
- cdp.exp_info.software_setup(name=CITE[keys[i][0]].name,
version=versions[i], vendor_name=CITE[keys[i][0]].authors,
url=CITE[keys[i][0]].url, cite_ids=cite_ids, tasks=CITE[keys[i][0]].tasks)
+ cdp.exp_info.software_setup(name=SOFTWARE[software_keys[i]].name,
version=versions[i], vendor_name=SOFTWARE[software_keys[i]].authors,
url=SOFTWARE[software_keys[i]].url, cite_ids=cite_ids,
tasks=SOFTWARE[software_keys[i]].tasks)
def thiol_state(state=None):
r9855 - in /branches/bmrb/generic_fns: bmrb.py exp_info.py