Author: bugman Date: Wed Jul 4 11:09:10 2012 New Revision: 17183 URL: http://svn.gna.org/viewcvs/relax?rev=17183&view=rev Log: Merged revisions 17139,17142,17156,17174,17179-17181 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk ................ r17139 | bugman | 2012-07-02 21:36:49 +0200 (Mon, 02 Jul 2012) | 6 lines The spin container hidden objects are now replicated when the object is copied. The old Prototype.__deepcopy__() method was skipping all hidden objects, but now only objects starting with '__' are skipped. ................ r17142 | bugman | 2012-07-02 22:07:41 +0200 (Mon, 02 Jul 2012) | 5 lines Improvement for the RelaxNoVectorsError class - the data pipe name is now optional. The print outs have been improved as well. ................ r17156 | bugman | 2012-07-03 14:20:16 +0200 (Tue, 03 Jul 2012) | 6 lines Bug fix for the Value GUI input element for integer values. This is only uncovered when remotely running the GUI - e.g. through the test suite - and an integer value is set. ................ r17174 | bugman | 2012-07-04 09:32:35 +0200 (Wed, 04 Jul 2012) | 5 lines Bug fix for the Palmer system tests for the changed spin ID syntax. The spin Gly 2 can no longer be selected with ':2&:Gly', the '&' symbol is not allowed here. ................ r17179 | bugman | 2012-07-04 10:51:03 +0200 (Wed, 04 Jul 2012) | 3 lines Initialized merge tracking via "svnmerge" with revisions "1-16843" from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/interatomic ................ r17180 | bugman | 2012-07-04 11:04:16 +0200 (Wed, 04 Jul 2012) | 1195 lines Merged revisions 16844-16845,16848-16849,16852-16855,16858-16865,16867-16878,16883,16917,16919-16956,16961-16991,16994-16997,17000-17008,17011-17016,17023-17027,17032-17038,17042-17043,17046-17065,17067-17113,17123-17138,17141,17143-17144,17146-17155,17158-17173,17175-17177 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/interatomic ........ r16844 | bugman | 2012-06-11 19:37:17 +0200 (Mon, 11 Jun 2012) | 6 lines Created the interatomic data list and containers, and added these to the data pipe structures. This is modelled on the molecule/residue/spin structures. The new containers have is_empty(), from_xml() and to_xml() methods and should be fully functional with the relax infrastructure. ........ r16845 | bugman | 2012-06-11 19:43:02 +0200 (Mon, 11 Jun 2012) | 3 lines A large number of missing imports for the new data.interatomic module! ........ r16848 | bugman | 2012-06-11 19:55:51 +0200 (Mon, 11 Jun 2012) | 3 lines Fix for the BMRB system tests for the new interatomic data pipe object. ........ r16849 | bugman | 2012-06-11 20:08:22 +0200 (Mon, 11 Jun 2012) | 5 lines Converted the rdc.read user function definition to use the interatomic data objects. This is currently only for the front ends of the user function. ........ r16852 | bugman | 2012-06-11 20:15:20 +0200 (Mon, 11 Jun 2012) | 3 lines Converted the stereochemistry auto-analysis to use the new rdc.read definition. ........ r16853 | bugman | 2012-06-11 20:16:21 +0200 (Mon, 11 Jun 2012) | 3 lines Converted the rdc.read user function backend to the new interatomic data design. ........ r16854 | bugman | 2012-06-11 20:17:55 +0200 (Mon, 11 Jun 2012) | 3 lines Converted the only sample script which uses the rdc.read user function to the changed definition. ........ r16855 | bugman | 2012-06-11 20:20:01 +0200 (Mon, 11 Jun 2012) | 3 lines Converted some of the test suite RDC data to use the double spin ID format for interatomic data. ........ r16858 | bugman | 2012-06-11 20:40:39 +0200 (Mon, 11 Jun 2012) | 3 lines Converted a few of the N-state model system tests to use the new rdc.read definition. ........ r16859 | bugman | 2012-06-11 20:41:25 +0200 (Mon, 11 Jun 2012) | 3 lines Created the InteratomContainer.id_match() method for checking the spin IDs in both directions for a match. ........ r16860 | bugman | 2012-06-11 20:47:41 +0200 (Mon, 11 Jun 2012) | 3 lines Created the generic_fns.interatomic module and added the return_container() method. ........ r16861 | bugman | 2012-06-11 20:55:27 +0200 (Mon, 11 Jun 2012) | 3 lines Fix for the InteratomList.add_item() method. ........ r16862 | bugman | 2012-06-11 20:56:57 +0200 (Mon, 11 Jun 2012) | 3 lines Added checks to the InteratomList.add_item() method to make sure that the spin IDs already exist. ........ r16863 | bugman | 2012-06-11 20:57:56 +0200 (Mon, 11 Jun 2012) | 3 lines Created the generic_fns.interatomic.create_interatom() function for creating interatomic data containers. ........ r16864 | bugman | 2012-06-11 21:01:22 +0200 (Mon, 11 Jun 2012) | 3 lines The rdc.read user function backend is now adding the RDCs to the interatomic data containers. ........ r16865 | bugman | 2012-06-11 21:03:50 +0200 (Mon, 11 Jun 2012) | 5 lines Shifted some code from InteratomList.add_item() to generic_fns.interatomic.create_interatom(). This is to break a circular import problem. ........ r16867 | bugman | 2012-06-11 21:06:51 +0200 (Mon, 11 Jun 2012) | 5 lines Renamed the interatomic function return_container() to return_interatom(). This is to make the name more unique. ........ r16868 | bugman | 2012-06-11 21:07:40 +0200 (Mon, 11 Jun 2012) | 3 lines Missing imports. ........ r16869 | bugman | 2012-06-11 22:25:24 +0200 (Mon, 11 Jun 2012) | 5 lines The generic_fns.interatomic.create_interatom() function now returns the created container. This comes from the InteratomicContainer.add_item() method which now also returns the container. ........ r16870 | bugman | 2012-06-11 22:26:03 +0200 (Mon, 11 Jun 2012) | 3 lines Updated another N-state model system test script to the new rdc.read interatomic data design. ........ r16871 | bugman | 2012-06-11 22:27:24 +0200 (Mon, 11 Jun 2012) | 3 lines Shifted the id_match() method to the correct class! ........ r16872 | bugman | 2012-06-11 22:31:00 +0200 (Mon, 11 Jun 2012) | 3 lines Fix for the id_match() method - there are no indices. ........ r16873 | bugman | 2012-06-11 22:31:33 +0200 (Mon, 11 Jun 2012) | 3 lines Lots of updates to the rdc.read user function backend. ........ r16874 | bugman | 2012-06-11 22:35:57 +0200 (Mon, 11 Jun 2012) | 3 lines Created the generic_fns.interatomic.interatomic_loop() generator function. ........ r16875 | bugman | 2012-06-11 22:56:07 +0200 (Mon, 11 Jun 2012) | 3 lines Started to convert the N-state model optimisation code to handle RDCs as interatomic data. ........ r16876 | bugman | 2012-06-11 22:57:09 +0200 (Mon, 11 Jun 2012) | 5 lines The N-state model specific analysis code is now handling RDCs as interatomic data. This still has a lot of work before it will be functional. ........ r16877 | bugman | 2012-06-11 22:59:17 +0200 (Mon, 11 Jun 2012) | 3 lines Syntax error fix. ........ r16878 | bugman | 2012-06-11 23:09:37 +0200 (Mon, 11 Jun 2012) | 3 lines Converted the structure.vectors user function definition to the new interatomic data design. ........ r16883 | bugman | 2012-06-12 17:45:59 +0200 (Tue, 12 Jun 2012) | 3 lines Expanded the description of the negative gyromagnetic ratio flag for the rdc.read user function. ........ r16917 | bugman | 2012-06-17 09:14:35 +0200 (Sun, 17 Jun 2012) | 3 lines Started to change the structure.vectors backend to handle two spin IDs. ........ r16919 | bugman | 2012-06-17 10:25:20 +0200 (Sun, 17 Jun 2012) | 9 lines Redesigned the model-free dauvergne_protocol.py system test script for the interatomic concept. The new script will be used to redesign how to set up a model-free analysis using the interatomic data concept. It adds the new relax_data.dipole_pair user function which will be used to define the dipolar relaxation interaction (this will inadvertently allow multi-dipole relation). The heteronuc_type and proton_type parameters have been replaced with the spin_type parameter, as now both the heternuclear and homonuclear spins need to be loaded into relax. ........ r16920 | bugman | 2012-06-17 11:46:11 +0200 (Sun, 17 Jun 2012) | 3 lines Added the definition for the new relax_data.dipole_pair user function. ........ r16921 | bugman | 2012-06-17 13:54:03 +0200 (Sun, 17 Jun 2012) | 5 lines The bond length setting via value.set has no been merged into relax_data.dipole_pair. This averaged length is dipole-dipole distance and does not need to be a model-free parameter. ........ r16922 | bugman | 2012-06-17 13:54:24 +0200 (Sun, 17 Jun 2012) | 3 lines Removed the bond length from the model-free parameter list. ........ r16923 | bugman | 2012-06-17 22:37:23 +0200 (Sun, 17 Jun 2012) | 3 lines Created graphics for the magnetic dipole-dipole interaction. ........ r16924 | bugman | 2012-06-17 22:37:57 +0200 (Sun, 17 Jun 2012) | 3 lines Shifted the dipole-dipole graphics to the Wizard directory, as this is a wizard graphic. ........ r16925 | bugman | 2012-06-17 23:22:09 +0200 (Sun, 17 Jun 2012) | 3 lines A few changes to the relax_data.dipole_pair user function definition. ........ r16926 | bugman | 2012-06-18 00:12:09 +0200 (Mon, 18 Jun 2012) | 3 lines Started to add the backend of the relax_data.dipole_pair user function. ........ r16927 | bugman | 2012-06-18 09:50:31 +0200 (Mon, 18 Jun 2012) | 5 lines Created the structural API base are_bonded() method - this is for determining if 2 atoms are bonded. This is a method stub which raises a RelaxImplementError. ........ r16928 | bugman | 2012-06-18 11:06:35 +0200 (Mon, 18 Jun 2012) | 3 lines Implemented the are_bonded() structural API method for the internal structural object. ........ r16929 | bugman | 2012-06-18 11:14:59 +0200 (Mon, 18 Jun 2012) | 6 lines Added CONECT records to the sphere.pdb file to allow connectivities to be more easily determined. This is for the internal reader, as the current algorithm for finding attached atoms is distance based, and as all N atoms of all residues are at [0, 0, 0], this algorithm fails. ........ r16930 | bugman | 2012-06-18 11:45:51 +0200 (Mon, 18 Jun 2012) | 3 lines The relax_data.dipole_pair backend now uses the direct_bond flag. ........ r16931 | bugman | 2012-06-18 14:10:00 +0200 (Mon, 18 Jun 2012) | 7 lines Shifted the relax_data.dipole_pair user function into the new dipole_pair user function class. This has also been split into two new user functions: dipole_pair.define used to set up the magnetic dipole-dipole interactions. dipole_pair.set_dist used to set up the r^-3 averaged interatomic distances. ........ r16932 | bugman | 2012-06-18 14:28:36 +0200 (Mon, 18 Jun 2012) | 3 lines Created a set of icons for the dipole_pair user functions. ........ r16933 | bugman | 2012-06-18 14:41:55 +0200 (Mon, 18 Jun 2012) | 3 lines Refinement of the dipole_pair user function definitions. ........ r16934 | bugman | 2012-06-18 14:48:01 +0200 (Mon, 18 Jun 2012) | 3 lines More refinements of the dipole_pair.define user function definition. ........ r16935 | bugman | 2012-06-18 14:48:49 +0200 (Mon, 18 Jun 2012) | 3 lines Fix for the dipole_pair.define user function - the interatom object can pre-exist, containing other data. ........ r16936 | bugman | 2012-06-18 17:27:16 +0200 (Mon, 18 Jun 2012) | 6 lines Created the dipole_pair.read_dist user function definitions. This new user function is for simplifying the loading of many different interatomic distances into relax. ........ r16937 | bugman | 2012-06-18 17:35:23 +0200 (Mon, 18 Jun 2012) | 3 lines Created the backend of the dipole_pair.read_dist user function. ........ r16938 | bugman | 2012-06-18 17:59:49 +0200 (Mon, 18 Jun 2012) | 3 lines Created the dipole_pair.unit_vectors user function definition. ........ r16939 | bugman | 2012-06-18 18:19:51 +0200 (Mon, 18 Jun 2012) | 3 lines Refinement of the dipole_pair user function definitions. ........ r16940 | bugman | 2012-06-18 18:21:06 +0200 (Mon, 18 Jun 2012) | 3 lines Fixed the call to dipole_pair.unit_vectors in the dauvergne_protocol.py system test script. ........ r16941 | bugman | 2012-06-18 20:34:12 +0200 (Mon, 18 Jun 2012) | 7 lines Implemented the dipole_pair.unit_vectors user function backend. This code originates from the generic_fns.structure.main.vectors() function (the structure.vectors user function backend). The dipole_pair.unit_vectors user function is designed to replace structure.vectors. ........ r16942 | bugman | 2012-06-19 10:03:29 +0200 (Tue, 19 Jun 2012) | 6 lines Deletion of the structure.vectors user function as it has been superseded by dipole_pair.unit_vectors. Only the user function definition has deleted - the backend code will remain so that it can be used internally. ........ r16943 | bugman | 2012-06-19 10:48:23 +0200 (Tue, 19 Jun 2012) | 3 lines Added a set of icons for nuclear or isotope related usage. ........ r16944 | bugman | 2012-06-19 10:49:24 +0200 (Tue, 19 Jun 2012) | 3 lines Added the nuclear symbol as a wizard graphic. ........ r16945 | bugman | 2012-06-19 10:54:07 +0200 (Tue, 19 Jun 2012) | 6 lines Created the spin.isotope user function. This is designed to be a permanent replacement for the specific analysis API 'heteronuc_type' and 'proton_type' parameters. ........ r16946 | bugman | 2012-06-19 11:01:47 +0200 (Tue, 19 Jun 2012) | 11 lines Eliminated a number of the specific API parameters relating to dipole-dipole interactions. These are now provided by the spin.isotope user function and the dipole_pair user functions. The eliminated parameters are: 'r' - replaced by dipole_pair.set_dist or dipole_pair.read_dist, 'xh_vect' - replaced by dipole_pair.unit_vectors, 'heteronuc_type' - replaced by spin.isotope, 'proton_type' - replaced by spin.isotope, 'attached_proton' - replaced by dipole_pair.define. ........ r16947 | bugman | 2012-06-19 11:10:47 +0200 (Tue, 19 Jun 2012) | 5 lines Changed the dauvergne_protocol.py system test script value.set calls with spin.isotope. The nuclear isotope is now defined via spin.isotope. ........ r16948 | bugman | 2012-06-19 11:22:16 +0200 (Tue, 19 Jun 2012) | 5 lines Expanded the RelaxNoValueError to handle one or two spin IDs as arguments. This is to better identify which spins or interatomic data containers are deficient. ........ r16949 | bugman | 2012-06-19 11:24:39 +0200 (Tue, 19 Jun 2012) | 7 lines Modified the check_args() method of the dauvergne_protocol model-free auto-analysis for the new data. The heteronuc_type and proton_type are now in the spin's isotope variable, and the bond length 'r' is now the interatomic distance variable 'r'. All spin containers and interatomic data containers are being checked. ........ r16950 | bugman | 2012-06-19 11:38:32 +0200 (Tue, 19 Jun 2012) | 5 lines Expanded the return_interatom() function to handle a single spin ID. This function now returns a list of matching interatomic data containers. ........ r16951 | bugman | 2012-06-19 11:49:07 +0200 (Tue, 19 Jun 2012) | 3 lines Started to convert the model-free analysis code to the new interatomic data container design. ........ r16952 | bugman | 2012-06-19 12:42:49 +0200 (Tue, 19 Jun 2012) | 3 lines The interatomic data container now has the dipole_pair flag initialised to False. ........ r16953 | bugman | 2012-06-19 12:58:44 +0200 (Tue, 19 Jun 2012) | 3 lines The model-free analysis is now fully using the new interatomic data container design. ........ r16954 | bugman | 2012-06-19 14:10:20 +0200 (Tue, 19 Jun 2012) | 3 lines Created the RelaxInteratomError and RelaxNoInteratomError classes for interatomic data errors. ........ r16955 | bugman | 2012-06-19 14:12:23 +0200 (Tue, 19 Jun 2012) | 8 lines Expanded the functionality of the generic_fns.interatomic module. The copy() and exists_data() functions have been added to copy all interatomic data from one data pipe to another and to check if interatomic data exists within a data pipe respectively. The create_interatom() function now also accepts a 'pipe' argument so that non-current pipes can be used. ........ r16956 | bugman | 2012-06-19 14:18:15 +0200 (Tue, 19 Jun 2012) | 3 lines Fixes for the model-free support of the interatomic data container design. ........ r16961 | bugman | 2012-06-19 16:21:59 +0200 (Tue, 19 Jun 2012) | 7 lines Fix for the model-free duplicate_data() method for interatomic data. This is used by the model_selection user function. The problem was that no proton spins where being copied as previously there were no proton spins in a model-free analysis. This spins are now needed to define the dipolar relaxation mechanism. ........ r16962 | bugman | 2012-06-19 16:25:34 +0200 (Tue, 19 Jun 2012) | 3 lines Added a check to the model-free overfit_deselect() to see if a relaxation mechanism is present. ........ r16963 | bugman | 2012-06-19 16:38:57 +0200 (Tue, 19 Jun 2012) | 3 lines The CSA value is now only set for the 15N spins in the dauvergne_protocol.py system test script. ........ r16964 | bugman | 2012-06-19 18:30:04 +0200 (Tue, 19 Jun 2012) | 6 lines The Mf.test_dauvergne_protocol system test now passes with the new interatomic data container design! This involves lots of changes to the model-free specific code, the dauvergne_protocol auto-analysis, and modification of the checks in the system test for the additional proton spin containers. ........ r16965 | bugman | 2012-06-19 18:40:20 +0200 (Tue, 19 Jun 2012) | 3 lines Added a verbose flag to the generic_fns.dipole_pair.define() function. ........ r16966 | bugman | 2012-06-19 18:54:29 +0200 (Tue, 19 Jun 2012) | 5 lines Bug fix for the printing out of interatomic data containers. The __repr__() method wasn't skipping all methods. ........ r16967 | bugman | 2012-06-19 19:43:18 +0200 (Tue, 19 Jun 2012) | 3 lines Basic docstring edit. ........ r16968 | bugman | 2012-06-19 19:44:14 +0200 (Tue, 19 Jun 2012) | 3 lines The import of old relax 1.2 results files is now operational under the interatomic data design. ........ r16969 | bugman | 2012-06-19 19:44:36 +0200 (Tue, 19 Jun 2012) | 3 lines Updated the final_results_trunc_1.3_pre_py2.7.3_v2.bz2 results file for the interatomic data design. ........ r16970 | bugman | 2012-06-19 20:13:18 +0200 (Tue, 19 Jun 2012) | 5 lines Fixes for the dipolar_pair.define user function backend. The return_interatom() function now returns a list! ........ r16971 | bugman | 2012-06-19 20:15:04 +0200 (Tue, 19 Jun 2012) | 6 lines Added a backwards compatibility hook for converting old XML files to the interatomic data design. This will convert the variable names, deleting the old, and create proton spins and interatomic data [... 1485 lines stripped ...]