Author: bugman
Date: Fri Feb 20 16:01:28 2015
New Revision: 27702
URL: http://svn.gna.org/viewcvs/relax?rev=27702&view=rev
Log:
Merged revisions 27698-27701 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27698 | bugman | 2015-02-20 14:56:11 +0100 (Fri, 20 Feb 2015) | 5 lines
Added one more check to the Structure.test_bug_23295_ss_metadata_merge
system test.
The test would pass if no HELIX or SHEET records were to be written to the
PDB file.
........
r27699 | bugman | 2015-02-20 15:41:11 +0100 (Fri, 20 Feb 2015) | 3 lines
Fix for the Structure.test_bug_23295_ss_metadata_merge system test and
additional printouts.
........
r27700 | bugman | 2015-02-20 15:49:23 +0100 (Fri, 20 Feb 2015) | 9 lines
Bug fix for the SHEET PDB records created by the structure.write_pdb user
function.
The current and previous atom parts of the record were not being correctly
formatted. This was
simply using the %4s formatting string. However the PDB atom format is
rather more complicated. To
handle this, the new _handle_atom_name() helper function has been added to
the
lib.structure.pdb_write module. This is now used in the atom() and sheet()
functions for
consistently formatting the atom name field.
........
r27701 | bugman | 2015-02-20 15:50:52 +0100 (Fri, 20 Feb 2015) | 6 lines
Fix for the Structure.test_pdb_combined_secondary_structure system test.
The SHEET PDB record check was incorrect and was checking for the
improperly formatted atom name
field, which has now been fixed in relax.
........
Modified:
branches/nmrglue/ (props changed)
branches/nmrglue/lib/structure/internal/object.py
branches/nmrglue/lib/structure/pdb_write.py
branches/nmrglue/test_suite/system_tests/structure.py
Propchange: branches/nmrglue/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Feb 20 16:01:28 2015
@@ -1 +1 @@
-/trunk:1-27695
+/trunk:1-27701
Modified: branches/nmrglue/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/lib/structure/internal/object.py?rev=27702&r1=27701&r2=27702&view=diff
==============================================================================
--- branches/nmrglue/lib/structure/internal/object.py (original)
+++ branches/nmrglue/lib/structure/internal/object.py Fri Feb 20 16:01:28
2015
@@ -3070,15 +3070,8 @@
if mol.pdb_record[i] in [None, 'ATOM']:
atom_record = True
- # Handle the funky atom name alignment. From the
PDB format documents:
- # "Alignment of one-letter atom name such as C
starts at column 14, while two-letter atom name such as FE starts at column
13."
- if len(mol.atom_name[i]) == 1:
- atom_name = " %s" % mol.atom_name[i]
- else:
- atom_name = "%s" % mol.atom_name[i]
-
# Write out.
- pdb_write.atom(file, serial=ser_num, name=atom_name,
res_name=mol.res_name[i], chain_id=CHAIN_ID_LIST[index],
res_seq=mol.res_num[i], x=mol.x[i], y=mol.y[i], z=mol.z[i], occupancy=1.0,
temp_factor=0, element=mol.element[i])
+ pdb_write.atom(file, serial=ser_num,
name=mol.atom_name[i], res_name=mol.res_name[i],
chain_id=CHAIN_ID_LIST[index], res_seq=mol.res_num[i], x=mol.x[i],
y=mol.y[i], z=mol.z[i], occupancy=1.0, temp_factor=0, element=mol.element[i])
num_atom += 1
ser_num += 1
Modified: branches/nmrglue/lib/structure/pdb_write.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/lib/structure/pdb_write.py?rev=27702&r1=27701&r2=27702&view=diff
==============================================================================
--- branches/nmrglue/lib/structure/pdb_write.py (original)
+++ branches/nmrglue/lib/structure/pdb_write.py Fri Feb 20 16:01:28 2015
@@ -30,6 +30,40 @@
# relax module imports.
from lib.errors import RelaxError
+
+
+def _handle_atom_name(name):
+ """Handle the funky PDB atom name alignment.
+
+ From the PDB format documents:
+
+ "Alignment of one-letter atom name such as C starts at column 14,
while two-letter atom name such as FE starts at column 13."
+
+
+ @param name: The atom name.
+ @type name: str or None
+ @return: The whitespace padded and PDB formatted atom name. This
will be exactly 4 characters.
+ @rtype: str
+ """
+
+ # Handle none.
+ if name == None:
+ name = " "
+
+ # Single letter name.
+ if len(name) == 1:
+ name = " %s " % name
+
+ # Two letter name.
+ elif len(name) == 2:
+ name = "%s " % name
+
+ # Three letter name.
+ elif len(name) == 3:
+ name = "%s " % name
+
+ # Return the name.
+ return name
def _handle_none(value):
@@ -283,7 +317,7 @@
text = "%-6s%5s %-4s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f
%2s%2s" % (
'ATOM',
_handle_none(serial),
- _handle_none(name),
+ _handle_atom_name(name),
_handle_none(alt_loc),
_handle_none(res_name),
_handle_none(chain_id),
@@ -1725,12 +1759,12 @@
_handle_none(end_seq_num),
_handle_none(end_icode),
_handle_none(sense),
- _handle_none(cur_atom),
+ _handle_atom_name(cur_atom),
_handle_none(cur_res_name),
_handle_none(cur_chain_id),
_handle_none(cur_res_seq),
_handle_none(cur_icode),
- _handle_none(prev_atom),
+ _handle_atom_name(prev_atom),
_handle_none(prev_res_name),
_handle_none(prev_chain_id),
_handle_none(prev_res_seq),
Modified: branches/nmrglue/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/system_tests/structure.py?rev=27702&r1=27701&r2=27702&view=diff
==============================================================================
--- branches/nmrglue/test_suite/system_tests/structure.py (original)
+++ branches/nmrglue/test_suite/system_tests/structure.py Fri Feb 20
16:01:28 2015
@@ -1036,10 +1036,15 @@
continue
# Check the line.
+ print("\nOrig: %s" % repr(contents[index]))
+ print("New: %s" % repr(line))
self.assertEqual(contents[index], line)
# Increment the secondary structure index.
index += 1
+
+ # Check the count to make sure that secondary structure records have
at all been created.
+ self.assertEqual(len(contents), index)
def test_bug_sr_2998_broken_conect_records(self):
@@ -4155,7 +4160,7 @@
"HELIX 7 3 THR B 117 ASP B 129 1
13 \n",
"HELIX 8 4 TYR B 138 THR B 146 1
9 \n",
"SHEET 1 A 2 TYR B 99 ILE B 100 0
\n",
- "SHEET 2 A 2 VAL B 136 ASN B 137 -1 OVAL B 136 NILE
B 100 \n"
+ "SHEET 2 A 2 VAL B 136 ASN B 137 -1 O VAL B 136 N ILE
B 100 \n"
]
# Check secondary structure contents of the created PDB file.
r27702 - in /branches/nmrglue: ./ lib/structure/ lib/structure/internal/ test_suite/system_tests/