Author: bugman
Date: Mon Mar 4 14:23:47 2013
New Revision: 18607
URL: http://svn.gna.org/viewcvs/relax?rev=18607&view=rev
Log:
Large improvements to the checking for all the rdc and pcs user functions.
The new methods check_pipe_setup() have been added to replace all other
checking. This
standardises all error checking and provides much better coverage. The
results is that a user will
be much less likely to encounter a Python traceback when they forget
something, and will be told via
a RelaxError what they are missing.
Modified:
trunk/generic_fns/pcs.py
trunk/generic_fns/rdc.py
Modified: trunk/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/pcs.py?rev=18607&r1=18606&r2=18607&view=diff
==============================================================================
--- trunk/generic_fns/pcs.py (original)
+++ trunk/generic_fns/pcs.py Mon Mar 4 14:23:47 2013
@@ -50,9 +50,8 @@
@type align_id: str
"""
- # Arg check.
- if align_id and align_id not in cdp.align_ids:
- raise RelaxError("The alignment ID '%s' is not in the alignment ID
list %s." % (align_id, cdp.align_ids))
+ # Check the pipe setup.
+ check_pipe_setup(pcs_id=align_id, sequence=True, N=True, tensors=True,
paramag_centre=True)
# Convert the align IDs to an array, or take all IDs.
if align_id:
@@ -135,8 +134,8 @@
if pipe == None:
pipe = pipes.cdp_name()
- # Test the data pipe.
- pipes.test(pipe)
+ # Check the pipe setup.
+ check_pipe_setup(pipe=pipe)
# Get the data pipes.
source_dp = pipes.get_pipe(pipe)
@@ -204,6 +203,64 @@
cdp.paramagnetic_centre = full_pos_list
+def check_pipe_setup(pipe=None, pcs_id=None, sequence=False, N=False,
tensors=False, pcs=False, paramag_centre=False):
+ """Check that the current data pipe has been setup sufficiently.
+
+ @keyword pipe: The data pipe to check, defaulting to the
current pipe.
+ @type pipe: None or str
+ @keyword pcs_id: The PCS ID string to check for in
cdp.pcs_ids.
+ @type pcs_id: None or str
+ @keyword sequence: A flag which when True will invoke the
sequence data check.
+ @type sequence: bool
+ @keyword N: A flag which if True will check that cdp.N
is set.
+ @type N: bool
+ @keyword tensors: A flag which if True will check that
alignment tensors exist.
+ @type tensors: bool
+ @keyword pcs: A flag which if True will check that PCSs
exist.
+ @type pcs: bool
+ @keyword paramag_centre: A flag which if True will check that the
paramagnetic centre has been set.
+ @type paramag_centre: bool
+ """
+
+ # The data pipe.
+ if pipe == None:
+ pipe = pipes.cdp_name()
+
+ # Get the data pipe.
+ dp = pipes.get_pipe(pipe)
+
+ # Test if the current data pipe exists.
+ pipes.test(pipe)
+
+ # Test if sequence data exists.
+ if sequence and not exists_mol_res_spin_data(pipe):
+ raise RelaxNoSequenceError(pipe)
+
+ # Check for dp.N.
+ if N and not hasattr(dp, 'N'):
+ raise RelaxError("The number of states N has not been set.")
+
+ # Check that alignment tensors are present.
+ if tensors and (not hasattr(dp, 'align_tensors') or
len(dp.align_tensors) == 0):
+ raise RelaxNoTensorError('alignment')
+
+ # Test for the alignment ID.
+ if pcs_id and (not hasattr(dp, 'align_ids') or pcs_id not in
dp.align_ids):
+ raise RelaxNoAlignError(pcs_id, pipe)
+
+ # Test if PCS data exists.
+ if pcs and not hasattr(dp, 'align_ids'):
+ raise RelaxNoAlignError()
+ if pcs and not hasattr(dp, 'pcs_ids'):
+ raise RelaxNoPCSError()
+ elif pcs and pcs_id and pcs_id not in dp.pcs_ids:
+ raise RelaxNoPCSError(pcs_id)
+
+ # Test if the paramagnetic centre is set.
+ if paramag_centre and not hasattr(cdp, 'paramagnetic_centre'):
+ raise RelaxError("The paramagnetic centre has not been defined.")
+
+
def copy(pipe_from=None, pipe_to=None, align_id=None):
"""Copy the PCS data from one data pipe to another.
@@ -223,31 +280,13 @@
elif pipe_to == None:
pipe_to = pipes.cdp_name()
- # Test if the pipe_from and pipe_to data pipes exist.
- pipes.test(pipe_from)
- pipes.test(pipe_to)
+ # Check the pipe setup.
+ check_pipe_setup(pipe=pipe_from, pcs_id=align_id, sequence=True,
pcs=True)
+ check_pipe_setup(pipe=pipe_to, sequence=True)
# Get the data pipes.
dp_from = pipes.get_pipe(pipe_from)
dp_to = pipes.get_pipe(pipe_to)
-
- # Test if pipe_from contains sequence data.
- if not exists_mol_res_spin_data(pipe_from):
- raise RelaxNoSequenceError
-
- # Test if pipe_to contains sequence data.
- if not exists_mol_res_spin_data(pipe_to):
- raise RelaxNoSequenceError
-
- # Test if alignment ID string exists for pipe_from.
- if align_id and (not hasattr(dp_from, 'align_ids') or align_id not in
dp_from.align_ids):
- raise RelaxNoAlignError(align_id, pipe_from)
-
- # Test if PCS data for the alignment ID exists.
- if not hasattr(dp_from, 'pcs_ids'):
- raise RelaxError("No PCS data exists.")
- elif align_id and align_id not in dp_from.pcs_ids:
- raise RelaxNoPCSError(align_id)
# The IDs.
if align_id == None:
@@ -305,12 +344,8 @@
@type force: bool
"""
- # Test if the current pipe exists.
- pipes.test()
-
- # Test if the sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True)
# Does PCS data exist?
if not hasattr(cdp, 'pcs_ids') or not cdp.pcs_ids:
@@ -412,16 +447,8 @@
@type align_id: str or None
"""
- # Test if the current data pipe exists.
- pipes.test()
-
- # Test if sequence data exists.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Check that the ID exists.
- if align_id and not align_id in cdp.pcs_ids:
- raise RelaxError("The PCS alignment id '%s' does not exist" %
align_id)
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True, pcs_id=align_id, pcs=True)
# The IDs.
if not align_id:
@@ -462,6 +489,9 @@
@type bc: bool
"""
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True, pcs_id=align_id, pcs=True)
+
# Call the write method with sys.stdout as the file.
write(align_id=align_id, file=sys.stdout, bc=bc)
@@ -472,6 +502,9 @@
@keyword spin_id: The spin ID string used to restrict the Q-factor
calculation to a subset of all spins.
@type spin_id: None or str
"""
+
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True)
# No PCSs, so no Q factors can be calculated.
if not hasattr(cdp, 'pcs_ids') or not len(cdp.pcs_ids):
@@ -572,8 +605,8 @@
@type spin_id: None or str
"""
- # Test if the current data pipe exists.
- pipes.test()
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True)
# Test if sequence data exists.
if not exists_mol_res_spin_data():
@@ -681,21 +714,8 @@
@type sd: float or int.
"""
- # Test if sequence data exists.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test if PCS data exists.
- if not hasattr(cdp, 'pcs_ids'):
- raise RelaxNoPCSError()
-
- # Test if data corresponding to 'align_id' exists.
- if align_id and align_id not in cdp.pcs_ids:
- raise RelaxNoPCSError(align_id)
-
- # Arg check.
- if align_id and align_id not in cdp.pcs_ids:
- raise RelaxError("The alignment ID '%s' is not in the PCS ID list
%s." % (align_id, cdp.pcs_ids))
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True, pcs_id=align_id, pcs=True)
# Convert the align IDs to an array, or take all IDs.
if align_id:
@@ -756,22 +776,8 @@
@type force: bool
"""
- # Test if the current pipe exists.
- pipes.test()
-
- # Test if sequence data exists.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test if data corresponding to 'align_id' exists.
- if not hasattr(cdp, 'pcs_ids'):
- raise RelaxNoPCSError(align_id)
- if align_id and align_id not in cdp.pcs_ids:
- raise RelaxNoPCSError(align_id)
-
- # Arg check.
- if align_id and align_id not in cdp.align_ids:
- raise RelaxError("The alignment ID '%s' is not in the alignment ID
list %s." % (align_id, cdp.align_ids))
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True, pcs_id=align_id, pcs=True,
paramag_centre=True)
# Convert the align IDs to an array, or take all IDs.
if align_id:
@@ -901,13 +907,8 @@
@type weight: float or int.
"""
- # Test if sequence data exists.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test if data corresponding to 'align_id' exists.
- if not hasattr(cdp, 'pcs_ids') or align_id not in cdp.pcs_ids:
- raise RelaxNoPCSError(align_id)
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True, pcs_id=align_id, pcs=True)
# Loop over the spins.
for spin in spin_loop(spin_id):
@@ -934,16 +935,8 @@
@type force: bool
"""
- # Test if the current pipe exists.
- pipes.test()
-
- # Test if the sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test if data corresponding to 'align_id' exists.
- if not hasattr(cdp, 'pcs_ids') or align_id not in cdp.pcs_ids:
- raise RelaxNoPCSError(align_id)
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True, pcs_id=align_id, pcs=True)
# Open the file for writing.
file = open_write_file(file, dir, force)
Modified: trunk/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/rdc.py?rev=18607&r1=18606&r2=18607&view=diff
==============================================================================
--- trunk/generic_fns/rdc.py (original)
+++ trunk/generic_fns/rdc.py Mon Mar 4 14:23:47 2013
@@ -51,9 +51,8 @@
@type align_id: str
"""
- # Arg check.
- if align_id and align_id not in cdp.align_ids:
- raise RelaxError("The alignment ID '%s' is not in the alignment ID
list %s." % (align_id, cdp.align_ids))
+ # Check the pipe setup.
+ check_pipe_setup(rdc_id=align_id, sequence=True, N=True, tensors=True)
# Convert the align IDs to an array, or take all IDs.
if align_id:
@@ -122,6 +121,58 @@
# The absolute value.
if hasattr(interatom, 'absolute_rdc') and id in
interatom.absolute_rdc.keys() and interatom.absolute_rdc[id]:
interatom.rdc_bc[id] = abs(interatom.rdc_bc[id])
+
+
+def check_pipe_setup(pipe=None, rdc_id=None, sequence=False, N=False,
tensors=False, rdc=False):
+ """Check that the current data pipe has been setup sufficiently.
+
+ @keyword pipe: The data pipe to check, defaulting to the current
pipe.
+ @type pipe: None or str
+ @keyword rdc_id: The RDC ID string to check for in cdp.rdc_ids.
+ @type rdc_id: None or str
+ @keyword sequence: A flag which when True will invoke the sequence data
check.
+ @type sequence: bool
+ @keyword N: A flag which if True will check that cdp.N is set.
+ @type N: bool
+ @keyword tensors: A flag which if True will check that alignment
tensors exist.
+ @type tensors: bool
+ @keyword rdc: A flag which if True will check that RDCs exist.
+ @type rdc: bool
+ """
+
+ # The data pipe.
+ if pipe == None:
+ pipe = pipes.cdp_name()
+
+ # Get the data pipe.
+ dp = pipes.get_pipe(pipe)
+
+ # Test if the current data pipe exists.
+ pipes.test(pipe)
+
+ # Test if sequence data exists.
+ if sequence and not exists_mol_res_spin_data(pipe):
+ raise RelaxNoSequenceError(pipe)
+
+ # Check for dp.N.
+ if N and not hasattr(dp, 'N'):
+ raise RelaxError("The number of states N has not been set.")
+
+ # Check that alignment tensors are present.
+ if tensors and (not hasattr(dp, 'align_tensors') or
len(dp.align_tensors) == 0):
+ raise RelaxNoTensorError('alignment')
+
+ # Test for the alignment ID.
+ if rdc_id and (not hasattr(dp, 'align_ids') or rdc_id not in
dp.align_ids):
+ raise RelaxNoAlignError(rdc_id, pipe)
+
+ # Test if RDC data exists.
+ if rdc and not hasattr(dp, 'align_ids'):
+ raise RelaxNoAlignError()
+ if rdc and not hasattr(dp, 'rdc_ids'):
+ raise RelaxNoRDCError()
+ elif rdc and rdc_id and rdc_id not in dp.rdc_ids:
+ raise RelaxNoRDCError(rdc_id)
def convert(value, align_id, to_intern=False):
@@ -175,31 +226,13 @@
elif pipe_to == None:
pipe_to = pipes.cdp_name()
- # Test if the pipe_from and pipe_to data pipes exist.
- pipes.test(pipe_from)
- pipes.test(pipe_to)
+ # Check the pipe setup.
+ check_pipe_setup(pipe=pipe_from, rdc_id=align_id, sequence=True,
rdc=True)
+ check_pipe_setup(pipe=pipe_to, sequence=True)
# Get the data pipes.
dp_from = pipes.get_pipe(pipe_from)
dp_to = pipes.get_pipe(pipe_to)
-
- # Test if pipe_from contains sequence data.
- if not exists_mol_res_spin_data(pipe_from):
- raise RelaxNoSequenceError
-
- # Test if pipe_to contains sequence data.
- if not exists_mol_res_spin_data(pipe_to):
- raise RelaxNoSequenceError
-
- # Test if alignment ID string exists for pipe_from.
- if align_id and (not hasattr(dp_from, 'align_ids') or align_id not in
dp_from.align_ids):
- raise RelaxNoAlignError(align_id, pipe_from)
-
- # Test if RDC data for the alignment ID exists.
- if not hasattr(dp_from, 'rdc_ids'):
- raise RelaxError("No RDC data exists.")
- elif align_id and align_id not in dp_from.rdc_ids:
- raise RelaxNoRDCError(align_id)
# Test that the interatomic data is consistent between the two data pipe.
consistent_interatomic_data(pipe1=pipe_to, pipe2=pipe_from)
@@ -260,12 +293,8 @@
@type force: bool
"""
- # Test if the current pipe exists.
- pipes.test()
-
- # Test if the sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True)
# Does RDC data exist?
if not hasattr(cdp, 'rdc_ids') or not cdp.rdc_ids:
@@ -341,16 +370,8 @@
@type align_id: str or None
"""
- # Test if the current data pipe exists.
- pipes.test()
-
- # Test if sequence data exists.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Check that the ID exists.
- if align_id and not align_id in cdp.rdc_ids:
- raise RelaxError("The RDC alignment id '%s' does not exist" %
align_id)
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True, rdc_id=align_id, rdc=True)
# The IDs.
if not align_id:
@@ -391,6 +412,9 @@
@type bc: bool
"""
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True, rdc_id=align_id, rdc=True)
+
# Call the write method with sys.stdout as the file.
write(align_id=align_id, file=sys.stdout, bc=bc)
@@ -401,6 +425,9 @@
@keyword spin_id: The spin ID string used to restrict the Q-factor
calculation to a subset of all spins.
@type spin_id: None or str
"""
+
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True)
# No RDCs, so no Q factors can be calculated.
if not hasattr(cdp, 'rdc_ids') or not len(cdp.rdc_ids):
@@ -535,12 +562,8 @@
@type absolute: bool
"""
- # Test if the current data pipe exists.
- pipes.test()
-
- # Test if sequence data exists.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True)
# Either the data or error column must be supplied.
if data_col == None and error_col == None:
@@ -721,21 +744,8 @@
@type sd: float or int.
"""
- # Test if sequence data exists.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test if RDC data exists.
- if not hasattr(cdp, 'rdc_ids'):
- raise RelaxNoRDCError()
-
- # Test if data corresponding to 'align_id' exists.
- if align_id and align_id not in cdp.rdc_ids:
- raise RelaxNoRDCError(align_id)
-
- # Arg check.
- if align_id and align_id not in cdp.rdc_ids:
- raise RelaxError("The alignment ID '%s' is not in the RDC ID list
%s." % (align_id, cdp.rdc_ids))
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True, rdc_id=align_id, rdc=True)
# Convert the align IDs to an array, or take all IDs.
if align_id:
@@ -765,13 +775,8 @@
@type weight: float or int.
"""
- # Test if sequence data exists.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test if data corresponding to 'align_id' exists.
- if not hasattr(cdp, 'rdc_ids') or align_id not in cdp.rdc_ids:
- raise RelaxNoRDCError(align_id)
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True, rdc_id=align_id, rdc=True)
# Loop over the interatomic data.
for interatom in interatomic_loop():
@@ -798,16 +803,8 @@
@type force: bool
"""
- # Test if the current pipe exists.
- pipes.test()
-
- # Test if the sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Test if data corresponding to 'align_id' exists.
- if not hasattr(cdp, 'rdc_ids') or align_id not in cdp.rdc_ids:
- raise RelaxNoRDCError(align_id)
+ # Check the pipe setup.
+ check_pipe_setup(sequence=True, rdc_id=align_id, rdc=True)
# Open the file for writing.
file = open_write_file(file, dir, force)
r18607 - in /trunk/generic_fns: pcs.py rdc.py