Have a look at my last message ;) Regards,
Edward On 23 June 2011 15:26, Han Sun <[email protected]> wrote: > Hi Edward, > > I added the residue check as you suggested. A new problem was coming out. > Firstly, a single atom 2 can be loaded properly. But if all atoms are > loaded, then it complains that the second atom exists and a new spin with > the same name can not be generated again. I guess the code can not check > properly that the atom 2 has been loaded, but I could not find the problem > in the code. Could you help me with that? > > Best, > Han > > > On Jun 23, 2011, at 3:19 PM, [email protected] wrote: > >> Author: han87 >> Date: Thu Jun 23 15:19:45 2011 >> New Revision: 13180 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=13180&view=rev >> Log: >> Debugging the user function load_spins() and changing the system test >> test_read_xyz_internal2(). >> >> In the user function load_spins() in generic_fns/structure/main.py a check >> whether the residue name exists or not has been included. The code is >> similiar to the molecule check. Also see email: >> https://mail.gna.org/public/relax-devel/2011-06/msg00226.html. And in the >> system test 'test_read_xyz_internal2()' all models were loaded instead of 2 >> and the line for loading proton was removed. >> >> Modified: >> branches/xyz/generic_fns/structure/main.py >> branches/xyz/test_suite/system_tests/structure.py >> >> Modified: branches/xyz/generic_fns/structure/main.py >> URL: >> http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/structure/main.py?rev=13180&r1=13179&r2=13180&view=diff >> >> ============================================================================== >> --- branches/xyz/generic_fns/structure/main.py (original) >> +++ branches/xyz/generic_fns/structure/main.py Thu Jun 23 15:19:45 2011 >> @@ -236,11 +236,26 @@ >> >> # Add the residue if it doesn't exist. >> if res_cont == None: >> - # Add the residue. >> - mol_cont.res.add_item(res_name=res_name, res_num=res_num) >> - >> - # Get the container. >> - res_cont = mol_cont.res[-1] >> + # Get the unnamed residue, assuming there is only one: >> + res_cont = return_residue() >> + >> + # Got something! >> + if res_cont != None: >> + # Rename the residue name if the res name is given and >> the sole container is unnamed. >> + if res_cont.name == None and res_name: >> + # Print out. >> + print(("Renaming the unnamed sole residue container >> to '%s'." % res_name)) >> + >> + # Get the name. >> + res_cont.name = res_name >> + >> + # Nothing exists yet. >> + else: >> + # Add the residue. >> + mol_cont.res.add_item(res_name=res_name, res_num=res_num) >> + >> + # Get the container. >> + res_cont = mol_cont.res[-1] >> >> # Add the atom number to the ID string (atom name is ignored >> because only the number is unique). >> id = id + '@' + repr(atom_num) >> >> Modified: branches/xyz/test_suite/system_tests/structure.py >> URL: >> http://svn.gna.org/viewcvs/relax/branches/xyz/test_suite/system_tests/structure.py?rev=13180&r1=13179&r2=13180&view=diff >> >> ============================================================================== >> --- branches/xyz/test_suite/system_tests/structure.py (original) >> +++ branches/xyz/test_suite/system_tests/structure.py Thu Jun 23 15:19:45 >> 2011 >> @@ -656,7 +656,7 @@ >> path = status.install_path + >> sep+'test_suite'+sep+'shared_data'+sep+'structures' >> >> # Read the xyz. >> - >> self.interpreter.structure.read_xyz(file='SSS-cluster4-new-test.xyz', >> dir=path, read_model=[1,3]) >> + >> self.interpreter.structure.read_xyz(file='SSS-cluster4-new-test.xyz', >> dir=path) >> >> # Test the molecule name. >> self.assertEqual(cdp.structure.structural_data[0].mol[0].mol_name, >> 'SSS-cluster4-new-test_mol1') >> @@ -666,8 +666,8 @@ >> self.assertEqual(count_spins(), 1) >> >> # Try loading a few protons. >> - self.interpreter.structure.load_spins('@*H*') >> - >> - # And now all the rest of the atoms. >> - self.interpreter.structure.load_spins() >> - >> + #self.interpreter.structure.load_spins('@H') >> + >> + # And now all the rest of the atoms. >> + self.interpreter.structure.load_spins() >> + >> >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-commits mailing list >> [email protected] >> >> 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 [email protected] 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
