Author: bugman
Date: Thu Jul 14 15:30:47 2011
New Revision: 13620
URL: http://svn.gna.org/viewcvs/relax?rev=13620&view=rev
Log:
Converted the noe user function docstrings to the new design.
Modified:
branches/gui_testing/prompt/noe.py
Modified: branches/gui_testing/prompt/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/prompt/noe.py?rev=13620&r1=13619&r2=13620&view=diff
==============================================================================
--- branches/gui_testing/prompt/noe.py (original)
+++ branches/gui_testing/prompt/noe.py Thu Jul 14 15:30:47 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2010 Edward d'Auvergne
#
+# Copyright (C) 2004-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -25,7 +25,7 @@
__docformat__ = 'plaintext'
# relax module imports.
-from base_class import User_fn_class
+from base_class import User_fn_class, _build_doc
import arg_check
from generic_fns import noesy
from specific_fns.setup import noe_obj
@@ -35,50 +35,6 @@
"""Class for handling steady-state NOE and NOESY data."""
def read_restraints(self, file=None, dir=None, proton1_col=None,
proton2_col=None, lower_col=None, upper_col=None, sep=None):
- """Read NOESY or ROESY restraints from a file.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- file: The name of the file containing the relaxation data.
-
- dir: The directory where the file is located.
-
- proton1_col: The column containing the first proton of the NOE or
ROE cross peak.
-
- proton2_col: The column containing the second proton of the NOE or
ROE cross peak.
-
- lower_col: The column containing the lower NOE bound.
-
- upper_col: The column containing the upper NOE bound.
-
- sep: The column separator (the default is white space).
-
-
- Description
- ~~~~~~~~~~~
-
- This function can automatically determine the format of the file,
for example Xplor
- formatted restraint files. A generically formatted file is also
supported if it contains
- minimally four columns with the two proton names and the upper and
lower bounds, as
- specified by the *_col arguments. The proton names need to be in
the spin identification
- string format.
-
-
- Examples
- ~~~~~~~~
-
- To read the Xplor formatted restraint file 'NOE.xpl', type one of:
-
- relax> noe.read_restraints('NOE.xpl')
- relax> noe.read_restraints(file='NOE.xpl')
-
-
- To read the generic formatted file 'noes', type one of:
-
- relax> noe.read_restraints(file='NOE.xpl', proton1_col=0,
proton2_col=1, lower_col=2, upper_col=3)
- """
-
# Function intro text.
if self._exec_info.intro:
text = self._exec_info.ps3 + "noe.read_restraints("
@@ -103,30 +59,36 @@
# Execute the functional code.
noesy.read_restraints(file=file, dir=dir, proton1_col=proton1_col,
proton2_col=proton2_col, lower_col=lower_col, upper_col=upper_col, sep=sep)
+ # The function doc info.
+ read_restraints._doc_title = "Read NOESY or ROESY restraints from a
file."
+ read_restraints._doc_title_short = "NOESY or ROESY restraint reading."
+ read_restraints._doc_args = [
+ ["file", "The name of the file containing the relaxation data."],
+ ["dir", "The directory where the file is located."],
+ ["proton1_col", "The column containing the first proton of the NOE
or ROE cross peak."],
+ ["proton2_col", "The column containing the second proton of the NOE
or ROE cross peak."],
+ ["lower_col", "The column containing the lower NOE bound."],
+ ["upper_col", "The column containing the upper NOE bound."],
+ ["sep", "The column separator (the default is white space)."]
+ ]
+ read_restraints._doc_desc = """
+ This can automatically determine the format of the file, for example
Xplor formatted restraint files. A generically formatted file is also
supported if it contains minimally four columns with the two proton names and
the upper and lower bounds, as specified by the column numbers. The proton
names need to be in the spin ID string format.
+ """
+ read_restraints._doc_examples = """
+ To read the Xplor formatted restraint file 'NOE.xpl', type one of:
+
+ relax> noe.read_restraints('NOE.xpl')
+ relax> noe.read_restraints(file='NOE.xpl')
+
+
+ To read the generic formatted file 'noes', type one of:
+
+ relax> noe.read_restraints(file='NOE.xpl', proton1_col=0,
proton2_col=1, lower_col=2, upper_col=3)
+ """
+ _build_doc(read_restraints)
+
def spectrum_type(self, spectrum_type=None, spectrum_id=None):
- """Set the steady-state NOE spectrum type for pre-loaded peak
intensities.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- spectrum_type: The type of steady-state NOE spectrum, one of 'ref'
or 'sat'.
-
- spectrum_id: The spectrum identification string.
-
-
- Description
- ~~~~~~~~~~~
-
- The spectrum_type argument can have the following values:
- 'ref': The steady-state NOE reference spectrum.
- 'sat': The steady-state NOE spectrum with proton saturation
turned on.
-
- Peak intensities should be loaded before calling this user function
via the
- 'spectrum.read_intensities()' user function. The intensity values
will then be associated
- with a spectrum identifier which can be used here.
- """
-
# Function intro text.
if self._exec_info.intro:
text = self._exec_info.ps3 + "noe.spectrum_type("
@@ -136,7 +98,24 @@
# The argument checks.
arg_check.is_str(spectrum_type, 'spectrum type')
- arg_check.is_str(spectrum_id, 'spectrum identification string')
+ arg_check.is_str(spectrum_id, 'spectrum ID string')
# Execute the functional code.
noe_obj._spectrum_type(spectrum_type=spectrum_type,
spectrum_id=spectrum_id)
+
+ # The function doc info.
+ spectrum_type._doc_title = "Set the steady-state NOE spectrum type for
pre-loaded peak intensities."
+ spectrum_type._doc_title = "Steady-state NOE spectrum type."
+ spectrum_type._doc_args = [
+ ["spectrum_type", "The type of steady-state NOE spectrum, one of
'ref' or 'sat'."],
+ ["spectrum_id", "The spectrum ID string."]
+ ]
+ spectrum_type._doc_desc = """
+ The spectrum_type argument can have the following values:
+
+ 'ref': The steady-state NOE reference spectrum.
+ 'sat': The steady-state NOE spectrum with proton saturation
turned on.
+
+ Peak intensities should be loaded before this user function via the
spectrum.read_intensities user function. The intensity values will then be
associated with a spectrum ID string which can be used here.
+ """
+ _build_doc(spectrum_type)
r13620 - /branches/gui_testing/prompt/noe.py