Author: bugman
Date: Mon Feb 16 11:34:05 2009
New Revision: 8806
URL: http://svn.gna.org/viewcvs/relax?rev=8806&view=rev
Log:
The RDC data is now formatted for Pales, to check the synthetic test model
and relax.
Added:
1.3/test_suite/shared_data/align_data/CaM/pales.in
Modified:
1.3/test_suite/shared_data/align_data/CaM/generate_data.py
Modified: 1.3/test_suite/shared_data/align_data/CaM/generate_data.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/align_data/CaM/generate_data.py?rev=8806&r1=8805&r2=8806&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/align_data/CaM/generate_data.py (original)
+++ 1.3/test_suite/shared_data/align_data/CaM/generate_data.py Mon Feb 16
11:34:05 2009
@@ -80,6 +80,16 @@
rdc_file = open('synth_rdc', 'w')
pcs_file = open('synth_pcs', 'w')
+# Open the Pales input file.
+pales_file = open('pales.in', 'w')
+
+# The Pales header.
+pales_file.write("DATA SEQUENCE
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLT\n")
+pales_file.write("DATA SEQUENCE
MMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREANIDGDGQVNYEE\n")
+pales_file.write("DATA SEQUENCE FVQMMTAK\n\n")
+pales_file.write("VARS RESID_I RESNAME_I ATOMNAME_I RESID_J RESNAME_J
ATOMNAME_J D DD W\n")
+pales_file.write("FORMAT %5d %6s %6s %5d %6s %6s
%9.3f %9.3f %.2f\n\n")
+
# Loop over the N spins.
for spin, mol, res_num, res_name in spin_loop(full_info=True):
# Skip deselected spins.
@@ -116,6 +126,9 @@
rdc = dip_const * dot(transpose(spin.xh_vect), dot(tensor, spin.xh_vect))
rdc_file.write("%20s%10s%10s%10s%10s%30.11f\n" % (mol, res_num,
res_name, spin.num, spin.name, rdc))
+ # The Pales data line (equal weight, no errors).
+ pales_file.write("%5d %6s %6s %5d %6s %6s
%9.3f %9.3f %.2f\n" % (res_num, res_name, spin.name, res_num, res_name,
spin.attached_atom, rdc, 0.0, 1.0))
+
# Print outs.
print "\nAlignment tensor (A):\n" + `tensor`
print "Eigenvalues: " + `eigvals(tensor)`
Added: 1.3/test_suite/shared_data/align_data/CaM/pales.in
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/align_data/CaM/pales.in?rev=8806&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/align_data/CaM/pales.in (added)
+++ 1.3/test_suite/shared_data/align_data/CaM/pales.in Mon Feb 16 11:34:05
2009
@@ -1,0 +1,36 @@
+DATA SEQUENCE
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLT
+DATA SEQUENCE
MMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREANIDGDGQVNYEE
+DATA SEQUENCE FVQMMTAK
+
+VARS RESID_I RESNAME_I ATOMNAME_I RESID_J RESNAME_J ATOMNAME_J D DD
W
+FORMAT %5d %6s %6s %5d %6s %6s %9.3f %9.3f
%.2f
+
+ 83 GLU N 83 GLU H
5.949 0.000 1.00
+ 84 GLU N 84 GLU H
14.153 0.000 1.00
+ 85 ILE N 85 ILE H
7.482 0.000 1.00
+ 111 ASN N 111 ASN H
-3.607 0.000 1.00
+ 112 LEU N 112 LEU H
-2.223 0.000 1.00
+ 113 GLY N 113 GLY H
12.165 0.000 1.00
+ 114 GLU N 114 GLU H
-9.635 0.000 1.00
+ 115 LYS N 115 LYS H
2.484 0.000 1.00
+ 116 LEU N 116 LEU H
-6.181 0.000 1.00
+ 117 THR N 117 THR H
13.928 0.000 1.00
+ 118 ASP N 118 ASP H
2.688 0.000 1.00
+ 119 GLU N 119 GLU H
-5.002 0.000 1.00
+ 120 GLU N 120 GLU H
4.337 0.000 1.00
+ 121 VAL N 121 VAL H
6.676 0.000 1.00
+ 122 ASP N 122 ASP H
-4.988 0.000 1.00
+ 123 GLU N 123 GLU H
-2.490 0.000 1.00
+ 124 MET N 124 MET H
4.141 0.000 1.00
+ 126 ARG N 126 ARG H
-5.862 0.000 1.00
+ 127 GLU N 127 GLU H
0.767 0.000 1.00
+ 128 ALA N 128 ALA H
4.056 0.000 1.00
+ 130 ILE N 130 ILE H
-11.570 0.000 1.00
+ 131 ASP N 131 ASP H
-1.766 0.000 1.00
+ 132 GLY N 132 GLY H
4.570 0.000 1.00
+ 143 GLN N 143 GLN H
4.751 0.000 1.00
+ 144 MET N 144 MET H
7.439 0.000 1.00
+ 145 MET N 145 MET H
-2.422 0.000 1.00
+ 146 THR N 146 THR H
3.873 0.000 1.00
+ 147 ALA N 147 ALA H
7.271 0.000 1.00
+ 148 LYS N 148 LYS H
-3.397 0.000 1.00
r8806 - in /1.3/test_suite/shared_data/align_data/CaM: generate_data.py pales.in