Re: r13900 - /branches/xyz/generic_fns/structure/main.pyRe: r13900 - /branches/xyz/generic_fns/structure/main.pyHi Edward, Ok, thanks! I think I need some time to fully understand this logic. Best, Han On Jul 27, 2011, at 1:49 PM, Edward d'Auvergne wrote:
Hi, The svnmerge update will clear some things up. I've now tracked this to the load_spins() function of generic_fns/structure/main.py. The logic is not very flexible in here, and I think we will need to redesign this function. It is safe to do the redesign in the xyz branch as the 1.3 line is working perfectly at the moment. The redesign is only needed for the XYZ files. This is just because the code was not designed with this type of flexibility in mind. I would suggest that the logic should follow these options (the container would be either a molecule container, a residue container, or a spin container, and the same logic would be applied to all three): (1) The container name (and number) was not supplied, so check that there is only a single container in the relax data store and that it is unnamed and unnumbered (throw a RelaxError otherwise).(2) The container already exists in the relax data store, so do nothing. (3) There is only a single container in the relax data store and it is empty.(4) The container does not exist, so add it. The order of these would need to be determined. I would suggest we also use a number of pre-written functions from relax: - To get the ID strings, we can use generic_fns.mol_res_spin.generate_spin_id(). This replaces all of the 'id' string manipulation in the current code. - The container objects have is_empty() methods for determining if they are empty. This should be used to identify if the container should be renamed and renumbered in (3). Because of the difficulty of this design, I might try to solve it myself and commit the code to the xyz branch. Regards, Edward On 27 July 2011 12:15, Han Sun <hasu@xxxxxxxxxxxxxxxxx> wrote:Hi Edward,ok, I will have a look. I think the problem is that the return_residue function does not work properly. I hope the 1.3 line has already solved thisproblem. Best, Han On Jul 27, 2011, at 12:04 PM, Edward d'Auvergne wrote:Hi Han,I think you'll need to merge the 1.3 line changes into your branch to root out this problem. That will simplify the amount of changed codeto search for the problem. If you don't know how to do this, see section 9.5 of the relax manual for details (http://www.nmr-relax.com/manual/1.3/9_5_Branches.html). Note that svnmerge for the xyz branch has already been initialised. Regards, EdwardOn 27 July 2011 11:52, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:Hi, This seems quite strange. When running the test suite, the systemtests have 11 failures and 44 errors. There appears to be a problem whereby all spins are being put into the first residue. I.e. multiple residues are no longer supported. This will require a bit of digging.Regards, Edward On 26 July 2011 18:57, Han Sun <hasu@xxxxxxxxxxxxxxxxx> wrote:Hi Edward,Now the test passes for reading the xyz file and loading the spins. But there is a problem for loading the spins in the pdb file. The reason isinthe generic_fns/structure/main.py function load_spins. We added a checktosee whether the residue name exists or not. When not, it will add one.And Ifound this rises the problem now for loading the spins of a pdb fileproperly. Do you have a idea how to solve it? Best, Han Begin forwarded message: From: hasu@xxxxxxxxxxxxxxxxx Date: July 26, 2011 6:47:49 PM GMT+02:00 To: relax-commits@xxxxxxx Subject: r13900 - /branches/xyz/generic_fns/structure/main.py Reply-To: relax-devel@xxxxxxx Author: han87 Date: Tue Jul 26 18:47:49 2011 New Revision: 13900 URL: http://svn.gna.org/viewcvs/relax?rev=13900&view=rev Log: Changing the code in the generic_fns/structure/main.py For printing out of modified spins, a test to check whether the spin_name exists or not is added. Modified: branches/xyz/generic_fns/structure/main.py Modified: branches/xyz/generic_fns/structure/main.py URL:http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/ structure/main.py?rev=13900&r1=13899&r2=13900&view=diff================================================================== ============--- branches/xyz/generic_fns/structure/main.py (original)+++ branches/xyz/generic_fns/structure/main.py Tue Jul 26 18:47:49 2011@@ -602,7 +602,10 @@ # Print out of modified spins. if verbosity: - print(("Extracted " + str(spin.num) + "-" + str(attached_name) + " vectors for " + repr(id) + '.')) + if spin.name: + print(("Extracted " + spin.name + "-" + str(attached_name) + " vectors for " + repr(id) + '.')) + else: + print(("Extracted " + str(spin.num) + "-" + str(attached_name) + " vectors for " + repr(id) + '.'))# Right, catch the problem of missing vectors to prevent massiveuser confusion! if no_vectors: _______________________________________________ relax (http://nmr-relax.com) This is the relax-commits mailing list relax-commits@xxxxxxx 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-commits _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list relax-devel@xxxxxxx 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