Author: bugman
Date: Wed Jun 27 18:00:59 2012
New Revision: 17079
URL: http://svn.gna.org/viewcvs/relax?rev=17079&view=rev
Log:
Started to convert the Frame Order test suite RDC data to the new interatomic
data design.
Modified:
branches/interatomic/test_suite/shared_data/frame_order/free_rotor/back_calc.py
branches/interatomic/test_suite/shared_data/frame_order/free_rotor/rdc_dy.txt
Modified:
branches/interatomic/test_suite/shared_data/frame_order/free_rotor/back_calc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/shared_data/frame_order/free_rotor/back_calc.py?rev=17079&r1=17078&r2=17079&view=diff
==============================================================================
---
branches/interatomic/test_suite/shared_data/frame_order/free_rotor/back_calc.py
(original)
+++
branches/interatomic/test_suite/shared_data/frame_order/free_rotor/back_calc.py
Wed Jun 27 18:00:59 2012
@@ -1,6 +1,7 @@
# Script for calculation RDCs and PCSs for the rigid frame order model.
# relax module imports.
+from generic_fns.interatomic import interatomic_loop
from generic_fns.mol_res_spin import spin_loop
@@ -14,13 +15,14 @@
structure.load_spins('@N')
structure.load_spins('@H')
-# Load the NH vectors.
-structure.vectors(spin_id='@N', attached='H', ave=False)
+# Define the magnetic dipole-dipole relaxation interaction.
+dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.041 * 1e-10)
+dipole_pair.unit_vectors(ave=False)
-# Set the values needed to calculate the dipolar constant.
-value.set(1.041 * 1e-10, 'r', spin_id="@N")
-value.set('15N', 'heteronuc_type', spin_id="@N")
-value.set('1H', 'proton_type', spin_id="@N")
+# Set the nuclear isotope type.
+spin.isotope(isotope='15N', spin_id='@N')
+spin.isotope(isotope='1H', spin_id='@H')
# Load the tensors.
execfile('../tensors.py')
@@ -45,16 +47,22 @@
rdc.back_calc(tag)
pcs.back_calc(tag)
- # Set 1 Hz and 0.1 ppm errors on all data.
+ # Set 1 Hz errors on all RDC data.
+ for interatom in interatomic_loop():
+ # Init.
+ if not hasattr(interatom, 'rdc_err'):
+ interatom.rdc_err = {}
+
+ # Set the errors.
+ interatom.rdc_err[tag] = 1.0
+
+ # Set 0.1 ppm errors on all PCS data.
for spin in spin_loop():
# Init.
- if not hasattr(spin, 'rdc_err'):
- spin.rdc_err = {}
if not hasattr(spin, 'pcs_err'):
spin.pcs_err = {}
# Set the errors.
- spin.rdc_err[tag] = 1.0
spin.pcs_err[tag] = 0.1
# Write the data.
Modified:
branches/interatomic/test_suite/shared_data/frame_order/free_rotor/rdc_dy.txt
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/shared_data/frame_order/free_rotor/rdc_dy.txt?rev=17079&r1=17078&r2=17079&view=diff
==============================================================================
---
branches/interatomic/test_suite/shared_data/frame_order/free_rotor/rdc_dy.txt
(original)
+++
branches/interatomic/test_suite/shared_data/frame_order/free_rotor/rdc_dy.txt
Wed Jun 27 18:00:59 2012
@@ -1,68 +1,68 @@
-# mol_name res_num res_name spin_num spin_name RDCs
RDC_error
-distribution.pdb_mol1 83 GLU 2 N
-22.6435685973 1.0
-distribution.pdb_mol1 84 GLU 4 N
-10.154888962 1.0
-distribution.pdb_mol1 85 ILE 6 N
-18.2259647699 1.0
-distribution.pdb_mol1 86 ARG 8 N
-25.6971161012 1.0
-distribution.pdb_mol1 87 GLU 10 N
-17.3206535892 1.0
-distribution.pdb_mol1 88 ALA 12 N
-10.2308247788 1.0
-distribution.pdb_mol1 89 PHE 14 N
-23.2941623978 1.0
-distribution.pdb_mol1 90 ARG 16 N
-23.8906721963 1.0
-distribution.pdb_mol1 91 VAL 18 N
-5.33650980844 1.0
-distribution.pdb_mol1 92 PHE 20 N
-8.46166125859 1.0
-distribution.pdb_mol1 93 ASP 22 N
-28.3779817572 1.0
-distribution.pdb_mol1 94 LYS 24 N
-3.14292711728 1.0
-distribution.pdb_mol1 95 ASP 26 N
8.16819366171 1.0
-distribution.pdb_mol1 96 GLY 28 N
14.7393319277 1.0
-distribution.pdb_mol1 97 ASN 30 N
-1.22674090881 1.0
-distribution.pdb_mol1 98 GLY 32 N
14.9684904628 1.0
-distribution.pdb_mol1 99 TYR 34 N
10.2865609146 1.0
-distribution.pdb_mol1 100 ILE 36 N
8.06424488819 1.0
-distribution.pdb_mol1 101 SER 38 N
12.816161544 1.0
-distribution.pdb_mol1 102 ALA 40 N
6.58997285878 1.0
-distribution.pdb_mol1 103 ALA 42 N
12.962028849 1.0
-distribution.pdb_mol1 104 GLU 44 N
15.7047968343 1.0
-distribution.pdb_mol1 105 LEU 46 N
5.95759325856 1.0
-distribution.pdb_mol1 106 ARG 48 N
8.30000950097 1.0
-distribution.pdb_mol1 107 HIS 50 N
15.8902329653 1.0
-distribution.pdb_mol1 108 VAL 52 N
15.0956142239 1.0
-distribution.pdb_mol1 109 MET 54 N
9.34098342259 1.0
-distribution.pdb_mol1 110 THR 56 N
14.4125982957 1.0
-distribution.pdb_mol1 111 ASN 58 N
15.6438153059 1.0
-distribution.pdb_mol1 112 LEU 60 N
7.9736667163 1.0
-distribution.pdb_mol1 113 GLY 62 N
-1.84634178244 1.0
-distribution.pdb_mol1 114 GLU 64 N
3.94061971615 1.0
-distribution.pdb_mol1 115 LYS 66 N
15.9362722226 1.0
-distribution.pdb_mol1 116 LEU 68 N
6.5529938029 1.0
-distribution.pdb_mol1 117 THR 70 N
13.816693482 1.0
-distribution.pdb_mol1 118 ASP 72 N
-15.2595590232 1.0
-distribution.pdb_mol1 119 GLU 74 N
0.0101362010849 1.0
-distribution.pdb_mol1 120 GLU 76 N
0.946484578587 1.0
-distribution.pdb_mol1 121 VAL 78 N
-14.9893503588 1.0
-distribution.pdb_mol1 122 ASP 80 N
-12.1012805359 1.0
-distribution.pdb_mol1 123 GLU 82 N
2.82497482803 1.0
-distribution.pdb_mol1 124 MET 84 N
-0.0112811928562 1.0
-distribution.pdb_mol1 125 ILE 86 N
-14.5178859705 1.0
-distribution.pdb_mol1 126 ARG 88 N
-6.5238695499 1.0
-distribution.pdb_mol1 127 GLU 90 N
7.8152544798 1.0
-distribution.pdb_mol1 128 ALA 92 N
-5.39866767071 1.0
-distribution.pdb_mol1 129 ASP 94 N
-12.2433682215 1.0
-distribution.pdb_mol1 130 ILE 96 N
-9.77258720562 1.0
-distribution.pdb_mol1 131 ASP 98 N
10.2841384286 1.0
-distribution.pdb_mol1 132 GLY 100 N
0.0177592051639 1.0
-distribution.pdb_mol1 133 ASP 102 N
-25.3287740069 1.0
-distribution.pdb_mol1 134 GLY 104 N
2.97365619424 1.0
-distribution.pdb_mol1 135 GLN 106 N
10.0156587013 1.0
-distribution.pdb_mol1 136 VAL 108 N
11.753914627 1.0
-distribution.pdb_mol1 137 ASN 110 N
14.6719877841 1.0
-distribution.pdb_mol1 138 TYR 112 N
15.9030345333 1.0
-distribution.pdb_mol1 139 GLU 114 N
12.2703580007 1.0
-distribution.pdb_mol1 140 GLU 116 N
10.3174884305 1.0
-distribution.pdb_mol1 141 PHE 118 N
15.8390388894 1.0
-distribution.pdb_mol1 142 VAL 120 N
15.9444755585 1.0
-distribution.pdb_mol1 143 GLN 122 N
12.9003762876 1.0
-distribution.pdb_mol1 144 MET 124 N
15.1315625138 1.0
-distribution.pdb_mol1 145 MET 126 N
14.3796783524 1.0
-distribution.pdb_mol1 146 THR 128 N
5.25699800283 1.0
-distribution.pdb_mol1 147 ALA 130 N
-5.21671483632 1.0
-distribution.pdb_mol1 148 LYS 132 N
14.8439380803 1.0
+# Spin_id1 Spin_id2 RDCs RDC_error
+:83@N :83@H -22.6435685973 1.0
+:84@N :84@H -10.154888962 1.0
+:85@N :85@H -18.2259647699 1.0
+:86@N :86@H -25.6971161012 1.0
+:87@N :87@H -17.3206535892 1.0
+:88@N :88@H -10.2308247788 1.0
+:89@N :89@H -23.2941623978 1.0
+:90@N :90@H -23.8906721963 1.0
+:91@N :91@H -5.33650980844 1.0
+:92@N :92@H -8.46166125859 1.0
+:93@N :93@H -28.3779817572 1.0
+:94@N :94@H -3.14292711728 1.0
+:95@N :95@H 8.16819366171 1.0
+:96@N :96@H 14.7393319277 1.0
+:97@N :97@H -1.22674090881 1.0
+:98@N :98@H 14.9684904628 1.0
+:99@N :99@H 10.2865609146 1.0
+:100@N :100@H 8.06424488819 1.0
+:101@N :101@H 12.816161544 1.0
+:102@N :102@H 6.58997285878 1.0
+:103@N :103@H 12.962028849 1.0
+:104@N :104@H 15.7047968343 1.0
+:105@N :105@H 5.95759325856 1.0
+:106@N :106@H 8.30000950097 1.0
+:107@N :107@H 15.8902329653 1.0
+:108@N :108@H 15.0956142239 1.0
+:109@N :109@H 9.34098342259 1.0
+:110@N :110@H 14.4125982957 1.0
+:111@N :111@H 15.6438153059 1.0
+:112@N :112@H 7.9736667163 1.0
+:113@N :113@H -1.84634178244 1.0
+:114@N :114@H 3.94061971615 1.0
+:115@N :115@H 15.9362722226 1.0
+:116@N :116@H 6.5529938029 1.0
+:117@N :117@H 13.816693482 1.0
+:118@N :118@H -15.2595590232 1.0
+:119@N :119@H 0.0101362010849 1.0
+:120@N :120@H 0.946484578587 1.0
+:121@N :121@H -14.9893503588 1.0
+:122@N :122@H -12.1012805359 1.0
+:123@N :123@H 2.82497482803 1.0
+:124@N :124@H -0.0112811928562 1.0
+:125@N :125@H -14.5178859705 1.0
+:126@N :126@H -6.5238695499 1.0
+:127@N :127@H 7.8152544798 1.0
+:128@N :128@H -5.39866767071 1.0
+:129@N :129@H -12.2433682215 1.0
+:130@N :130@H -9.77258720562 1.0
+:131@N :131@H 10.2841384286 1.0
+:132@N :132@H 0.0177592051639 1.0
+:133@N :133@H -25.3287740069 1.0
+:134@N :134@H 2.97365619424 1.0
+:135@N :135@H 10.0156587013 1.0
+:136@N :136@H 11.753914627 1.0
+:137@N :137@H 14.6719877841 1.0
+:138@N :138@H 15.9030345333 1.0
+:139@N :139@H 12.2703580007 1.0
+:140@N :140@H 10.3174884305 1.0
+:141@N :141@H 15.8390388894 1.0
+:142@N :142@H 15.9444755585 1.0
+:143@N :143@H 12.9003762876 1.0
+:144@N :144@H 15.1315625138 1.0
+:145@N :145@H 14.3796783524 1.0
+:146@N :146@H 5.25699800283 1.0
+:147@N :147@H -5.21671483632 1.0
+:148@N :148@H 14.8439380803 1.0
r17079 - in /branches/interatomic/test_suite/shared_data/frame_order/free_rotor: back_calc.py rdc_dy.txt