Author: bugman
Date: Wed Jun 27 09:59:41 2012
New Revision: 17067
URL: http://svn.gna.org/viewcvs/relax?rev=17067&view=rev
Log:
Converted the population model RDC test data to the interatomic data design.
The RDC lists now consist of the two spin ID columns and a data column.
Modified:
branches/interatomic/test_suite/shared_data/align_data/population_model/generate.py
branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_0
branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_2
branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_3
Modified:
branches/interatomic/test_suite/shared_data/align_data/population_model/generate.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/shared_data/align_data/population_model/generate.py?rev=17067&r1=17066&r2=17067&view=diff
==============================================================================
---
branches/interatomic/test_suite/shared_data/align_data/population_model/generate.py
(original)
+++
branches/interatomic/test_suite/shared_data/align_data/population_model/generate.py
Wed Jun 27 09:59:41 2012
@@ -8,7 +8,8 @@
from re import search
# relax imports.
-from generic_fns.mol_res_spin import spin_loop
+from generic_fns.interatomic import interatomic_loop
+from generic_fns.mol_res_spin import return_spin, spin_loop
from status import Status; status = Status()
@@ -33,8 +34,15 @@
deselect.spin(spin_id=':UNK@H17')
deselect.spin(spin_id=':UNK@H18')
-# Load the CH vectors for the C atoms.
-structure.vectors(spin_id='@C*', attached='H*', ave=False)
+# Load the CH vectors.
+dipole_pair.define(spin_id1='@C*', spin_id2='@H*', direct_bond=True)
+dipole_pair.unit_vectors(ave=False)
+
+# Deselect the CH2 carbon-proton pairs.
+deselect.interatom(spin_id1=':UNK@C6', spin_id2=':UNK@H6')
+deselect.interatom(spin_id1=':UNK@C6', spin_id2=':UNK@H7')
+deselect.interatom(spin_id1=':UNK@C12', spin_id2=':UNK@H17')
+deselect.interatom(spin_id1=':UNK@C12', spin_id2=':UNK@H18')
# Init the alignment tensors.
A_5D = []
@@ -152,39 +160,40 @@
continue
# Header.
- out.write('%-10s %-10s %-10s %-10s %-10s %20s\n' % ('mol_name',
'res_num', 'res_name', 'spin.num', 'spin.name', 'rdc'))
+ out.write('# %-18s %-20s %20s\n' % ('spin_id1', 'spin_id2', 'rdc'))
- # Loop over the spins.
- for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
- # Skip protons.
- if spin.element == 'H':
+ # Loop over the interatomic data.
+ for interatom in interatomic_loop():
+ # Deselected containers.
+ if not interatom.select:
continue
- # Skip spin.
+ # Get the spins.
+ spin1 = return_spin(interatom.spin_id1)
+ spin2 = return_spin(interatom.spin_id2)
+
+ # Skip.
skip = False
for j in range(len(missing[i])):
- if missing[i][j][1] == '*' and res_num == missing[i][j][0]:
+ if missing[i][j][1] == '*' and spin1._res_num ==
missing[i][j][0]:
skip = True
- elif res_num == missing[i][j][0] and spin.name ==
missing[i][j][1]:
+ elif res_num == missing[i][j][0] and spin1.name ==
missing[i][j][1]:
skip = True
if skip:
continue
# No vector.
- if not hasattr(spin, 'xh_vect'):
+ if not hasattr(interatom, 'vector'):
continue
# Loop over the states.
rdc_full = 0.0
for j in range(len(pops)):
- # Unit vector.
- unit = spin.xh_vect[j] / norm(spin.xh_vect[j])
-
# Calculate the RDC.
- rdc = const * dot(unit, dot(A[i], unit))
+ rdc = const * dot(interatom.vector[j], dot(A[i],
interatom.vector[j]))
# Add to the full RDC.
rdc_full = rdc_full + pops[j] * rdc
# Output the rdc.
- out.write('%-10s %-10s %-10s %-10s %-10s %20s\n' % (mol_name,
res_num, res_name, spin.num, spin.name, rdc_full))
+ out.write('%-20s %-20s %20s\n' % (interatom.spin_id1,
interatom.spin_id2, rdc_full))
Modified:
branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_0
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_0?rev=17067&r1=17066&r2=17067&view=diff
==============================================================================
---
branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_0
(original)
+++
branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_0
Wed Jun 27 09:59:41 2012
@@ -1,10 +1,10 @@
-mol_name res_num res_name spin.num spin.name rdc
-LE 900 UNK 1 C1 -8.99008059436
-LE 900 UNK 2 C2 -11.1727013693
-LE 900 UNK 3 C3 -12.7645493632
-LE 900 UNK 4 C4 -25.6305124864
-LE 900 UNK 13 C7 -45.4329078085
-LE 900 UNK 14 C8 -45.6507371723
-LE 900 UNK 15 C9 -43.883378626
-LE 900 UNK 16 C10 -36.2358839976
-LE 900 UNK 17 C11 -43.6585501407
+# spin_id1 spin_id2 rdc
+#LE:900@C1 #LE:900@H1 -8.99008059436
+#LE:900@C2 #LE:900@H2 -11.1727013693
+#LE:900@C3 #LE:900@H3 -12.7645493632
+#LE:900@C4 #LE:900@H4 -25.6305124864
+#LE:900@C7 #LE:900@H12 -45.4329078085
+#LE:900@C8 #LE:900@H13 -45.6507371723
+#LE:900@C9 #LE:900@H14 -43.883378626
+#LE:900@C10 #LE:900@H15 -36.2358839976
+#LE:900@C11 #LE:900@H16 -43.6585501407
Modified:
branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_2
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_2?rev=17067&r1=17066&r2=17067&view=diff
==============================================================================
---
branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_2
(original)
+++
branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_2
Wed Jun 27 09:59:41 2012
@@ -1,10 +1,10 @@
-mol_name res_num res_name spin.num spin.name rdc
-LE 900 UNK 1 C1 0.0558217781223
-LE 900 UNK 2 C2 0.0749776961711
-LE 900 UNK 3 C3 0.0205783203822
-LE 900 UNK 4 C4 0.0412213151059
-LE 900 UNK 13 C7 0.0222255415748
-LE 900 UNK 14 C8 0.0196998835613
-LE 900 UNK 15 C9 0.0292391050148
-LE 900 UNK 16 C10 0.0735146554972
-LE 900 UNK 17 C11 0.0267010276098
+# spin_id1 spin_id2 rdc
+#LE:900@C1 #LE:900@H1 0.0558217781223
+#LE:900@C2 #LE:900@H2 0.0749776961711
+#LE:900@C3 #LE:900@H3 0.0205783203822
+#LE:900@C4 #LE:900@H4 0.0412213151059
+#LE:900@C7 #LE:900@H12 0.0222255415748
+#LE:900@C8 #LE:900@H13 0.0196998835613
+#LE:900@C9 #LE:900@H14 0.0292391050148
+#LE:900@C10 #LE:900@H15 0.0735146554972
+#LE:900@C11 #LE:900@H16 0.0267010276098
Modified:
branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_3
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_3?rev=17067&r1=17066&r2=17067&view=diff
==============================================================================
---
branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_3
(original)
+++
branches/interatomic/test_suite/shared_data/align_data/population_model/missing_rdc_3
Wed Jun 27 09:59:41 2012
@@ -1,9 +1,9 @@
-mol_name res_num res_name spin.num spin.name rdc
-LE 900 UNK 1 C1 24.7282064343
-LE 900 UNK 2 C2 24.9197912176
-LE 900 UNK 3 C3 27.8993003775
-LE 900 UNK 4 C4 0.948535173994
-LE 900 UNK 13 C7 2.09456125408
-LE 900 UNK 14 C8 6.74141169982
-LE 900 UNK 15 C9 8.69255563861
-LE 900 UNK 17 C11 -2.24181940515
+# spin_id1 spin_id2 rdc
+#LE:900@C1 #LE:900@H1 24.7282064343
+#LE:900@C2 #LE:900@H2 24.9197912176
+#LE:900@C3 #LE:900@H3 27.8993003775
+#LE:900@C4 #LE:900@H4 0.948535173994
+#LE:900@C7 #LE:900@H12 2.09456125408
+#LE:900@C8 #LE:900@H13 6.74141169982
+#LE:900@C9 #LE:900@H14 8.69255563861
+#LE:900@C11 #LE:900@H16 -2.24181940515
r17067 - /branches/interatomic/test_suite/shared_data/align_data/population_model/