Author: bugman
Date: Tue Jul 1 17:30:56 2014
New Revision: 24383
URL: http://svn.gna.org/viewcvs/relax?rev=24383&view=rev
Log:
Fixes for all system tests failing due to the expanded and improved PDB
REMARK section.
The system tests now remove all REMARK records prior to comparing file
contents. The special
strip_remarks() system test method has been created to simplify the stripping
process.
Modified:
trunk/test_suite/system_tests/structure.py
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=24383&r1=24382&r2=24383&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Tue Jul 1 17:30:56 2014
@@ -45,6 +45,17 @@
self.interpreter.pipe.create('mf', 'mf')
+ def strip_remarks(self, lines):
+ """Strip out all PDB remark lines.
+
+ @param lines: The list of PDB lines.
+ @type lines: list of str
+ """
+
+ # Rebuild the list.
+ lines[:] = [x for x in lines if x[:6] != 'REMARK']
+
+
def test_alt_loc_missing(self):
"""Test that a RelaxError occurs when the alternate location
indicator is present but not specified."""
@@ -112,10 +123,8 @@
file = DummyFileObject()
self.interpreter.structure.write_pdb(file=file, force=True)
- # The file contents, as they should be.
+ # The file contents, without remarks, as they should be.
contents = [
- "REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011.
\n",
- "REMARK 40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM).
\n",
"MODEL 1
\n",
"ATOM 1 N Pro A 2 1.000 2.000 3.000 1.00
0.00 N \n",
"TER 2 Pro A 2
\n",
@@ -130,6 +139,7 @@
# Check the created PDB file.
lines = file.readlines()
+ self.strip_remarks(lines)
for i in range(len(lines)):
self.assertEqual(contents[i], lines[i])
@@ -158,10 +168,8 @@
file = DummyFileObject()
self.interpreter.structure.write_pdb(file=file, force=True)
- # The file contents, as they should be.
+ # The file contents, without remarks, as they should be.
contents = [
- "REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011.
\n",
- "REMARK 40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM).
\n",
"HET CYN A 445 1
\n",
"HET CYN B 445 1
\n",
"HETNAM CYN UNKNOWN
\n",
@@ -192,6 +200,7 @@
# Check the created PDB file.
lines = file.readlines()
+ self.strip_remarks(lines)
for i in range(len(lines)):
self.assertEqual(contents[i], lines[i])
@@ -889,10 +898,8 @@
lines = file.readlines()
file.close()
- # What the contents should be.
+ # What the contents should be, without remarks.
real_data = [
- "REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011.
\n",
- "REMARK 40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM).
\n",
"HELIX 1 H1 ILE A 23 GLU A 34 1
12 \n",
"SHEET 1 BET 5 GLY A 10 VAL A 17 0
\n",
"SHEET 2 BET 5 MET A 1 THR A 7 -1
\n",
@@ -1170,6 +1177,7 @@
]
# Check the data.
+ self.strip_remarks(lines)
for i in range(len(real_data)):
self.assertEqual(real_data[i], lines[i])
@@ -1406,10 +1414,8 @@
file = DummyFileObject()
self.interpreter.structure.web_of_motion(file=file, models=[1, 2])
- # The result.
+ # The result, without remarks.
result = [
- "REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011.
",
- "REMARK 40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM).
",
"ATOM 1 N LEU A 4 9.464 -9.232 27.573 1.00
0.00 N ",
"ATOM 2 N LEU A 4 9.211 -9.425 26.970 1.00
0.00 N ",
"ATOM 3 H LEU A 4 8.575 -8.953 27.963 1.00
0.00 H ",
@@ -1449,6 +1455,7 @@
# Check the created PDB file.
lines = file.readlines()
+ self.strip_remarks(lines)
for i in range(len(lines)):
self.assertEqual(result[i]+'\n', lines[i])
@@ -1464,10 +1471,8 @@
file = DummyFileObject()
self.interpreter.structure.web_of_motion(file=file, models=[1, 3])
- # The result.
+ # The result, without remarks.
result = [
- "REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011.
",
- "REMARK 40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM).
",
"ATOM 1 N LEU A 4 9.464 -9.232 27.573 1.00
0.00 N ",
"ATOM 2 N LEU A 4 7.761 -6.392 27.161 1.00
0.00 N ",
"ATOM 3 H LEU A 4 8.575 -8.953 27.963 1.00
0.00 H ",
@@ -1507,6 +1512,7 @@
# Check the created PDB file.
lines = file.readlines()
+ self.strip_remarks(lines)
for i in range(len(lines)):
self.assertEqual(result[i]+'\n', lines[i])
@@ -1522,10 +1528,8 @@
file = DummyFileObject()
self.interpreter.structure.web_of_motion(file=file)
- # The result.
+ # The result, without remarks.
result = [
- "REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011.
",
- "REMARK 40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM).
",
"ATOM 1 N LEU A 4 9.464 -9.232 27.573 1.00
0.00 N ",
"ATOM 2 N LEU A 4 9.211 -9.425 26.970 1.00
0.00 N ",
"ATOM 3 N LEU A 4 7.761 -6.392 27.161 1.00
0.00 N ",
@@ -1581,5 +1585,6 @@
# Check the created PDB file.
lines = file.readlines()
+ self.strip_remarks(lines)
for i in range(len(lines)):
self.assertEqual(result[i]+'\n', lines[i])
r24383 - /trunk/test_suite/system_tests/structure.py