Author: bugman
Date: Thu Nov 14 11:54:27 2013
New Revision: 21440
URL: http://svn.gna.org/viewcvs/relax?rev=21440&view=rev
Log:
Clean ups and improvements for the pipe_control.rdc.check_rdcs() function.
Pseudo-atoms are now handled much better and correctly in all cases. And
many RelaxErrors have been
converted to RelaxWarnings followed by a 'return False' statement.
Modified:
trunk/pipe_control/rdc.py
trunk/specific_analyses/n_state_model/__init__.py
Modified: trunk/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/rdc.py?rev=21440&r1=21439&r2=21440&view=diff
==============================================================================
--- trunk/pipe_control/rdc.py (original)
+++ trunk/pipe_control/rdc.py Thu Nov 14 11:54:27 2013
@@ -37,7 +37,7 @@
from lib.errors import RelaxError, RelaxNoAlignError, RelaxNoJError,
RelaxNoRDCError, RelaxNoSequenceError, RelaxSpinTypeError
from lib.io import extract_data, open_write_file, strip, write_data
from lib.physical_constants import dipolar_constant,
return_gyromagnetic_ratio
-from lib.warnings import RelaxWarning
+from lib.warnings import RelaxWarning, RelaxSpinTypeWarning
from pipe_control import grace, pipes
from pipe_control.align_tensor import get_tensor_index, get_tensor_object,
opt_uses_align_data, opt_uses_tensor
from pipe_control.interatomic import consistent_interatomic_data,
create_interatom, interatomic_loop, return_interatom
@@ -190,27 +190,19 @@
raise RelaxNoRDCError(rdc_id)
-def check_rdcs(interatom, spin1, spin2):
- """Check if the RDCs for the given interatomic data container should be
used.
+def check_rdcs(interatom):
+ """Check if all data required for calculating the RDC is present.
@param interatom: The interatomic data container.
@type interatom: InteratomContainer instance
- @param spin1: The first spin container.
- @type spin1: SpinContainer instance
- @param spin2: The second spin container.
- @type spin2: SpinContainer instance
- @return: True if the RDCs should be used, False otherwise.
+ @return: True if all data required for calculating the RDC is
present, False otherwise.
+ @rtype: bool
"""
# Skip deselected interatomic data containers.
if not interatom.select:
return False
- # Skip deselected spins.
- # FIXME: These checks could be fatal in the future if a user has good
RDCs and one of the two spins are deselected!
- if not spin1.select or not spin2.select:
- return False
-
# Only use interatomic data containers with RDC data.
if not hasattr(interatom, 'rdc'):
return False
@@ -219,33 +211,22 @@
if opt_uses_j_couplings() and not hasattr(interatom, 'j_coupling'):
return False
- # RDC data exists but the interatomic vectors are missing?
- if not hasattr(interatom, 'vector'):
- # Throw a warning.
- warn(RelaxWarning("RDC data exists but the interatomic vectors are
missing, skipping the spin pair '%s' and '%s'." % (interatom.spin_id1,
interatom.spin_id2)))
-
- # Jump to the next spin.
+ # Get the spins.
+ spin1 = return_spin(interatom.spin_id1)
+ spin2 = return_spin(interatom.spin_id2)
+
+ # Spin information checks.
+ if not hasattr(spin1, 'isotope'):
+ warn(RelaxSpinTypeWarning(interatom.spin_id1))
return False
-
- # Skip non-Me pseudo-atoms for the first spin.
- if hasattr(spin1, 'members') and len(spin1.members) != 3:
- warn(RelaxWarning("Only methyl group pseudo atoms are supported due
to their fast rotation, skipping the spin pair '%s' and '%s'." %
(interatom.spin_id1, interatom.spin_id2)))
+ if not hasattr(spin2, 'isotope'):
+ warn(RelaxSpinTypeWarning(interatom.spin_id2))
return False
-
- # Skip non-Me pseudo-atoms for the second spin.
- if hasattr(spin2, 'members') and len(spin2.members) != 3:
- warn(RelaxWarning("Only methyl group pseudo atoms are supported due
to their fast rotation, skipping the spin pair '%s' and '%s'." %
(interatom.spin_id1, interatom.spin_id2)))
+ if is_pseudoatom(spin1) and is_pseudoatom(spin2):
+ warn(RelaxWarning("Support for both spins being in a dipole pair
being pseudo-atoms is not implemented yet."))
return False
- # Checks.
- if not hasattr(spin1, 'isotope'):
- raise RelaxSpinTypeError(interatom.spin_id1)
- if not hasattr(spin2, 'isotope'):
- raise RelaxSpinTypeError(interatom.spin_id2)
- if is_pseudoatom(spin1) and is_pseudoatom(spin2):
- raise RelaxError("Support for both spins being in a dipole pair
being pseudo-atoms is not implemented yet.")
-
- # Interatomic distance checking (pseudo-atoms).
+ # Pseudo-atom checks.
if is_pseudoatom(spin1) or is_pseudoatom(spin2):
# Alias the pseudo and normal atoms.
pseudospin = spin1
@@ -261,14 +242,27 @@
# Get the corresponding interatomic data container.
pseudo_interatom = return_interatom(spin_id1=spin_id,
spin_id2=base_spin_id)
+ # Unit vector check.
+ if not hasattr(pseudo_interatom, 'vector'):
+ warn(RelaxWarning("The interatomic vector is missing for the
spin pair '%s' and '%s' of the pseudo-atom '%s', skipping the RDC for the
spin pair '%s' and '%s'." % (pseudo_interatom.spin_id1,
pseudo_interatom.spin_id2, pseudospin_id, base_spin_id, pseudospin_id)))
+ return False
+
# Check.
if not hasattr(pseudo_interatom, 'r'):
- raise RelaxError("The averaged interatomic distance between
spins '%s' and '%s' for the pseudo-atom '%s' has not been set yet." %
(spin_id, base_spin_id, pseudospin_id))
-
- # Interatomic distance checking (normal atoms).
+ warn(RelaxWarning("The averaged interatomic distance between
spins '%s' and '%s' for the pseudo-atom '%s' has not been set yet." %
(spin_id, base_spin_id, pseudospin_id)))
+ return False
+
+ # Normal atoms checks.
else:
+ # Unit vector check.
+ if not hasattr(interatom, 'vector'):
+ warn(RelaxWarning("The interatomic vector is missing, skipping
the spin pair '%s' and '%s'." % (interatom.spin_id1, interatom.spin_id2)))
+ return False
+
+ # Distance information check.
if not hasattr(interatom, 'r'):
- raise RelaxError("The averaged interatomic distance between
spins '%s' and '%s' has not been set yet." % (interatom.spin_id1,
interatom.spin_id2))
+ warn(RelaxWarning("The averaged interatomic distance between
spins '%s' and '%s' has not been set yet." % (interatom.spin_id1,
interatom.spin_id2)))
+ return False
# Everything is ok.
return True
@@ -946,7 +940,7 @@
spin2 = return_spin(interatom.spin_id2)
# RDC checks.
- if not check_rdcs(interatom, spin1, spin2):
+ if not check_rdcs(interatom):
continue
# Gyromagnetic ratios.
@@ -1064,12 +1058,9 @@
spin1 = return_spin(interatom.spin_id1)
spin2 = return_spin(interatom.spin_id2)
- # Skip deselected spins.
- if not spin1.select or not spin2.select:
- continue
-
- # Only use interatomic data containers with RDC and vector data.
- if not hasattr(interatom, 'rdc') or not hasattr(interatom,
'vector'):
+ print interatom.spin_id1, interatom.spin_id2
+ # RDC checks.
+ if not check_rdcs(interatom):
continue
# T-type data.
Modified: trunk/specific_analyses/n_state_model/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/n_state_model/__init__.py?rev=21440&r1=21439&r2=21440&view=diff
==============================================================================
--- trunk/specific_analyses/n_state_model/__init__.py (original)
+++ trunk/specific_analyses/n_state_model/__init__.py Thu Nov 14 11:54:27 2013
@@ -314,7 +314,7 @@
spin2 = return_spin(interatom.spin_id2)
# RDC checks.
- if not check_rdcs(interatom, spin1, spin2):
+ if not check_rdcs(interatom):
continue
# Containers with RDC data.
r21440 - in /trunk: pipe_control/rdc.py specific_analyses/n_state_model/__init__.py