Author: bugman
Date: Mon Nov 17 12:17:22 2014
New Revision: 26598
URL: http://svn.gna.org/viewcvs/relax?rev=26598&view=rev
Log:
Converted all ATOM records to HETATM in the sphere.pdb file.
Modified:
trunk/test_suite/shared_data/model_free/sphere/create_sphere.py
trunk/test_suite/shared_data/model_free/sphere/sphere.pdb
Modified: trunk/test_suite/shared_data/model_free/sphere/create_sphere.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/sphere/create_sphere.py?rev=26598&r1=26597&r2=26598&view=diff
==============================================================================
--- trunk/test_suite/shared_data/model_free/sphere/create_sphere.py
(original)
+++ trunk/test_suite/shared_data/model_free/sphere/create_sphere.py Mon
Nov 17 12:17:22 2014
@@ -5,7 +5,7 @@
from math import acos, cos, pi, sin, sqrt
# relax module imports.
-from lib.structure.pdb_write import atom, conect, ter
+from lib.structure.pdb_write import conect, hetatm
# Number of increments.
@@ -78,10 +78,10 @@
continue
# Nitrogen line.
- atom(file=file, serial=atom_num, name='N', res_seq=res_num,
res_name='GLY', x=0.0, y=0.0, z=0.0)
+ hetatm(file=file, serial=atom_num, name='N', res_seq=res_num,
res_name='GLY', x=0.0, y=0.0, z=0.0)
# Hydrogen line.
- atom(file=file, serial=atom_num+1, name='H', res_seq=res_num,
res_name='GLY', x=vectors[i][0], y=vectors[i][1], z=vectors[i][2])
+ hetatm(file=file, serial=atom_num+1, name='H', res_seq=res_num,
res_name='GLY', x=vectors[i][0], y=vectors[i][1], z=vectors[i][2])
# Increment the atom number and residue number.
atom_num = atom_num + 2
@@ -91,11 +91,8 @@
used.append(vectors[i])
# Add a Trp indole NH for luck ;)
-atom(file=file, serial=atom_num, name='NE1', res_seq=res_num-1,
res_name='GLY', x=0.0, y=0.0, z=0.0)
-atom(file=file, serial=atom_num+1, name='HE1', res_seq=res_num-1,
res_name='GLY', x=1/sqrt(3), y=1/sqrt(3), z=1/sqrt(3))
-
-# Add a TER record.
-ter(file=file, serial=atom_num+2, res_name='GLY')
+hetatm(file=file, serial=atom_num, name='NE1', res_seq=res_num-1,
res_name='GLY', x=0.0, y=0.0, z=0.0)
+hetatm(file=file, serial=atom_num+1, name='HE1', res_seq=res_num-1,
res_name='GLY', x=1/sqrt(3), y=1/sqrt(3), z=1/sqrt(3))
# Connect everything.
atom_num = 1
Modified: trunk/test_suite/shared_data/model_free/sphere/sphere.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/sphere/sphere.pdb?rev=26598&r1=26597&r2=26598&view=diff
==============================================================================
--- trunk/test_suite/shared_data/model_free/sphere/sphere.pdb (original)
+++ trunk/test_suite/shared_data/model_free/sphere/sphere.pdb Mon Nov 17
12:17:22 2014
@@ -1,24 +1,23 @@
-ATOM 1 N GLY 1 0.000 0.000 0.000 1.00 0.00
-ATOM 2 H GLY 1 0.745 0.000 -0.667 1.00 0.00
-ATOM 3 N GLY 2 0.000 0.000 0.000 1.00 0.00
-ATOM 4 H GLY 2 -0.373 0.645 -0.667 1.00 0.00
-ATOM 5 N GLY 3 0.000 0.000 0.000 1.00 0.00
-ATOM 6 H GLY 3 -0.373 -0.645 -0.667 1.00 0.00
-ATOM 7 N GLY 4 0.000 0.000 0.000 1.00 0.00
-ATOM 8 H GLY 4 1.000 0.000 0.000 1.00 0.00
-ATOM 9 N GLY 5 0.000 0.000 0.000 1.00 0.00
-ATOM 10 H GLY 5 -0.500 0.866 0.000 1.00 0.00
-ATOM 11 N GLY 6 0.000 0.000 0.000 1.00 0.00
-ATOM 12 H GLY 6 -0.500 -0.866 0.000 1.00 0.00
-ATOM 13 N GLY 7 0.000 0.000 0.000 1.00 0.00
-ATOM 14 H GLY 7 0.745 0.000 0.667 1.00 0.00
-ATOM 15 N GLY 8 0.000 0.000 0.000 1.00 0.00
-ATOM 16 H GLY 8 -0.373 0.645 0.667 1.00 0.00
-ATOM 17 N GLY 9 0.000 0.000 0.000 1.00 0.00
-ATOM 18 H GLY 9 -0.373 -0.645 0.667 1.00 0.00
-ATOM 19 NE1 GLY 9 0.000 0.000 0.000 1.00 0.00
-ATOM 20 HE1 GLY 9 0.577 0.577 0.577 1.00 0.00
-TER 21 GLY
+HETATM 1 N GLY 1 0.000 0.000 0.000 1.00 0.00
+HETATM 2 H GLY 1 0.745 0.000 -0.667 1.00 0.00
+HETATM 3 N GLY 2 0.000 0.000 0.000 1.00 0.00
+HETATM 4 H GLY 2 -0.373 0.645 -0.667 1.00 0.00
+HETATM 5 N GLY 3 0.000 0.000 0.000 1.00 0.00
+HETATM 6 H GLY 3 -0.373 -0.645 -0.667 1.00 0.00
+HETATM 7 N GLY 4 0.000 0.000 0.000 1.00 0.00
+HETATM 8 H GLY 4 1.000 0.000 0.000 1.00 0.00
+HETATM 9 N GLY 5 0.000 0.000 0.000 1.00 0.00
+HETATM 10 H GLY 5 -0.500 0.866 0.000 1.00 0.00
+HETATM 11 N GLY 6 0.000 0.000 0.000 1.00 0.00
+HETATM 12 H GLY 6 -0.500 -0.866 0.000 1.00 0.00
+HETATM 13 N GLY 7 0.000 0.000 0.000 1.00 0.00
+HETATM 14 H GLY 7 0.745 0.000 0.667 1.00 0.00
+HETATM 15 N GLY 8 0.000 0.000 0.000 1.00 0.00
+HETATM 16 H GLY 8 -0.373 0.645 0.667 1.00 0.00
+HETATM 17 N GLY 9 0.000 0.000 0.000 1.00 0.00
+HETATM 18 H GLY 9 -0.373 -0.645 0.667 1.00 0.00
+HETATM 19 NE1 GLY 9 0.000 0.000 0.000 1.00 0.00
+HETATM 20 HE1 GLY 9 0.577 0.577 0.577 1.00 0.00
CONECT 1 2
CONECT 2 1
CONECT 3 4
r26598 - in /trunk/test_suite/shared_data/model_free/sphere: create_sphere.py sphere.pdb