Author: bugman
Date: Thu Nov 20 15:27:47 2014
New Revision: 26662
URL: http://svn.gna.org/viewcvs/relax?rev=26662&view=rev
Log:
Added the missing_error keyword argument to the pipe_centre_of_mass() function.
This is from the pipe_control.structure.mass module. The new keyword controls
what happens with the
absence of structural data. The
pipe_control.structure.checks.check_structure() function is now
being used to either throw a warning and return [0, 0, 0] or to raise a
RelaxError.
Modified:
trunk/pipe_control/structure/mass.py
Modified: trunk/pipe_control/structure/mass.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/mass.py?rev=26662&r1=26661&r2=26662&view=diff
==============================================================================
--- trunk/pipe_control/structure/mass.py (original)
+++ trunk/pipe_control/structure/mass.py Thu Nov 20 15:27:47 2014
@@ -26,9 +26,10 @@
from lib.errors import RelaxNoPdbError
from lib.structure.mass import centre_of_mass
from lib.warnings import RelaxWarning
+from pipe_control.structure.checks import check_structure
-def pipe_centre_of_mass(atom_id=None, model=None, return_mass=False,
verbosity=1):
+def pipe_centre_of_mass(atom_id=None, model=None, return_mass=False,
verbosity=1, missing_error=True):
"""Calculate and return the centre of mass of the structures in the
current data pipe.
@keyword atom_id: The molecule, residue, and atom identifier string.
Only atoms matching this selection will be used.
@@ -39,13 +40,18 @@
@type return_mass: bool
@keyword verbosity: The amount of text to print out. 0 results in no
printouts, 1 the full amount.
@type verbosity: int
+ @keyword missing_error: A flag which if True will cause an error to be
raised if structural data is absent. Otherwise if False, a warning will be
given and the CoM of [0, 0, 0] will be returned.
+ @type missing_error: bool
@return: The centre of mass vector, and additionally the
mass.
@rtype: list of 3 floats (or tuple of a list of 3 floats
and one float)
"""
# Test if a structure has been loaded.
- if not hasattr(cdp, 'structure') or cdp.structure.num_models() == 0:
- raise RelaxNoPdbError
+ if missing_error:
+ check_structure()
+ else:
+ if not check_structure(escalate=1):
+ return [0.0, 0.0, 0.0]
# The selection object.
selection = cdp.structure.selection(atom_id=atom_id)
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