Author: bugman
Date: Tue Feb 17 09:47:03 2015
New Revision: 27657
URL: http://svn.gna.org/viewcvs/relax?rev=27657&view=rev
Log:
Merged revisions 27654-27655 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27654 | bugman | 2015-02-17 09:27:42 +0100 (Tue, 17 Feb 2015) | 3 lines
Small correction for the structure.read_pdb user function description.
........
r27655 | bugman | 2015-02-17 09:31:42 +0100 (Tue, 17 Feb 2015) | 6 lines
Created the Structure.test_read_merge_simultaneous system test.
This is to demonstrate a failure in the structure.read_pdb user function
when merging multiple
molecules from one file into one molecule simultaneously with a single user
function call.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/test_suite/system_tests/structure.py
branches/frame_order_cleanup/user_functions/structure.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Feb 17 09:47:03 2015
@@ -1 +1 @@
-/trunk:1-27639
+/trunk:1-27639,27654-27655
Modified: branches/frame_order_cleanup/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/structure.py?rev=27657&r1=27656&r2=27657&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/structure.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/structure.py Tue
Feb 17 09:47:03 2015
@@ -4025,6 +4025,19 @@
cdp.structure.validate_models()
+ def test_read_merge_simultaneous(self):
+ """Test the simultaneous merging of two molecules into one."""
+
+ # Path of the files.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+
+ # Read the PDB files.
+ self.interpreter.structure.read_pdb(file='2BE6_core_I_IV.pdb',
dir=path, read_mol=[1, 3], set_mol_name='CaM A')
+
+ # Check that everything is ok.
+ cdp.structure.validate_models()
+
+
def test_read_not_pdb(self):
"""Test the reading of a file by structure.read_pdb that is not a
PDB."""
Modified: branches/frame_order_cleanup/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/structure.py?rev=27657&r1=27656&r2=27657&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/structure.py (original)
+++ branches/frame_order_cleanup/user_functions/structure.py Tue Feb 17
09:47:03 2015
@@ -1002,7 +1002,7 @@
uf.desc[-1].add_paragraph("Setting the molecule name allows the molecule
within the PDB (within one model) to have a custom name. If not set, then
the molecules will be named after the file name, with the molecule number
appended if more than one exists.")
uf.desc[-1].add_paragraph("Note that relax will complain if it cannot work
out what to do.")
uf.desc[-1].add_paragraph("This is able to handle uncompressed, bzip2
compressed files, or gzip compressed files automatically. The full file name
including extension can be supplied, however, if the file cannot be found,
this function will search for the file name with '.bz2' appended followed by
the file name with '.gz' appended.")
-uf.desc[-1].add_paragraph("If a PDB file contains alternative atomic
locations, then the alternate location indicator must be specified to allow
one of the multiple coordinate sets to be select.")
+uf.desc[-1].add_paragraph("If a PDB file contains alternative atomic
locations, then the alternate location indicator must be specified to allow
one of the multiple coordinate sets to be selected.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To load all structures from the PDB file
'test.pdb' in the directory '~/pdb', including all models and all molecules,
type one of:")
r27657 - in /branches/frame_order_cleanup: ./ test_suite/system_tests/structure.py user_functions/structure.py