relax (molecular dynamics analysis)

URL: <http://gna.org/bugs/?23293> Summary: PDB HETATM loading error - the last HETATM record is sometimes not read from the PDB file. Project: relax Submitted by: bugman Submitted on: ... [More] Thu 19 Feb 2015 01:17:04 PM UTC Category: relax's source code Specific analysis category: All analyses Priority: 5 - Normal Severity: 2 - Minor Status: None Assigned to: bugman Originator Name: Originator Email: Open/Closed: Open Release: 3.3.6 Discussion Lock: Any Operating System: All systems _______________________________________________________ Details: The last HETATM record of a molecule, when multiple molecules are present in the PDB file, will not be read. This does not affect the last molecule. The following files are attached: - A test PDB file 'in.pdb'. - A simple relax script 'test.py' which cre [Less]

Update of bug #23288 (project relax): Status: None => Fixed Open/Closed: Open => Closed ... [More] _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?23288> _______________________________________________ Message sent via/by Gna! http://gna.org/ [Less]

Hi Troels, If possible, we don't need the entire extern/nmrglue/nmrglue_0_5/tests/ directory. This is far, far too big! As I mentioned in earlier messages, we only need the nmrglue package or subdirectory from the entire nmrglue distribution. The ... [More] rest can be accessed by a user by installing another copy of nmrglue themselves, if they need it. However note that installing nmrglue will only copy the nmrglue package and ignore all other directories (doc/, examples/, and tests/). Also, I would suggest renaming extern/nmrglue/README.txt to extern/README.nmrglue and to change the contents to: """ To get new version from: https://github.com/jjhelmus/nmrglue/releases # Put an empty __init__.py into the extern/nmrglue folder. # Version 0.5 ## Get the tar file wget https://github.com/jjhelmus/nmrglue/archive/v0.5.tar.gz ## Unpack tar zxvf v0.5.tar.gz ## Remove tar file. rm v0.5.tar.gz ## Rename directory to not contain "-" and "." rm -rf nmrglue mv nmrglue-0.5/nmrglue nmrglue """ This will save future inf [Less]

Hi Troels, Rather than using this import, the code would be much cleaner if extern.nmrglue.nmrglue_0_5.nmrglue was simply located at extern.nmrglue (see my comment at http://thread.gmane.org/gmane.science.nmr.relax.scm/24920/focus=7468). It will ... [More] also force the size of the extern/nmrglue directory to be much more reasonable. Cheers, Edward On 14 January 2015 at 17:05, <tlinnet-kqII41Zox2pDPfheJLI6IQ< at >public.gmane.org> wrote: [Less]

Hi Troels, For any test data in "status.install_path +sep+ 'extern' +sep+ 'nmrglue' +sep+ 'nmrglue_0_5' +sep+ 'tests' +sep+ 'pipe_proc_tests'" that you use in the relax system tests, this could be copied into test_suite/shared_data/nmrglue/. The ... [More] extern/nmrglue/nmrglue_0_5/tests directory is far too big to be redistributed with relax. Cheers, Edward On 14 January 2015 at 17:05, <tlinnet-kqII41Zox2pDPfheJLI6IQ< at >public.gmane.org> wrote: [Less]

Update of task #7873 (project relax): Status: Gone walkabout => Ready For Test Percent Complete: 10% => 100% Effort: 10.00 ... [More] => 100 _______________________________________________________ Follow-up Comment #93: This needs to be verified for python 3 and relax. _______________________________________________________ Reply to this item at: <http://gna.org/task/?7873> _______________________________________________ Message sent via/by Gna! http://gna.org/ [Less]

Follow-up Comment #94, task #7873 (project relax): When I run the Nmrglue system tests in Python 2, they pass. However in Python 3 I see: $ python3 ./relax -s --time Nmrglue Echoing of user function calls has been enabled. ... [More] ============================= = System / functional tests = ============================= . 0.00 s for Nmrglue.test_nmrglue_read . 0.00 s for Nmrglue.test_nmrglue_read_several . 0.16 s for Nmrglue.test_plot_contour . 0.10 s for Nmrglue.test_plot_contour_cpmg . 0.12 s for Nmrglue.test_plot_correlation . 2.90 s for Nmrglue.test_plot_hist_cpmg . 3.44 s for Nmrglue.test_plot_hist_cpmg_several E 0.00 s for Nmrglue.test_save_state . 0.00 s for Nmrglue.test_version ====================================================================== ERROR: test_save_state (test_suite.system_tests.nmrglue.Nmrglue) Test saving a state with numpy arrays, reset relax, and read the state again. ---------------------------------------------------------------------- relax> p [Less]

Update of bug #23187 (project relax): Status: None => Fixed Assigned to: None => bugman Open/Closed: Open ... [More] => Closed Summary: Deleting residue in GUI, and then open spin viewer crashes relax. => Opening the spin viewer GUI window, deleting a residue, and then reopening the spin viewer crashes relax. _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?23187> _______________________________________________ Message sent via/by Gna! http://gna.org/ [Less]

Follow-up Comment #9, bug #23187 (project relax): Unfortunately I don't think that this bug can be caught in the relax test suite as the wxPython RuntimeError handler seems to be completely incompatible with the Python unittest framework. ... [More] _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?23187> _______________________________________________ Message sent via/by Gna! http://gna.org/ [Less]

I already have a patch which fixes the error, but I'd like to work out how we can catch it first. Regards, Edward On 14 January 2015 at 16:17, Edward d'Auvergne <edward< at >nmr-relax.com> wrote: ... [More] _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel< at >gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel [Less]