Author: bugman
Date: Tue Oct 7 23:04:49 2008
New Revision: 7565
URL: http://svn.gna.org/viewcvs/relax?rev=7565&view=rev
Log:
Converted the noe.error() user function front and back-end to the new design.
Modified:
1.3/prompt/noe.py
1.3/specific_fns/noe.py
Modified: 1.3/prompt/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/noe.py?rev=7565&r1=7564&r2=7565&view=diff
==============================================================================
--- 1.3/prompt/noe.py (original)
+++ 1.3/prompt/noe.py Tue Oct 7 23:04:49 2008
@@ -42,7 +42,7 @@
self.__relax__ = relax
- def error(self, error=0.0, spectrum_type=None, res_num=None,
res_name=None):
+ 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
@@ -52,9 +52,7 @@
spectrum_type: The type of spectrum.
- res_num: The residue number.
-
- res_name: The residue name.
+ spin_id: The spin identification string.
Description
@@ -76,8 +74,7 @@
text = sys.ps3 + "noe.error("
text = text + "error=" + `error`
text = text + ", spectrum_type=" + `spectrum_type`
- text = text + ", res_num=" + `res_num`
- text = text + ", res_name=" + `res_name` + ")"
+ text = text + ", spin_id=" + `spin_id` + ")"
print text
# The error.
@@ -88,16 +85,12 @@
if type(spectrum_type) != str:
raise RelaxStrError, ('spectrum type', spectrum_type)
- # Residue number.
- if res_num != None and type(res_num) != int and type(res_num) != str:
- raise RelaxNoneIntStrError, ('residue number', res_num)
-
- # Residue name.
- if res_name != None and type(res_name) != str:
- raise RelaxNoneStrError, ('residue name', res_name)
+ # 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,
res_num=res_num, res_name=res_name)
+ 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):
Modified: 1.3/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe.py?rev=7565&r1=7564&r2=7565&view=diff
==============================================================================
--- 1.3/specific_fns/noe.py (original)
+++ 1.3/specific_fns/noe.py Tue Oct 7 23:04:49 2008
@@ -27,7 +27,7 @@
# relax module imports.
from data import Relax_data_store; ds = Relax_data_store()
from generic_fns import intensity, pipes
-from generic_fns.mol_res_spin import exists_mol_res_spin_data
+from generic_fns.mol_res_spin import exists_mol_res_spin_data, spin_loop
from relax_errors import RelaxArgNotInListError, RelaxError,
RelaxInvalidDataError, RelaxNoSequenceError, RelaxRegExpError
from relax_io import open_write_file
@@ -349,14 +349,17 @@
return value, error
- def set_error(self, run=None, error=0.0, spectrum_type=None,
res_num=None, res_name=None):
- """Function for setting the errors."""
-
- # Arguments.
- self.run = run
- self.spectrum_type = spectrum_type
- self.res_num = res_num
- self.res_name = res_name
+ def set_error(self, error=0.0, spectrum_type=None, spin_id=None):
+ """Set the peak intensity errors.
+
+ @param error: The peak intensity error value defined as
the RMSD of the base plane
+ noise.
+ @type error: float
+ @keyword spectrum_type: The type of spectrum, one of 'ref' or 'sat'.
+ @type spectrum_type: str
+ @param spin_id: The spin identification string.
+ @type spin_id: str
+ """
# Test if the current pipe exists
pipes.test()
@@ -365,44 +368,17 @@
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
- # Test if the residue number is a valid regular expression.
- if type(res_num) == str:
- try:
- compile(res_num)
- except:
- raise RelaxRegExpError, ('residue number', res_num)
-
- # Test if the residue name is a valid regular expression.
- if res_name:
- try:
- compile(res_name)
- except:
- raise RelaxRegExpError, ('residue name', res_name)
-
- # Loop over the sequence.
- for i in xrange(len(ds.res[run])):
- # Remap the data structure 'ds.res[self.run][i]'.
- data = ds.res[self.run][i]
-
- # Skip deselected residues.
- if not data.select:
+ # Loop over the spins.
+ for spin in spin_loop(spin_id):
+ # Skip deselected spins.
+ if not spin.select:
continue
- # If 'res_num' is not None, skip the residue if there is no
match.
- if type(res_num) == int and not data.num == res_num:
- continue
- elif type(res_num) == str and not match(res_num, `data.num`):
- continue
-
- # If 'res_name' is not None, skip the residue if there is no
match.
- if res_name != None and not match(res_name, data.name):
- continue
-
# Set the error.
- if self.spectrum_type == 'ref':
- data.ref_err = float(error)
- elif self.spectrum_type == 'sat':
- data.sat_err = float(error)
+ if spectrum_type == 'ref':
+ spin.ref_err = float(error)
+ elif spectrum_type == 'sat':
+ spin.sat_err = float(error)
def write(self, run=None, file=None, dir=None, force=False):
r7565 - in /1.3: prompt/noe.py specific_fns/noe.py