Author: bugman
Date: Tue Oct 21 16:04:32 2008
New Revision: 7883
URL: http://svn.gna.org/viewcvs/relax?rev=7883&view=rev
Log:
Renamed the noe module to spectrum.
The noe module only contains user functions will are to be merged into the
spectrum user function
class, hence will be deleted anyway.
Added:
branches/spectral_errors/prompt/spectrum.py
- copied unchanged from r7880, branches/spectral_errors/prompt/noe.py
Removed:
branches/spectral_errors/prompt/noe.py
Removed: branches/spectral_errors/prompt/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/prompt/noe.py?rev=7882&view=auto
==============================================================================
--- branches/spectral_errors/prompt/noe.py (original)
+++ branches/spectral_errors/prompt/noe.py (removed)
@@ -1,214 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2004-2005 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax.
#
-#
#
-# relax is free software; you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation; either version 2 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# relax is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with relax; if not, write to the Free Software
#
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
-#
#
-###############################################################################
-
-# Python module imports.
-import sys
-
-# relax module imports.
-import help
-from relax_errors import RelaxNoneIntError, RelaxNoneIntStrError,
RelaxNoneStrError, RelaxNumError, RelaxStrError
-from specific_fns.setup import noe_obj
-
-
-class Noe:
- def __init__(self, relax):
- # Help.
- self.__relax_help__ = \
- """Class for calculating NOE data."""
-
- # Add the generic help string.
- self.__relax_help__ = self.__relax_help__ + "\n" +
help.relax_class_help
-
- # Place relax in the class namespace.
- self.__relax__ = relax
-
-
- def error(self, error=0.0, spectrum_type=None, spin_id=None):
- """Function for setting the errors in the reference or saturated NOE
spectra.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- error: The error.
-
- spectrum_type: The type of spectrum.
-
- spin_id: The spin identification string.
-
-
- Description
- ~~~~~~~~~~~
-
- The spectrum_type argument can have the following values:
- 'ref': The NOE reference spectrum.
- 'sat': The NOE spectrum with proton saturation turned on.
-
- If the 'res_num' and 'res_name' arguments are left as the defaults
of None, then the error
- value for all residues will be set to the supplied value. Otherwise
the residue number can
- be set to either an integer for selecting a single residue or a
python regular expression
- string for selecting multiple residues. The residue name argument
must be a string and can
- use regular expression as well.
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "noe.error("
- text = text + "error=" + `error`
- text = text + ", spectrum_type=" + `spectrum_type`
- text = text + ", spin_id=" + `spin_id` + ")"
- print text
-
- # The error.
- if type(error) != float and type(error) != int:
- raise RelaxNumError, ('error', error)
-
- # The spectrum type.
- if type(spectrum_type) != str:
- raise RelaxStrError, ('spectrum type', spectrum_type)
-
- # Spin identification string.
- if spin_id != None and type(spin_id) != str:
- raise RelaxNoneStrError, ('spin identification string', spin_id)
-
- # Execute the functional code.
- noe_obj.set_error(error=error, spectrum_type=spectrum_type,
spin_id=spin_id)
-
-
- def read(self, file=None, dir=None, spectrum_type=None, format='sparky',
heteronuc='N', proton='HN', int_col=None):
- """Function for reading peak intensities from a file for NOE
calculations.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- file: The name of the file containing the sequence data.
-
- dir: The directory where the file is located.
-
- spectrum_type: The type of spectrum.
-
- format: The type of file containing peak intensities.
-
- heteronuc: The name of the heteronucleus as specified in the peak
intensity file.
-
- proton: The name of the proton as specified in the peak intensity
file.
-
- int_col: The column containing the peak intensity data (for a
non-standard formatted file).
-
-
- Description
- ~~~~~~~~~~~
-
- The peak intensity can either be from peak heights or peak volumes.
-
-
- The 'spectrum_type' argument can have the following values:
- 'ref': The NOE reference spectrum.
- 'sat': The NOE spectrum with proton saturation turned on.
-
-
- The 'format' argument can currently be set to:
- 'sparky'
- 'xeasy'
- 'nmrview'
-
- If the 'format' argument is set to 'sparky', the file should be a
Sparky peak list saved
- after typing the command 'lt'. The default is to assume that
columns 0, 1, 2, and 3 (1st,
- 2nd, 3rd, and 4th) contain the Sparky assignment, w1, w2, and peak
intensity data
- respectively. The frequency data w1 and w2 are ignored while the
peak intensity data can
- either be the peak height or volume displayed by changing the window
options. If the peak
- intensity data is not within column 3, set the argument 'int_col' to
the appropriate value
- (column numbering starts from 0 rather than 1).
-
- If the 'format' argument is set to 'xeasy', the file should be the
saved XEasy text window
- output of the list peak entries command, 'tw' followed by 'le'. As
the columns are fixed,
- the peak intensity column is hardwired to number 10 (the 11th
column) which contains either
- the peak height or peak volume data. Because the columns are fixed,
the 'int_col' argument
- will be ignored.
-
- If the 'format' argument is set to 'nmrview', the file should be a
NMRView peak list. The
- default is to use column 16 (which contains peak heights) for peak
intensities. To use
- use peak volumes (or evolumes), int_col must be set to 15.
-
-
- The 'heteronuc' and 'proton' arguments should be set respectively to
the name of the
- heteronucleus and proton in the file. Only those lines which match
these labels will be
- used.
-
-
- Examples
- ~~~~~~~~
-
- To read the reference and saturated spectra peak heights from the
Sparky formatted files
- 'ref.list' and 'sat.list', type:
-
- relax> noe.read(file='ref.list', spectrum_type='ref')
- relax> noe.read(file='sat.list', spectrum_type='sat')
-
- To read the reference and saturated spectra peak heights from the
XEasy formatted files
- 'ref.text' and 'sat.text', type:
-
- relax> noe.read(file='ref.text', spectrum_type='ref', format='xeasy')
- relax> noe.read(file='sat.text', spectrum_type='sat', format='xeasy')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "noe.read("
- text = text + "file=" + `file`
- text = text + ", dir=" + `dir`
- text = text + ", spectrum_type=" + `spectrum_type`
- text = text + ", format=" + `format`
- text = text + ", heteronuc=" + `heteronuc`
- text = text + ", proton=" + `proton`
- text = text + ", int_col=" + `int_col` + ")"
- print text
-
- # The file name.
- if type(file) != str:
- raise RelaxStrError, ('file name', file)
-
- # Directory.
- if dir != None and type(dir) != str:
- raise RelaxNoneStrError, ('directory name', dir)
-
- # The spectrum type.
- if type(spectrum_type) != str:
- raise RelaxStrError, ('spectrum type', spectrum_type)
-
- # The format.
- if type(format) != str:
- raise RelaxStrError, ('format', format)
-
- # The heteronucleus name.
- if type(heteronuc) != str:
- raise RelaxStrError, ('heteronucleus name', heteronuc)
-
- # The proton name.
- if type(proton) != str:
- raise RelaxStrError, ('proton name', proton)
-
- # The intensity column.
- if int_col and type(int_col) != int:
- raise RelaxNoneIntError, ('intensity column', int_col)
-
- # Execute the functional code.
- noe_obj.read(file=file, dir=dir, spectrum_type=spectrum_type,
format=format, heteronuc=heteronuc, proton=proton, int_col=int_col)
r7883 - in /branches/spectral_errors/prompt: noe.py spectrum.py