Author: bugman
Date: Thu Oct 29 14:31:33 2009
New Revision: 9843
URL: http://svn.gna.org/viewcvs/relax?rev=9843&view=rev
Log:
Created the bmrb.script() user function for specifying the scripts used in
the analysis.
Modified:
branches/bmrb/data/exp_info.py
branches/bmrb/generic_fns/exp_info.py
branches/bmrb/prompt/bmrb.py
Modified: branches/bmrb/data/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/data/exp_info.py?rev=9843&r1=9842&r2=9843&view=diff
==============================================================================
--- branches/bmrb/data/exp_info.py (original)
+++ branches/bmrb/data/exp_info.py Thu Oct 29 14:31:33 2009
@@ -169,6 +169,73 @@
return self.temp_control[i].method
+ def setup_thiol(self, state):
+ """Set up the thiol state of the system.
+
+ @param thiol_state: The thiol state of the molecule.
+ @type thiol_state: str
+ """
+
+ # Check.
+ if hasattr(self, "thiol_state"):
+ raise RelaxError("The thiol state has already been specified")
+
+ # Set the attribute.
+ self.thiol_state = state
+
+
+ def setup_script(self, file=None, text=None, analysis_type=None,
model_selection=None, engine=None, model_elim=False,
universal_solution=False):
+ """Specify the scripts used in the analysis.
+
+ @param file: The name of the script file.
+ @type file: str
+ @param text: The script text.
+ @type text: str
+ @keyword analysis_type: The type of analysis performed.
+ @type analysis_type: str
+ @keyword model_selection: The model selection technique used,
if relevant.
+ @type model_selection: None or str
+ @keyword engine: The software engine used in the
analysis.
+ @type engine: str
+ @keyword model_elim: A model-free specific flag
specifying if model elimination was performed.
+ @type model_elim: bool
+ @keyword universal_solution: A model-free specific flag
specifying if the universal solution was sought after.
+ @type universal_solution: bool
+ """
+
+ # Initialise the container if needed.
+ if not hasattr(self, "scripts"):
+ # The list.
+ self.scripts = ContainerList()
+
+ # The name of the container.
+ self.scripts.container_name = "script_list"
+
+ # The description of the container.
+ self.scripts.container_desc = "List of scripts used for the
analysis"
+
+ # Init the container.
+ script = Element()
+
+ # The name of the container.
+ script.element_name = "script"
+
+ # The description of the container.
+ script.element_desc = "Script used for the analysis"
+
+ # Set the attributes.
+ script.file = file
+ script.text = text
+ script.analysis_type = analysis_type
+ script.model_selection = model_selection
+ script.engine = engine
+ script.model_elim = model_elim
+ script.universal_solution = universal_solution
+
+ # Append the container.
+ self.scripts.append(script)
+
+
def software_setup(self, name, version=None, url=None, vendor_name=None,
cite_ids=None, tasks=None):
"""Set up the software information.
@@ -306,18 +373,3 @@
# Append the container.
self.temp_control.append(temp_control)
-
-
- def setup_thiol(self, state):
- """Set up the thiol state of the system.
-
- @param thiol_state: The thiol state of the molecule.
- @type thiol_state: str
- """
-
- # Check.
- if hasattr(self, "thiol_state"):
- raise RelaxError("The thiol state has already been specified")
-
- # Set the attribute.
- self.thiol_state = state
Modified: branches/bmrb/generic_fns/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/exp_info.py?rev=9843&r1=9842&r2=9843&view=diff
==============================================================================
--- branches/bmrb/generic_fns/exp_info.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Thu Oct 29 14:31:33 2009
@@ -26,6 +26,7 @@
# relax module imports.
from data.exp_info import ExpInfo
from relax_errors import RelaxError
+from relax_io import open_read_file
from version import version_full
@@ -189,6 +190,50 @@
cdp.exp_info.add_citation(cite_id=cite_id, 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 script(file=None, dir=None, analysis_type=None, model_selection=None,
engine=None, model_elim=False, universal_solution=False):
+ """Specify the scripts used in the analysis.
+
+ @param file: The name of the file to open.
+ @type file: str
+ @param dir: The directory containing the file
(defaults to the current directory if None).
+ @type dir: None or str
+ @keyword analysis_type: The type of analysis performed.
+ @type analysis_type: str
+ @keyword model_selection: The model selection technique used, if
relevant.
+ @type model_selection: None or str
+ @keyword engine: The software engine used in the analysis.
+ @type engine: str
+ @keyword model_elim: A model-free specific flag specifying if
model elimination was performed.
+ @type model_elim: bool
+ @keyword universal_solution: A model-free specific flag specifying if
the universal solution was sought after.
+ @type universal_solution: bool
+ """
+
+ # Check.
+ allowed = ['frame order',
+ 'jw',
+ 'mf',
+ 'N-state',
+ 'noe',
+ 'relax_fit',
+ 'srls'
+ ]
+ if analysis_type not in allowed:
+ raise RelaxError("The analysis type '%s' should be one of %s." %
(analysis_type, allowed))
+
+ # Set up the experimental info data container, if needed.
+ if not hasattr(cdp, 'exp_info'):
+ cdp.exp_info = ExpInfo()
+
+ # Extract the text.
+ file = open_read_file(file, dir)
+ text = file.read()
+ file.close()
+
+ # Place the data in the container.
+ cdp.exp_info.setup_script(file=file, text=text,
analysis_type=analysis_type, model_selection=model_selection, engine=engine,
model_elim=model_elim, universal_solution=universal_solution)
+
+
def software(name=None, version=None, url=None, vendor_name=None,
cite_ids=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=9843&r1=9842&r2=9843&view=diff
==============================================================================
--- branches/bmrb/prompt/bmrb.py (original)
+++ branches/bmrb/prompt/bmrb.py Thu Oct 29 14:31:33 2009
@@ -212,6 +212,117 @@
bmrb.read(file=file, directory=dir, version=version)
+ def script(self, file='reduced', dir=None, analysis_type=None,
model_selection=None, engine='relax', model_elim=False,
universal_solution=False):
+ """Specify the scripts used in the analysis.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ file: The script file name.
+
+ dir: The directory name.
+
+ analysis_type: The type of analysis performed.
+
+ model_selection: The model selection technique used, if relevant.
+
+ engine: The software engine used in the analysis.
+
+ model_elim: A model-free specific flag specifying if model
elimination was performed.
+
+ universal_solution: A model-free specific flag specifying if the
universal solution was
+ sought after.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ This user function allows scripts used in the analysis to be
included in the BMRB
+ deposition. The following addition information may need to be
specified with the script.
+
+ The analysis_type must be set. Allowable values include all the
data pipe types used in
+ relax, ie:
+
+ 'frame order': The Frame Order theories,
+ 'jw': Reduced spectral density mapping,
+ 'mf': Model-free analysis,
+ 'N-state': N-state model of domain motions,
+ 'noe': Steady state NOE calculation,
+ 'relax_fit': Relaxation curve fitting,
+ 'srls': SRLS analysis.
+
+ The model_selection argument only needs to be set if the script
selects between different
+ mathematical models. This can be anything, but the following are
recommended:
+
+ 'AIC': Akaike's Information Criteria.
+ 'AICc': Small sample size corrected AIC.
+ 'BIC': Bayesian or Schwarz Information Criteria.
+ 'Bootstrap': Bootstrap model selection.
+ 'CV': Single-item-out cross-validation.
+ 'Expect': The expected overall discrepancy (the true values of
the parameters are
+ required).
+ 'Farrow': Old model-free method by Farrow et al., 1994.
+ 'Palmer': Old model-free method by Mandel et al., 1995.
+ 'Overall': The realised overall discrepancy (the true values of
the parameters are
+ required).
+
+ The engine is the software used in the calculation, optimisation,
etc. This can be
+ anything, but those recognised by relax (automatic program info,
citations, etc. added)
+ include:
+
+ 'relax': hence relax was used for the full analysis.
+ 'modelfree4': Art Palmer's Modelfree4 program was used for
optimising the model-free
+ parameter values.
+ 'dasha': The Dasha program was used for optimising the
model-free parameter values.
+ 'curvefit': Art Palmer's curvefit program was used to determine
the R1 or R2 values.
+
+ The model_elim flag is model-free specific and should be set if the
methods from
+ "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." were
+ used. This should be set to True for the full_analysis.py script.
+
+ The universal_solution flag is model-free specific and should be set
if the methods from
+ "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." were used. This
+ should be set to True for the full_analysis.py script.
+
+
+ Examples
+ ~~~~~~~~
+
+ For BMRB deposition, to specify that the full_analysis.py script was
used, type one of:
+
+ relax> bmrb.script('full_analysis.py', 'model-free', 'AIC', 'relax',
True, True)
+ relax> bmrb.script(file='full_analysis.py', dir=None,
analysis_type='model-free',
+ model_selection='AIC', engine='relax',
model_elim=True,
+ universal_solution=True)
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "bmrb.script("
+ text = text + "file=" + repr(file)
+ text = text + ", dir=" + repr(dir)
+ text = text + ", analysis_type=" + repr(analysis_type)
+ text = text + ", model_selection=" + repr(model_selection)
+ text = text + ", engine=" + repr(engine)
+ text = text + ", model_elim=" + repr(model_elim)
+ text = text + ", universal_solution=" + repr(universal_solution)
+ ")"
+ print(text)
+
+ # The argument checks.
+ check.is_str(file, 'script file')
+ check.is_str(dir, 'directory', can_be_none=True)
+ check.is_str(analysis_type, 'analysis type')
+ check.is_str(model_selection, 'model selection', can_be_none=True)
+ check.is_str(engine, 'engine')
+ check.is_bool(model_elim, 'model elimination flag')
+ check.is_bool(universal_solution, 'universal solution flag')
+
+ # Execute the functional code.
+ exp_info.script(file=file, dir=dir, analysis_type=analysis_type,
model_selection=model_selection, engine=engine, model_elim=model_elim,
universal_solution=universal_solution)
+
+
def software(self, name=None, version=None, url=None, vendor_name=None,
cite_ids=None, tasks=None):
"""Specify the software used in the analysis.
r9843 - in /branches/bmrb: data/exp_info.py generic_fns/exp_info.py prompt/bmrb.py