Author: bugman Date: Tue Apr 28 17:59:52 2009 New Revision: 9026 URL: http://svn.gna.org/viewcvs/relax?rev=9026&view=rev Log: Merged revisions 8963,8971-8972,8974,8976-8977,8979-8990,8997-9003,9010-9011,9015-9017,9019-9024 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ................ r8963 | semor | 2009-03-10 20:52:43 +0100 (Tue, 10 Mar 2009) | 7 lines Fix for bug 13163 : latex_mf_table.py sample script broken. Discussion on this topic is in a thread at: https://mail.gna.org/public/relax-devel/2009-03/msg00007.html (Message-id: <49B6A6B1.4080305@xxxxxxxxx>) ................ r8971 | bugman | 2009-03-12 10:37:49 +0100 (Thu, 12 Mar 2009) | 3 lines Modified the full_analysis.py script to perform 500 MC sims and turned on automatic looping. ................ r8972 | bugman | 2009-03-12 11:25:53 +0100 (Thu, 12 Mar 2009) | 5 lines Added a line with the relax URL (http://nmr-relax.com) in the script docstring. This is in case someone has the script and not relax. ................ r8974 | semor | 2009-03-12 18:17:30 +0100 (Thu, 12 Mar 2009) | 7 lines Fix for bug 13162: Rex values in XML results file not in s-1. The units are now correctly given in the XML results fiel as discussed in a thread at: https://mail.gna.org/public/relax-devel/2009-03/msg00010.html (Message-id: <20090310-141629.sv7147.79009@xxxxxxx>) ................ r8976 | semor | 2009-03-12 18:56:28 +0100 (Thu, 12 Mar 2009) | 10 lines Reverted r8974. This follows a remark by Ed at: https://mail.gna.org/public/relax-devel/2009-03/msg00033.html (Message-id: <7f080ed10903121024h7a0a3808m3c268ca1f276ee4a@xxxxxxxxxxxxxx>) The command used was: svn merge -r8974:8973 . ................ r8977 | semor | 2009-03-12 19:01:24 +0100 (Thu, 12 Mar 2009) | 7 lines Now correctly fixed bug 13162: Rex values in XML results file not in s-1. This follows a remark by Ed at: https://mail.gna.org/public/relax-devel/2009-03/msg00033.html (Message-id: <7f080ed10903121024h7a0a3808m3c268ca1f276ee4a@xxxxxxxxxxxxxx>) ................ r8979 | semor | 2009-03-16 19:52:15 +0100 (Mon, 16 Mar 2009) | 9 lines Fix for bug 13032: Bug in structure.create diff tensor pdb The Dz unit in dependency_generator() were erroneous, inputing 'alpha' and 'beta' instead of 'beta' and 'gamma'. This had the effect of creating a weird shaped ellipsoid diffusion tensor representation when 'alpha' and 'beta' were set to unequal values. This is now fixed, yielding properly shaped diffusion tensor representations for any angles 'alpha', beta' and 'gamma'. ................ r8980 | semor | 2009-03-16 19:59:34 +0100 (Mon, 16 Mar 2009) | 11 lines Changed units of model-free parameters in the test suite results file according to r8977. ns -> seconds ps -> seconds Angstrom -> meters x MHz -> sigma_ex = Rex / omega**2 ppm -> unitless The bzipped file was changed directly with vim. The system tests now pass without error, ................ r8981 | bugman | 2009-03-18 15:48:09 +0100 (Wed, 18 Mar 2009) | 5 lines Bug fix! Debugged intensity_sparky() to handle a Sparky assignment such as '004N-H'. ................ r8982 | bugman | 2009-03-20 09:49:03 +0100 (Fri, 20 Mar 2009) | 5 lines Added the Bruker ncproc parameter to handle Topspin's integer scaling of FID intensities. The data is now internally scaled by 2**ncproc. ................ r8983 | bugman | 2009-03-20 11:28:13 +0100 (Fri, 20 Mar 2009) | 3 lines RMSD of baseplane noise is now scaled by NC_proc. ................ r8984 | bugman | 2009-03-20 15:22:14 +0100 (Fri, 20 Mar 2009) | 3 lines Fixed a bad apostrophe character causing the script to fail. ................ r8985 | bugman | 2009-03-20 15:28:37 +0100 (Fri, 20 Mar 2009) | 3 lines Comment fix - missing data and error column args. ................ r8986 | bugman | 2009-03-20 15:39:45 +0100 (Fri, 20 Mar 2009) | 3 lines Removed a check disallowing multiple NOE data sets at the same spectrometer frequency. ................ r8987 | bugman | 2009-03-20 16:55:06 +0100 (Fri, 20 Mar 2009) | 5 lines Bug fix for the results reading from_xml() method. The molecule name was being evaluated?!? ................ r8988 | bugman | 2009-03-20 17:35:00 +0100 (Fri, 20 Mar 2009) | 3 lines Allowed vectors() to generate vectors even if the spin numbers are different (for different PDBs). ................ r8989 | bugman | 2009-03-20 17:35:55 +0100 (Fri, 20 Mar 2009) | 3 lines Also removed the molecule name (for different PDBs). ................ r8990 | bugman | 2009-03-20 17:44:37 +0100 (Fri, 20 Mar 2009) | 5 lines Made the call to cdp.structure.bond_vectors() more fault tolerant. The molecule name, residue name, and spin number are removed to allow for different structures! ................ r8997 | bugman | 2009-03-25 21:49:55 +0100 (Wed, 25 Mar 2009) | 5 lines Modified the model elimination print out to show the data pipe name. This was picked up while trying to debug bug #13259 (https://gna.org/bugs/index.php?13259). ................ r8998 | bugman | 2009-03-25 22:26:06 +0100 (Wed, 25 Mar 2009) | 3 lines Clean up of the model_loop() checking. ................ r8999 | bugman | 2009-03-25 22:42:30 +0100 (Wed, 25 Mar 2009) | 6 lines Removed the check for spin selection so that determine_model_type() works with nothing selected. This is a partial response to bug #13259 (https://gna.org/bugs/index.php?13259) reported by Pierre-Yves Savard (pierre-yves dot savard att bcm dot ulaval dot ca). ................ r9000 | bugman | 2009-03-26 00:21:17 +0100 (Thu, 26 Mar 2009) | 3 lines Fixes for the MC sim methods for deselected spins. ................ r9001 | bugman | 2009-03-26 00:42:14 +0100 (Thu, 26 Mar 2009) | 5 lines Modified the structure.vectors() user function to fail if no vectors are found. This saves a lot of sanity when debugging a user script which fails. ................ r9002 | bugman | 2009-03-26 15:10:14 +0100 (Thu, 26 Mar 2009) | 7 lines Bug fix for bug #13259 (https://gna.org/bugs/index.php?13259). This bug was reported by Pierre-Yves Savard (pierre-yves dot savard att bcm dot ulaval dot ca). The bug may not be completely gone yet. ................ r9003 | bugman | 2009-03-26 16:40:57 +0100 (Thu, 26 Mar 2009) | 6 lines Fix for the regression of bug #12607 (https://gna.org/bugs/?12607). The determine_model_type() method now handles the strange case where no spins are selected (gracefully). ................ r9010 | bugman | 2009-04-15 14:33:53 +0200 (Wed, 15 Apr 2009) | 5 lines Expanded the test_read_pdb_internal3() and test_read_pdb_scientific3() system tests. Now the reading of atomic positions from different models is tested. ................ r9011 | bugman | 2009-04-15 15:28:15 +0200 (Wed, 15 Apr 2009) | 6 lines Removed a test in load_spins() causing a bug. This test is totally unnecessary as the structures are not created if they already exist. This was causing only the position from the first model to be extracted, if ave_pos was False. ................ r9015 | bugman | 2009-04-27 15:26:25 +0200 (Mon, 27 Apr 2009) | 5 lines Bug fix. The PyMOL code was failing because of the new design of the structural data object. ................ r9016 | bugman | 2009-04-28 13:47:51 +0200 (Tue, 28 Apr 2009) | 3 lines Added a catch for bug #13442 (https://gna.org/bugs/index.php?13442) to the test suite. ................ r9017 | bugman | 2009-04-28 14:02:02 +0200 (Tue, 28 Apr 2009) | 6 lines Fix for bug #13442 (https://gna.org/bugs/index.php?13442). The problem was that global minimisation objects were being accessed when the do not exist. These are now skipped. ................ r9019 | bugman | 2009-04-28 14:05:30 +0200 (Tue, 28 Apr 2009) | 3 lines Initialized merge tracking via "svnmerge" with revisions "1-8161" from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/ave_noe ................ r9020 | bugman | 2009-04-28 14:28:05 +0200 (Tue, 28 Apr 2009) | 321 lines Merged revisions 8162-8179,8181-8182,8643-8655,8657-8668,8671-8672,8674,8677,8679-8680,8689-8695,8700-8701,8710-8713,8716,9005-9009,9013 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/ave_noe ........ r8162 | bugman | 2008-12-08 16:41:32 +0100 (Mon, 08 Dec 2008) | 5 lines Fix for the noe.read_constraints() user function. The noe object is called noe_obj. ........ r8163 | bugman | 2008-12-08 16:46:53 +0100 (Mon, 08 Dec 2008) | 7 lines The noe.read_constraints() user function now calls generic_fns.noesy.read_constraints(). The noe user functions need not all point to the specific NOE object! Maybe later the steady-state NOE can be separated from the NOESY, but for now it isn't too illogical for both to be in the same user function class. ........ r8164 | bugman | 2008-12-08 16:48:34 +0100 (Mon, 08 Dec 2008) | 3 lines Created an empty module for NOESY data. ........ r8165 | bugman | 2008-12-09 10:30:36 +0100 (Tue, 09 Dec 2008) | 3 lines Wrote a stub function generic_fns.noesy.read_constraints(). ........ r8166 | bugman | 2008-12-09 10:37:16 +0100 (Tue, 09 Dec 2008) | 3 lines Added a directory to the test-suite for holding NOE restraint data. ........ r8167 | bugman | 2008-12-09 10:39:00 +0100 (Tue, 09 Dec 2008) | 5 lines Added an RNA H-bond Xplor restraint file. This comes from http://bass.chem.yale.edu/labdocs/packages/xplor.html. ........ r8168 | bugman | 2008-12-09 10:45:58 +0100 (Tue, 09 Dec 2008) | 5 lines Added the system test framework for NOE restraint reading tests. This includes one test for the reading of RNA H-bond restraints from an Xplor formatted input file. ........ r8169 | bugman | 2008-12-09 10:47:29 +0100 (Tue, 09 Dec 2008) | 3 lines Renamed 'constraints' to 'restraints' for the NOEs. ........ r8170 | bugman | 2008-12-09 11:04:24 +0100 (Tue, 09 Dec 2008) | 3 lines The RNA sequence of the noe_rna_hbond.dat file is now generated through a new class method. ........ r8171 | bugman | 2008-12-09 11:06:01 +0100 (Tue, 09 Dec 2008) | 3 lines Renamed all the noe.read_constraints() references in the unit tests to noe.read_restraints(). ........ r8172 | bugman | 2008-12-09 13:31:47 +0100 (Tue, 09 Dec 2008) | 5 lines Completed the test_read_xplor_rna() system test. Checks for the restraint list have now been added. ........ r8173 | bugman | 2008-12-09 13:32:57 +0100 (Tue, 09 Dec 2008) | 3 lines Activated the Noe_restraints system test framework. ........ r8174 | bugman | 2008-12-09 13:33:19 +0100 (Tue, 09 Dec 2008) | 3 lines Bug fix in the rna_seq() method. ........ r8175 | bugman | 2008-12-09 13:36:17 +0100 (Tue, 09 Dec 2008) | 3 lines Another bug fix for the rna_seq() sequence generation method. ........ r8176 | bugman | 2008-12-09 13:49:38 +0100 (Tue, 09 Dec 2008) | 3 lines Final fixes for the rna_seq() sequence generation method. ........ r8177 | bugman | 2008-12-09 13:50:30 +0100 (Tue, 09 Dec 2008) | 3 lines Fix for the call to noe.read_restraints() in test_read_xplor_rna(). ........ r8178 | bugman | 2008-12-09 13:57:32 +0100 (Tue, 09 Dec 2008) | 3 lines Removed the non-existent frq arg and a docstring clarification about the relax formatted file. ........ r8179 | bugman | 2008-12-09 14:02:53 +0100 (Tue, 09 Dec 2008) | 3 lines Missing import! ........ r8181 | bugman | 2008-12-10 14:30:44 +0100 (Wed, 10 Dec 2008) | 3 lines Added a missing import. ........ r8182 | bugman | 2008-12-10 15:18:38 +0100 (Wed, 10 Dec 2008) | 3 lines Added some more code to the read_restraints() function. ........ r8643 | bugman | 2009-01-26 11:52:11 +0100 (Mon, 26 Jan 2009) | 3 lines Wrote the __file_format() function for determining the NOE restraint file format. ........ r8644 | bugman | 2009-01-26 13:30:06 +0100 (Mon, 26 Jan 2009) | 3 lines The non-implemented function generic_fns.xplor.parse_noe_restraints() is now being called. ........ r8645 | bugman | 2009-01-26 13:44:06 +0100 (Mon, 26 Jan 2009) | 3 lines Reverted to calling file.readlines() rather than file.read(). ........ r8646 | bugman | 2009-01-26 15:01:10 +0100 (Mon, 26 Jan 2009) | 6 lines Created the Xplor module for handling Xplor formatted files. The function parse_noe_restraints() has been added to parse the NOE restraints. The function strip_comments() has been written to remove Xplor comments from the input data. ........ r8647 | bugman | 2009-01-26 15:24:53 +0100 (Mon, 26 Jan 2009) | 3 lines Created __convert_to_id() to convert from Xplor atom string to relax atom id. ........ r8648 | bugman | 2009-01-26 15:31:05 +0100 (Mon, 26 Jan 2009) | 3 lines Added checks to make sure spin containers corresponding to the Xplor atom strings exist. ........ r8649 | bugman | 2009-01-26 16:26:45 +0100 (Mon, 26 Jan 2009) | 3 lines Typo fix. 'H4' should have been 'N4'! ........ r8650 | bugman | 2009-01-26 16:32:49 +0100 (Mon, 26 Jan 2009) | 3 lines The NOE restraints are now stored in the current data pipe. ........ r8651 | bugman | 2009-01-26 16:39:22 +0100 (Mon, 26 Jan 2009) | 3 lines Fixes for the test_read_xplor_rna() system test. ........ r8652 | bugman | 2009-01-26 16:40:32 +0100 (Mon, 26 Jan 2009) | 5 lines Modified the NOE restraint list so that some restraints are spread across 2 lines. This should test the Xplor parsing code better. ........ r8653 | bugman | 2009-01-26 16:42:12 +0100 (Mon, 26 Jan 2009) | 5 lines Bug fix for the parse_noe_restraints() function. Xplor restraints spread across 2 lines are now properly handled. ........ r8654 | bugman | 2009-01-26 16:43:23 +0100 (Mon, 26 Jan 2009) | 3 lines Added a few comments to test the Xplor parsing even more. ........ r8655 | bugman | 2009-01-26 18:44:13 +0100 (Mon, 26 Jan 2009) | 3 lines Shifted the checks of the atom id strings from the Xplor parser to the NOE restraint reading fn. ........ r8657 | bugman | 2009-01-27 09:35:53 +0100 (Tue, 27 Jan 2009) | 3 lines Missing RelaxError import. ........ r8658 | bugman | 2009-01-27 09:44:38 +0100 (Tue, 27 Jan 2009) | 3 lines Added some test NOEs, in a generic formatted file, for phthalic acid and testing the NOE reading. ........ r8659 | bugman | 2009-01-27 10:01:41 +0100 (Tue, 27 Jan 2009) | 3 lines Created a system test for the reading of a generically formatted NOE restraint file. ........ r8660 | bugman | 2009-01-27 10:15:15 +0100 (Tue, 27 Jan 2009) | 3 lines Removed an unused import. ........ r8661 | bugman | 2009-01-27 10:16:04 +0100 (Tue, 27 Jan 2009) | 3 lines The generically formatted NOE restraint file is now being parsed. ........ r8662 | bugman | 2009-01-27 11:10:45 +0100 (Tue, 27 Jan 2009) | 3 lines Modified the phthalic acid NOE restraint reading test to include pseudo-atoms. ........ r8663 | bugman | 2009-01-27 13:45:15 +0100 (Tue, 27 Jan 2009) | 3 lines Removed the '@' from the pseudo-atom spin names. ........ r8664 | bugman | 2009-01-27 13:47:35 +0100 (Tue, 27 Jan 2009) | 3 lines Wrote a unit test for the creation of pseudo-atom spin containers. ........ r8665 | bugman | 2009-01-27 13:55:57 +0100 (Tue, 27 Jan 2009) | 3 lines Wrote 5 arg unit tests for the spin.create_pseudo() user function. ........ r8666 | bugman | 2009-01-27 14:00:37 +0100 (Tue, 27 Jan 2009) | 3 lines Wrote the interface for the spin.create_pseudo() user function. ........ r8667 | bugman | 2009-01-27 14:03:18 +0100 (Tue, 27 Jan 2009) | 3 lines Fixes for the arg unit tests of spin.create_pseudo(). ........ r8668 | bugman | 2009-01-27 14:06:13 +0100 (Tue, 27 Jan 2009) | 3 lines Imported the non-existant create_pseudo_spin() function. ........ r8671 | bugman | 2009-01-27 16:14:22 +0100 (Tue, 27 Jan 2009) | 3 lines Wrote the create_pseudo_spin() and __linear_ave() functions for pseudo-atom support. ........ r8672 | bugman | 2009-01-27 16:17:07 +0100 (Tue, 27 Jan 2009) | 5 lines Fix for the phthalic acid NOE restraint reading system test. Pseudo-atom creation was not correctly called. ........ r8674 | bugman | 2009-01-27 16:27:54 +0100 (Tue, 27 Jan 2009) | 3 lines Fixes for the create_pseudo_spin() and __linear_ave() functions. ........ r8677 | bugman | 2009-01-27 16:41:23 +0100 (Tue, 27 Jan 2009) | 3 lines Fixes for the 2 test_create_pseudo_spin() unit tests. ........ r8679 | bugman | 2009-01-27 16:49:58 +0100 (Tue, 27 Jan 2009) | 3 lines Fixes for the test_create_pseudo_spin() unit test. The atomic positions are now set. ........ r8680 | bugman | 2009-01-27 16:51:47 +0100 (Tue, 27 Jan 2009) | 3 lines The __linear_ave() now handles the coordinates as numpy arrays. ........ r8689 | bugman | 2009-01-28 11:24:04 +0100 (Wed, 28 Jan 2009) | 3 lines Added some more checks for the test_create_pseudo_spin() unit test. ........ r8690 | bugman | 2009-01-28 11:30:24 +0100 (Wed, 28 Jan 2009) | 3 lines Wrote a second unit test for the creation of a pseudo-spin. ........ r8691 | bugman | 2009-01-28 11:38:57 +0100 (Wed, 28 Jan 2009) | 3 lines Modified the checks for the pseudo-spin creation unit tests. ........ r8692 | bugman | 2009-01-28 11:40:14 +0100 (Wed, 28 Jan 2009) | 5 lines The pseudo-spin name and number is now stored in the member spin containers. This gives a mapping between from the spin to the pseudo-spin. ........ r8693 | bugman | 2009-01-28 11:40:50 +0100 (Wed, 28 Jan 2009) | 3 lines Fixes for test_create_pseudo_spin() and test_create_pseudo_spin2(). ........ r8694 | bugman | 2009-01-28 11:41:27 +0100 (Wed, 28 Jan 2009) | 3 lines One more fix for test_create_pseudo_spin(). ........ r8695 | bugman | 2009-01-28 11:42:32 +0100 (Wed, 28 Jan 2009) | 3 lines The members list is now stored in the pseudo-spin to map this to the respective spin containers. ........ r8700 | bugman | 2009-01-29 09:42:21 +0100 (Thu, 29 Jan 2009) | 3 lines Added a call to calc() to test the quadratic potential calculation. ........ r8701 | bugman | 2009-01-29 16:40:07 +0100 (Thu, 29 Jan 2009) | 5 lines Created a module for calculating different optimisation/energy potentials. The function quad_pot() has been written to provide a flat-bottom potential. ........ r8710 | bugman | 2009-02-02 10:44:48 +0100 (Mon, 02 Feb 2009) | 3 lines Added tests for the existence of the current data pipe. ........ r8711 | bugman | 2009-02-02 10:49:06 +0100 (Mon, 02 Feb 2009) | 3 lines Modified the RelaxNoModelError print out to be more informative, especially for the N-state model. ........ r8712 | bugman | 2009-02-02 10:51:17 +0100 (Mon, 02 Feb 2009) | 3 lines Added the start of the calculate() method. ........ r8713 | bugman | 2009-02-02 10:51:45 +0100 (Mon, 02 Feb 2009) | 3 lines The N-state model is now selected in the NOESY system test. ........ r8716 | bugman | 2009-02-02 11:05:21 +0100 (Mon, 02 Feb 2009) | 3 lines Modified __base_data_types() to include NOE restraints. ........ r9005 | bugman | 2009-04-09 19:33:13 +0200 (Thu, 09 Apr 2009) | 3 lines [... 174 lines stripped ...]