Author: bugman
Date: Tue Jun 26 14:27:37 2012
New Revision: 17060
URL: http://svn.gna.org/viewcvs/relax?rev=17060&view=rev
Log:
Converted all of the rdc related functions to the interatomic data container
design.
Modified:
branches/interatomic/generic_fns/rdc.py
Modified: branches/interatomic/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/rdc.py?rev=17060&r1=17059&r2=17060&view=diff
==============================================================================
--- branches/interatomic/generic_fns/rdc.py (original)
+++ branches/interatomic/generic_fns/rdc.py Tue Jun 26 14:27:37 2012
@@ -32,10 +32,11 @@
from warnings import warn
# relax module imports.
+from arg_check import is_float
from float import nan
from generic_fns import grace, pipes
from generic_fns.align_tensor import get_tensor_index
-from generic_fns.interatomic import create_interatom, return_interatom
+from generic_fns.interatomic import create_interatom, interatomic_loop,
return_interatom
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id, return_spin, spin_loop
from maths_fns.rdc import ave_rdc_tensor
from physical_constants import dipolar_constant, return_gyromagnetic_ratio
@@ -77,44 +78,46 @@
# Unit vector data structure init.
unit_vect = zeros((cdp.N, 3), float64)
- # Loop over the spins.
- for spin in spin_loop():
- # Skip spins with no bond vectors.
- if not hasattr(spin, 'bond_vect') and not hasattr(spin, 'xh_vect'):
- continue
-
- # Check.
- if not hasattr(spin, 'heteronuc_type'):
- raise RelaxSpinTypeError
-
- # Alias.
- if hasattr(spin, 'bond_vect'):
- vectors = spin.bond_vect
+ # Loop over the interatomic data.
+ for interatom in interatomic_loop():
+ # Skip containers with no interatomic vectors.
+ if not hasattr(interatom, 'vector'):
+ continue
+
+ # Get the spins.
+ spin1 = return_spin(interatom.spin_id1)
+ spin2 = return_spin(interatom.spin_id2)
+
+ # Checks.
+ if not hasattr(spin1, 'isotope'):
+ raise RelaxSpinTypeError(interatom.spin_id1)
+ if not hasattr(spin2, 'isotope'):
+ raise RelaxSpinTypeError(interatom.spin_id2)
+
+ # Single vector.
+ if is_float(interatom.vector[0], raise_error=False):
+ vectors = [interatom.vector]
else:
- vectors = spin.xh_vect
-
- # Single vector.
- if type(vectors[0]) in [float, float64]:
- vectors = [vectors]
+ vectors = interatom.vector
# Gyromagnetic ratios.
- gx = return_gyromagnetic_ratio(spin.heteronuc_type)
- gh = return_gyromagnetic_ratio(spin.proton_type)
+ g1 = return_gyromagnetic_ratio(spin1.isotope)
+ g2 = return_gyromagnetic_ratio(spin2.isotope)
# Calculate the RDC dipolar constant (in Hertz, and the 3 comes from
the alignment tensor), and append it to the list.
- dj = 3.0/(2.0*pi) * dipolar_constant(gx, gh, spin.r)
+ dj = 3.0/(2.0*pi) * dipolar_constant(g1, g2, interatom.r)
# Unit vectors.
for c in range(cdp.N):
unit_vect[c] = vectors[c] / norm(vectors[c])
# Initialise if necessary.
- if not hasattr(spin, 'rdc_bc'):
- spin.rdc_bc = {}
+ if not hasattr(interatom, 'rdc_bc'):
+ interatom.rdc_bc = {}
# Calculate the RDCs.
for id in align_ids:
- spin.rdc_bc[id] = ave_rdc_tensor(dj, unit_vect, cdp.N,
cdp.align_tensors[get_tensor_index(id)].A, weights=weights)
+ interatom.rdc_bc[id] = ave_rdc_tensor(dj, unit_vect, cdp.N,
cdp.align_tensors[get_tensor_index(id)].A, weights=weights)
def convert(value, align_id, to_intern=False):
@@ -190,38 +193,30 @@
# Errors present?
err_flag = False
- for spin in spin_loop():
- # Skip deselected spins.
- if not spin.select:
- continue
-
+ for interatom in interatomic_loop():
# Error present.
- if hasattr(spin, 'rdc_err') and align_id in spin.rdc_err.keys():
+ if hasattr(interatom, 'rdc_err') and align_id in
interatom.rdc_err.keys():
err_flag = True
break
- # Loop over the spins.
- for spin, spin_id in spin_loop(return_id=True):
- # Skip deselected spins.
- if not spin.select:
+ # Loop over the interatomic data.
+ for interatom in interatomic_loop():
+ # Skip if data is missing.
+ if not hasattr(interatom, 'rdc') or not hasattr(interatom,
'rdc_bc') or not align_id in interatom.rdc.keys() or not align_id in
interatom.rdc_bc.keys():
continue
- # Skip if data is missing.
- if not hasattr(spin, 'rdc') or not hasattr(spin, 'rdc_bc') or
not align_id in spin.rdc.keys() or not align_id in spin.rdc_bc.keys():
- continue
-
# Append the data.
- data[-1].append([convert(spin.rdc_bc[align_id], align_id),
convert(spin.rdc[align_id], align_id)])
+ data[-1].append([convert(interatom.rdc_bc[align_id], align_id),
convert(interatom.rdc[align_id], align_id)])
# Errors.
if err_flag:
- if hasattr(spin, 'rdc_err') and align_id in
spin.rdc_err.keys():
- data[-1][-1].append(convert(spin.rdc_err[align_id],
align_id))
+ if hasattr(interatom, 'rdc_err') and align_id in
interatom.rdc_err.keys():
+ data[-1][-1].append(convert(interatom.rdc_err[align_id],
align_id))
else:
data[-1][-1].append(None)
# Label.
- data[-1][-1].append(spin_id)
+ data[-1][-1].append("%s-%s" % (interatom.spin_id1,
interatom.spin_id2))
# The data size.
size = len(data)
@@ -277,15 +272,15 @@
if hasattr(cdp, 'rdc_data_types') and cdp.rdc_data_types.has_key(id):
cdp.rdc_data_types.pop(id)
- # The spin data.
- for spin in spin_loop():
+ # The interatomic data.
+ for interatom in interatomic_loop():
# The data.
- if hasattr(spin, 'rdc') and spin.rdc.has_key(id):
- spin.rdc.pop(id)
+ if hasattr(interatom, 'rdc') and interatom.rdc.has_key(id):
+ interatom.rdc.pop(id)
# The error.
- if hasattr(spin, 'rdc_err') and spin.rdc_err.has_key(id):
- spin.rdc_err.pop(id)
+ if hasattr(interatom, 'rdc_err') and
interatom.rdc_err.has_key(id):
+ interatom.rdc_err.pop(id)
# Clean the global data.
if not hasattr(cdp, 'pcs_ids') or id not in cdp.pcs_ids:
@@ -327,42 +322,42 @@
D2_sum = 0.0
sse = 0.0
- # Spin loop.
+ # Interatomic data loop.
dj = None
N = 0
- spin_count = 0
+ interatom_count = 0
rdc_data = False
rdc_bc_data = False
- for spin in spin_loop(spin_id):
- # Skip deselected spins.
- if not spin.select:
+ for interatom in interatomic_loop():
+ # Increment the counter.
+ interatom_count += 1
+
+ # Data checks.
+ if hasattr(interatom, 'rdc') and interatom.rdc.has_key(align_id):
+ rdc_data = True
+ if hasattr(interatom, 'rdc_bc') and
interatom.rdc_bc.has_key(align_id):
+ rdc_bc_data = True
+
+ # Skip containers without RDC data.
+ if not hasattr(interatom, 'rdc') or not hasattr(interatom,
'rdc_bc') or not interatom.rdc.has_key(align_id) or interatom.rdc[align_id]
== None or not interatom.rdc_bc.has_key(align_id) or
interatom.rdc_bc[align_id] == None:
continue
- # Increment the spin counter.
- spin_count += 1
-
- # Data checks.
- if hasattr(spin, 'rdc') and spin.rdc.has_key(align_id):
- rdc_data = True
- if hasattr(spin, 'rdc_bc') and spin.rdc_bc.has_key(align_id):
- rdc_bc_data = True
-
- # Skip spins without RDC data.
- if not hasattr(spin, 'rdc') or not hasattr(spin, 'rdc_bc') or
not spin.rdc.has_key(align_id) or spin.rdc[align_id] == None or not
spin.rdc_bc.has_key(align_id) or spin.rdc_bc[align_id] == None:
- continue
+ # Get the spins.
+ spin1 = return_spin(interatom.spin_id1)
+ spin2 = return_spin(interatom.spin_id2)
# Sum of squares.
- sse = sse + (spin.rdc[align_id] - spin.rdc_bc[align_id])**2
+ sse = sse + (interatom.rdc[align_id] -
interatom.rdc_bc[align_id])**2
# Sum the RDCs squared (for one type of normalisation).
- D2_sum = D2_sum + spin.rdc[align_id]**2
+ D2_sum = D2_sum + interatom.rdc[align_id]**2
# Gyromagnetic ratios.
- gx = return_gyromagnetic_ratio(spin.heteronuc_type)
- gh = return_gyromagnetic_ratio(spin.proton_type)
+ g1 = return_gyromagnetic_ratio(spin1.isotope)
+ g2 = return_gyromagnetic_ratio(spin2.isotope)
# Calculate the RDC dipolar constant (in Hertz, and the 3 comes
from the alignment tensor), and append it to the list.
- dj_new = 3.0/(2.0*pi) * dipolar_constant(gx, gh, spin.r)
+ dj_new = 3.0/(2.0*pi) * dipolar_constant(g1, g2, interatom.r)
if dj and dj_new != dj:
raise RelaxError("All the RDCs must come from the same
nucleus type.")
else:
@@ -372,8 +367,8 @@
N = N + 1
# Warnings (and then exit).
- if not spin_count:
- warn(RelaxWarning("No spins have been used in the calculation."))
+ if not interatom_count:
+ warn(RelaxWarning("No interatomic data containers have been used
in the calculation."))
return
if not rdc_data:
warn(RelaxWarning("No RDC data can be found."))
@@ -600,14 +595,14 @@
if not hasattr(cdp, 'rdc_ids') or align_id not in cdp.rdc_ids:
raise RelaxNoRDCError(align_id)
- # Loop over the spins.
- for spin in spin_loop(spin_id):
+ # Loop over the interatomic data.
+ for interatom in interatomic_loop():
# No data structure.
- if not hasattr(spin, 'rdc_weight'):
- spin.rdc_weight = {}
+ if not hasattr(interatom, 'rdc_weight'):
+ interatom.rdc_weight = {}
# Set the weight.
- spin.rdc_weight[align_id] = weight
+ interatom.rdc_weight[align_id] = weight
def write(align_id=None, file=None, dir=None, bc=False, force=False):
@@ -639,39 +634,31 @@
# Open the file for writing.
file = open_write_file(file, dir, force)
- # Loop over the spins and collect the data.
- mol_names = []
- res_nums = []
- res_names = []
- spin_nums = []
- spin_names = []
- values = []
- errors = []
- for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
- # Skip spins with no RDCs.
- if not bc and (not hasattr(spin, 'rdc') or align_id not in
spin.rdc.keys()):
- continue
- elif bc and (not hasattr(spin, 'rdc_bc') or align_id not in
spin.rdc_bc.keys()):
+ # Loop over the interatomic data containers and collect the data.
+ data = []
+ for interatom in interatomic_loop():
+ # Skip containers with no RDCs.
+ if not bc and (not hasattr(interatom, 'rdc') or align_id not in
interatom.rdc.keys()):
+ continue
+ elif bc and (not hasattr(interatom, 'rdc_bc') or align_id not in
interatom.rdc_bc.keys()):
continue
# Append the spin data.
- mol_names.append(mol_name)
- res_nums.append(res_num)
- res_names.append(res_name)
- spin_nums.append(spin.num)
- spin_names.append(spin.name)
+ data.append([])
+ data[-1].append(interatom.spin_id1)
+ data[-1].append(interatom.spin_id2)
# The value.
if bc:
- values.append(convert(spin.rdc_bc[align_id], align_id))
+ data[-1].append(convert(interatom.rdc_bc[align_id], align_id))
else:
- values.append(convert(spin.rdc[align_id], align_id))
+ data[-1].append(convert(interatom.rdc[align_id], align_id))
# The error.
- if hasattr(spin, 'rdc_err') and align_id in spin.rdc_err.keys():
- errors.append(convert(spin.rdc_err[align_id], align_id))
+ if hasattr(interatom, 'rdc_err') and align_id in
interatom.rdc_err.keys():
+ data[-1].append(convert(interatom.rdc_err[align_id], align_id))
else:
- errors.append(None)
+ data[-1].append(None)
# Write out.
- write_spin_data(file=file, mol_names=mol_names, res_nums=res_nums,
res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, data=values,
data_name='RDCs', error=errors, error_name='RDC_error')
+ write_data(out=file, headings=["Spin_ID1", "Spin_ID2", "RDCs",
"RDC_error"], data=data)
r17060 - /branches/interatomic/generic_fns/rdc.py