Author: bugman
Date: Tue Oct 21 17:22:49 2008
New Revision: 7892
URL: http://svn.gna.org/viewcvs/relax?rev=7892&view=rev
Log:
Added new arguments and improved the spectrum.read_intensities() docstring.
The mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col, and
sep args have been
added to support the generic intensity file format. This format has also had
a description in the
docstring written.
Modified:
branches/spectral_errors/prompt/spectrum.py
Modified: branches/spectral_errors/prompt/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/prompt/spectrum.py?rev=7892&r1=7891&r2=7892&view=diff
==============================================================================
--- branches/spectral_errors/prompt/spectrum.py (original)
+++ branches/spectral_errors/prompt/spectrum.py Tue Oct 21 17:22:49 2008
@@ -87,7 +87,7 @@
intensity.set_error(error=error, spectrum_id=spectrum_id,
spin_id=spin_id)
- def read_intensities(self, file=None, dir=None, spectrum_id=None,
heteronuc='N', proton='HN', int_col=None):
+ def read_intensities(self, file=None, dir=None, spectrum_id=None,
heteronuc='N', proton='HN', int_col=None, mol_name_col=None,
res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None,
sep=None):
"""Function for reading peak intensities from a file for NOE
calculations.
Keyword Arguments
@@ -103,7 +103,19 @@
proton: The name of the proton as specified in the peak intensity
file.
- int_col: The column(s) containing the peak intensity data (for a
non-standard formatted file).
+ int_col: The column(s) containing the peak intensity data (for a
non-standard format).
+
+ mol_name_col: The molecule name column used by the generic
intensity file format.
+
+ res_num_col: The residue number column used by the generic
intensity file format.
+
+ res_name_col: The residue name column used by the generic intensity
file format.
+
+ spin_num_col: The spin number column used by the generic intensity
file format.
+
+ spin_name_col: The spin name column used by the generic intensity
file format.
+
+ sep: The column separator used by the generic intensity format
(defaults to white space).
Description
@@ -112,9 +124,17 @@
The peak intensity can either be from peak heights or peak volumes.
- The 'spectrum_id' argument is a label which is subsequently used by
other user functions.
- This is a unique identifier, so the label must not already exist.
-
+ The 'spectrum_id' argument is a label which is subsequently utilised
by other user
+ functions. If this identifier matches that of a previously loaded
set of intensities, then
+ this indicates a replicated spectrum.
+
+ 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.
+
+
+ File formats
+ ~~~~~~~~~~~~
The peak list or intensity file will be automatically determined.
@@ -135,10 +155,16 @@
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.
+ Generic intensity file: This is a generic format which can be
created by scripting to
+ support non-supported peak lists. It should contain in the first
few columns enough
+ information to identify the spin. This can include columns for the
molecule name, residue
+ number, residue name, spin number, and spin name, with each optional
type positioned with
+ the *name_col and *num_col arguments. The peak intensities can be
placed in another column
+ specified by the int_col argument. Intensities from multiple
spectra can be placed into
+ different columns, and these can then be specified simultaneously by
setting the int_col
+ argument to a list of columns. This list must be matched by setting
the spectrum_id
+ argument to list of the same length. If columns are delimited by a
character other than
+ whitespace, this can be specified with the sep argument.
Examples
@@ -165,7 +191,13 @@
text = text + ", spectrum_id=" + `spectrum_id`
text = text + ", heteronuc=" + `heteronuc`
text = text + ", proton=" + `proton`
- text = text + ", int_col=" + `int_col` + ")"
+ text = text + ", int_col=" + `int_col`
+ text = text + ", mol_name_col=" + `mol_name_col`
+ text = text + ", res_num_col=" + `res_num_col`
+ text = text + ", res_name_col=" + `res_name_col`
+ text = text + ", spin_num_col=" + `spin_num_col`
+ text = text + ", spin_name_col=" + `spin_name_col`
+ text = text + ", sep=" + `sep` + ")"
print text
# The file name.
@@ -192,5 +224,29 @@
if int_col and type(int_col) != int:
raise RelaxNoneIntError, ('intensity column', int_col)
+ # Molecule name column.
+ if mol_name_col != None and type(mol_name_col) != int:
+ raise RelaxNoneIntError, ('molecule name column', mol_name_col)
+
+ # Residue number column.
+ if res_num_col != None and type(res_num_col) != int:
+ raise RelaxNoneIntError, ('residue number column', res_num_col)
+
+ # Residue name column.
+ if res_name_col != None and type(res_name_col) != int:
+ raise RelaxNoneIntError, ('residue name column', res_name_col)
+
+ # Spin number column.
+ if spin_num_col != None and type(spin_num_col) != int:
+ raise RelaxNoneIntError, ('spin number column', spin_num_col)
+
+ # Spin name column.
+ if spin_name_col != None and type(spin_name_col) != int:
+ raise RelaxNoneIntError, ('spin name column', spin_name_col)
+
+ # Column separator.
+ if sep != None and type(sep) != str:
+ raise RelaxNoneStrError, ('column separator', sep)
+
# Execute the functional code.
- intensity.read(file=file, dir=dir, spectrum_id=spectrum_id,
heteronuc=heteronuc, proton=proton, int_col=int_col)
+ intensity.read(file=file, dir=dir, spectrum_id=spectrum_id,
heteronuc=heteronuc, proton=proton, int_col=int_col,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, sep=sep)
r7892 - /branches/spectral_errors/prompt/spectrum.py