Author: bugman
Date: Tue Oct 6 13:20:57 2009
New Revision: 9580
URL: http://svn.gna.org/viewcvs/relax?rev=9580&view=rev
Log:
Converted spectrum.read_intensities() to use the new
relax_io.read_spin_data_file() function.
This is only for the generic formatted file.
Modified:
1.3/generic_fns/spectrum.py
1.3/prompt/spectrum.py
Modified: 1.3/generic_fns/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/spectrum.py?rev=9580&r1=9579&r2=9580&view=diff
==============================================================================
--- 1.3/generic_fns/spectrum.py (original)
+++ 1.3/generic_fns/spectrum.py Tue Oct 6 13:20:57 2009
@@ -698,7 +698,7 @@
return header_lines
-def read(file=None, dir=None, spectrum_id=None, heteronuc=None, proton=None,
int_col=None, int_method=None, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None,
ncproc=None):
+def read(file=None, dir=None, spectrum_id=None, heteronuc=None, proton=None,
int_col=None, int_method=None, spin_id_col=None, mol_name_col=None,
res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None,
sep=None, spin_id=None, ncproc=None):
"""Read the peak intensity data.
@keyword file: The name of the file containing the peak
intensities.
@@ -712,23 +712,35 @@
@type heteronuc: str
@keyword proton: The name of the proton as specified in the peak
intensity file.
@type proton: str
- @keyword int_col: The column containing the peak intensity data
(for a non-standard
- formatted file).
+ @keyword int_col: The column containing the peak intensity data
(used by the generic
+ intensity file format).
@type int_col: int
@keyword int_method: The integration method, one of 'height', 'point
sum' or 'other'.
@type int_method: str
- @keyword mol_name_col: The column containing the molecule name
information.
+ @keyword spin_id_col: The column containing the spin ID strings (used
by the generic intensity
+ file format). If supplied, the mol_name_col,
res_name_col, res_num_col,
+ spin_name_col, and spin_num_col arguments must
be none.
+ @type spin_id_col: int or None
+ @keyword mol_name_col: The column containing the molecule name
information (used by the generic
+ intensity file format). If supplied,
spin_id_col must be None.
@type mol_name_col: int or None
- @keyword res_name_col: The column containing the residue name
information.
+ @keyword res_name_col: The column containing the residue name
information (used by the generic
+ intensity file format). If supplied,
spin_id_col must be None.
@type res_name_col: int or None
- @keyword res_num_col: The column containing the residue number
information.
+ @keyword res_num_col: The column containing the residue number
information (used by the
+ generic intensity file format). If supplied,
spin_id_col must be None.
@type res_num_col: int or None
- @keyword spin_name_col: The column containing the spin name information.
+ @keyword spin_name_col: The column containing the spin name information
(used by the generic
+ intensity file format). If supplied,
spin_id_col must be None.
@type spin_name_col: int or None
- @keyword spin_num_col: The column containing the spin number
information.
+ @keyword spin_num_col: The column containing the spin number
information (used by the generic
+ intensity file format). If supplied,
spin_id_col must be None.
@type spin_num_col: int or None
@keyword sep: The column separator which, if None, defaults to
whitespace.
@type sep: str or None
+ @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all
+ spins.
+ @type spin_id: None or str
@keyword ncproc: The Bruker ncproc binary intensity scaling
factor.
@type ncproc: int or None
"""
@@ -761,10 +773,6 @@
if format == 'generic':
# Print out.
print("Generic formatted data file.\n")
-
- # Test that column numbers have been given.
- if max(mol_name_col, res_num_col, res_name_col, spin_num_col,
spin_name_col) == None:
- raise RelaxError("No column numbers have been supplied.")
# Set the intensity reading function.
intensity_fn = intensity_generic
Modified: 1.3/prompt/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/spectrum.py?rev=9580&r1=9579&r2=9580&view=diff
==============================================================================
--- 1.3/prompt/spectrum.py (original)
+++ 1.3/prompt/spectrum.py Tue Oct 6 13:20:57 2009
@@ -266,7 +266,7 @@
spectrum.integration_points(N=N, 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, int_method='height',
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None,
spin_name_col=None, sep=None, ncproc=None):
+ def read_intensities(self, file=None, dir=None, spectrum_id=None,
heteronuc='N', proton='HN', int_col=None, int_method='height',
spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None,
spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, ncproc=None):
"""Function for reading peak intensities from a file for NOE
calculations.
Keyword Arguments
@@ -282,21 +282,34 @@
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 format).
+ int_col: The column containing the peak intensity data (used by the
generic intensity file
+ format).
int_method: The integration method.
- 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).
+ spin_id_col: The spin ID string column used by the generic
intensity file format (an
+ alternative to the mol, res, and spin name and number columns).
+
+ mol_name_col: The molecule name column used by the generic
intensity file format
+ (alternative to the spid_id_col).
+
+ res_num_col: The residue number column used by the generic
intensity file format
+ (alternative to the spid_id_col).
+
+ res_name_col: The residue name column used by the generic intensity
file format
+ (alternative to the spid_id_col).
+
+ spin_num_col: The spin number column used by the generic intensity
file format
+ (alternative to the spid_id_col).
+
+ spin_name_col: The spin name column used by the generic intensity
file format
+ (alternative to the spid_id_col).
+
+ sep: The column separator used by the generic intensity format (the
default is white
+ space).
+
+ spin_id: The spin ID string used by the generic intensity file
format to restrict the
+ loading of data to certain spin subsets.
ncproc: The Bruker specific FID intensity scaling factor.
@@ -358,12 +371,14 @@
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.
+ the *name_col and *num_col arguments. Alternatively a spin ID
string column can be used.
+ 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. The spin_id argument can be used to restrict the loading
to specific spin
+ subsets.
Examples
@@ -392,12 +407,15 @@
text = text + ", proton=" + repr(proton)
text = text + ", int_col=" + repr(int_col)
text = text + ", int_method=" + repr(int_method)
+ text = text + ", spin_id_col=" + repr(spin_id_col)
text = text + ", mol_name_col=" + repr(mol_name_col)
text = text + ", res_num_col=" + repr(res_num_col)
text = text + ", res_name_col=" + repr(res_name_col)
text = text + ", spin_num_col=" + repr(spin_num_col)
text = text + ", spin_name_col=" + repr(spin_name_col)
- text = text + ", sep=" + repr(sep) + ")"
+ text = text + ", sep=" + repr(sep)
+ text = text + ", spin_id=" + repr(spin_id)
+ text = text + ", ncproc=" + repr(ncproc) + ")"
print(text)
# The argument checks.
@@ -408,16 +426,18 @@
check.is_str(proton, 'proton name')
check.is_int_or_int_list(int_col, 'intensity column',
can_be_none=True)
check.is_str(int_method, 'integration method')
+ check.is_int(spin_id_col, 'spin ID string column', can_be_none=True)
check.is_int(mol_name_col, 'molecule name column', can_be_none=True)
check.is_int(res_num_col, 'residue number column', can_be_none=True)
check.is_int(res_name_col, 'residue name column', can_be_none=True)
check.is_int(spin_num_col, 'spin number column', can_be_none=True)
check.is_int(spin_name_col, 'spin name column', can_be_none=True)
check.is_str(sep, 'column separator', can_be_none=True)
+ check.is_str(spin_id, 'spin ID string', can_be_none=True)
check.is_int(ncproc, 'Bruker ncproc parameter', can_be_none=True)
# Execute the functional code.
- spectrum.read(file=file, dir=dir, spectrum_id=spectrum_id,
heteronuc=heteronuc, proton=proton, int_col=int_col, int_method=int_method,
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, ncproc=ncproc)
+ spectrum.read(file=file, dir=dir, spectrum_id=spectrum_id,
heteronuc=heteronuc, proton=proton, int_col=int_col, int_method=int_method,
spin_id_col=spin_id_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, spin_id=spin_id, ncproc=ncproc)
def replicated(self, spectrum_ids=None):
r9580 - in /1.3: generic_fns/spectrum.py prompt/spectrum.py