Author: bugman
Date: Thu Feb 18 13:24:04 2010
New Revision: 10711
URL: http://svn.gna.org/viewcvs/relax?rev=10711&view=rev
Log:
The Q-factor calculation functions can now accept a spin_id arg.
As there can now be data problems, the functions check if there is any
selected spins looped over,
that the is RDC/PCS data, and that there is back-calculated RDC/PCS data.
Modified:
1.3/generic_fns/pcs.py
1.3/generic_fns/rdc.py
Modified: 1.3/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pcs.py?rev=10711&r1=10710&r2=10711&view=diff
==============================================================================
--- 1.3/generic_fns/pcs.py (original)
+++ 1.3/generic_fns/pcs.py Thu Feb 18 13:24:04 2010
@@ -27,12 +27,14 @@
from copy import deepcopy
from math import sqrt
from numpy import array, float64, zeros
+from warnings import warn
# relax module imports.
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_data_array, return_spin, spin_index_loop, spin_loop
from generic_fns import pipes
from relax_errors import RelaxError, RelaxNoPdbError, RelaxNoSequenceError,
RelaxNoSpinError, RelaxPCSError
from relax_io import read_spin_data
+from relax_warnings import RelaxWarning
def add_data_to_spin(spin=None, ri_labels=None, remap_table=None,
frq_labels=None, frq=None, values=None, errors=None, sim=False):
@@ -453,8 +455,12 @@
return index
-def q_factors():
- """Calculate the Q-factors for the PCS data."""
+def q_factors(spin_id=None):
+ """Calculate the Q-factors for the PCS data.
+
+ @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
+ """
# Q-factor list.
cdp.q_factors_pcs = []
@@ -466,11 +472,23 @@
sse = 0.0
# Spin loop.
- for spin in spin_loop():
+ spin_count = 0
+ pcs_data = False
+ pcs_bc_data = False
+ for spin in spin_loop(spin_id):
# Skip deselected spins.
if not spin.select:
continue
+ # Increment the spin counter.
+ spin_count += 1
+
+ # Data checks.
+ if hasattr(spin, 'pcs'):
+ pcs_data = True
+ if hasattr(spin, 'pcs_bc'):
+ pcs_bc_data = True
+
# Skip spins without PCS data.
if not hasattr(spin, 'pcs') or not hasattr(spin, 'pcs_bc') or
spin.pcs[i] == None:
continue
@@ -484,6 +502,17 @@
# The Q-factor for the alignment.
Q = sqrt(sse / pcs2_sum)
cdp.q_factors_pcs.append(Q)
+
+ # Warnings (and then exit).
+ if not spin_count:
+ warn(RelaxWarning("No spins have been used in the calculation."))
+ return
+ if not pcs_data:
+ warn(RelaxWarning("No PCS data can be found."))
+ return
+ if not pcs_bc_data:
+ warn(RelaxWarning("No back-calculated PCS data can be found."))
+ return
# The total Q-factor.
cdp.q_pcs = 0.0
Modified: 1.3/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/rdc.py?rev=10711&r1=10710&r2=10711&view=diff
==============================================================================
--- 1.3/generic_fns/rdc.py (original)
+++ 1.3/generic_fns/rdc.py Thu Feb 18 13:24:04 2010
@@ -29,6 +29,7 @@
from numpy import float64, ones, zeros
from numpy.linalg import norm
import sys
+from warnings import warn
# relax module imports.
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_data_array, return_spin, spin_index_loop, spin_loop
@@ -37,6 +38,7 @@
from physical_constants import dipolar_constant, g1H, pcs_constant,
return_gyromagnetic_ratio
from relax_errors import RelaxError, RelaxNoSequenceError, RelaxNoSpinError,
RelaxRDCError
from relax_io import read_spin_data, write_spin_data
+from relax_warnings import RelaxWarning
def add_data_to_spin(spin=None, ri_labels=None, remap_table=None,
frq_labels=None, frq=None, values=None, errors=None, sim=False):
@@ -410,8 +412,12 @@
return index
-def q_factors():
- """Calculate the Q-factors for the RDC data."""
+def q_factors(spin_id=None):
+ """Calculate the Q-factors for the RDC data.
+
+ @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
+ """
# Q-factor list.
cdp.q_factors_rdc = []
@@ -426,10 +432,22 @@
# Spin loop.
dj = None
N = 0
- for spin in spin_loop():
+ spin_count = 0
+ rdc_data = False
+ rdc_bc_data = False
+ for spin in spin_loop(spin_id):
# Skip deselected spins.
if not spin.select:
continue
+
+ # Increment the spin counter.
+ spin_count += 1
+
+ # Data checks.
+ if hasattr(spin, 'rdc'):
+ rdc_data = True
+ if hasattr(spin, 'rdc_bc'):
+ rdc_bc_data = True
# Skip spins without RDC data.
if not hasattr(spin, 'rdc') or not hasattr(spin, 'rdc_bc') or
spin.rdc[i] == None:
@@ -454,6 +472,17 @@
# Increment the number of data sets.
N = N + 1
+
+ # Warnings (and then exit).
+ if not spin_count:
+ warn(RelaxWarning("No spins have been used in the calculation."))
+ return
+ if not rdc_data:
+ warn(RelaxWarning("No RDC data can be found."))
+ return
+ if not rdc_bc_data:
+ warn(RelaxWarning("No back-calculated RDC data can be found."))
+ return
# Normalisation factor of 2Da^2(4 + 3R)/5.
D = dj * cdp.align_tensors[i].A_diag
r10711 - in /1.3/generic_fns: pcs.py rdc.py