Hi, I realise it is difficult. For now it would be best to state that. Maybe the description of using 2 file can be put into the user function documentation (in the prompt package). This design can change in the future, if there is a need.
Regards, Edward On 20 June 2011 11:39, Han Sun <[email protected]> wrote: > It is really hard to determine the correct connectivities for the chemical > compounds. If the two molecules are very close to each other, then it is > very probably to determine them wrong. Because unlike the protein and DNA, > in which you can only have the sp3 and sp2 hybridization, you can have here > from sp to sp3d2 hybridization. Therefore the angles as criteria for > determining the connectivities can not be used. In my opinion, the only > criteria is then the bond length. But it will not be valid any more, if the > two molecules are close to each other. Therefore I think the easiest > solution will be to separate different molecules into different xyz files, > if the users can accept this. > > Best > Han > > On Jun 20, 2011, at 11:27 AM, Edward d'Auvergne wrote: > >> That might be something we have to look at after implementing this. >> We can see how the current algorithm works. And we need to work out >> how useful it would be for organic chemists to be able to separate out >> two molecules in an XYZ file (i.e. should we implement it, or wait >> until a user asks for it). >> >> Cheers, >> >> Edward >> >> >> >> On 20 June 2011 11:26, Han Sun <[email protected]> wrote: >>> >>> Hi, >>> >>> I think the viewers determine the connectivities from the bond length. >>> But I >>> am not sure. >>> >>> Han >>> >>> On Jun 20, 2011, at 10:57 AM, Edward d'Auvergne wrote: >>> >>>> Hi, >>>> >>>> Do you know how organic molecule viewers determine this? Do they try >>>> to work out the connectivity in the molecules? The internal reader >>>> has a very, very basic algorithm for connectivity. See >>>> __find_bonded_atoms() in generic_fns/structure/internal.py. This >>>> might have to be improved for organic molecules, as my assumptions are >>>> ok for standard biomolecules, but maybe do not hold for all organic >>>> molecules. So in reality, so we need to be able to determine 2 >>>> molecules within one file using connectivities, or a lack of, between >>>> two group of atoms? >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> On 20 June 2011 10:48, Han Sun <[email protected]> wrote: >>>>> >>>>> Hi Edward, >>>>> >>>>> That is the problem. In the xyz file you can probably have several >>>>> molecules, but you can not recognized that. There is no parameter to >>>>> define >>>>> the molecule or the residue like in the pdb file. >>>>> >>>>> Best, >>>>> Han >>>>> >>>>> On Jun 20, 2011, at 10:41 AM, Edward d'Auvergne wrote: >>>>> >>>>>> Hi Han, >>>>>> >>>>>> It's now working, your ssh access :) I was just wondering why you had >>>>>> the statement: >>>>>> >>>>>> if mol_index==0: >>>>>> >>>>>> This could be problematic if you have multiple molecules in the XYZ >>>>>> file. Is it possible to have more than one in the format? >>>>>> >>>>>> Cheers, >>>>>> >>>>>> Edward >>>>>> >>>>>> >>>>>> >>>>>> On 20 June 2011 10:07, <[email protected]> wrote: >>>>>>> >>>>>>> Author: han87 >>>>>>> Date: Mon Jun 20 10:07:35 2011 >>>>>>> New Revision: 13121 >>>>>>> >>>>>>> URL: http://svn.gna.org/viewcvs/relax?rev=13121&view=rev >>>>>>> Log: >>>>>>> Debugging the user functions load_xyz() and >>>>>>> test_read_xyz_internal2(). >>>>>>> >>>>>>> The user functions load_xyz() in 'generic_fns/structure/internal.py' >>>>>>> and >>>>>>> test_read_xyz_internal2() in 'test_suite/system_tests/structure.py' >>>>>>> have >>>>>>> been changed so that the molecule name can be read properly. >>>>>>> >>>>>>> Modified: >>>>>>> branches/xyz/generic_fns/structure/internal.py >>>>>>> branches/xyz/test_suite/system_tests/structure.py >>>>>>> >>>>>>> Modified: branches/xyz/generic_fns/structure/internal.py >>>>>>> URL: >>>>>>> >>>>>>> >>>>>>> http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/structure/internal.py?rev=13121&r1=13120&r2=13121&view=diff >>>>>>> >>>>>>> >>>>>>> >>>>>>> ============================================================================== >>>>>>> --- branches/xyz/generic_fns/structure/internal.py (original) >>>>>>> +++ branches/xyz/generic_fns/structure/internal.py Mon Jun 20 >>>>>>> 10:07:35 >>>>>>> 2011 >>>>>>> @@ -853,8 +853,9 @@ >>>>>>> if set_mol_name: >>>>>>> new_mol_name.append(set_mol_name[mol_index]) >>>>>>> else: >>>>>>> - # Set the name to the file name plus the structure >>>>>>> number. >>>>>>> - new_mol_name.append(file_root(file) + '_mol' + >>>>>>> repr(mol_index)) >>>>>>> + if mol_index==0: >>>>>>> + #Set the name to the file name plus the structure >>>>>>> number. >>>>>>> + new_mol_name.append(file_root(file) + '_mol' + >>>>>>> repr(mol_index+1)) >>>>>>> >>>>>>> # Store the original mol number. >>>>>>> orig_mol_num.append(mol_index) >>>>>>> @@ -874,7 +875,8 @@ >>>>>>> >>>>>>> # Increment the model index. >>>>>>> model_index = model_index + 1 >>>>>>> - >>>>>>> + >>>>>>> + orig_mol_num=[0] >>>>>>> # Create the structural data data structures. >>>>>>> self.pack_structs(mol_conts, orig_model_num=orig_model_num, >>>>>>> set_model_num=set_model_num, orig_mol_num=orig_mol_num, >>>>>>> set_mol_name=new_mol_name, file_name=file, file_path=path) >>>>>>> >>>>>>> >>>>>>> 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=13121&r1=13120&r2=13121&view=diff >>>>>>> >>>>>>> >>>>>>> >>>>>>> ============================================================================== >>>>>>> --- branches/xyz/test_suite/system_tests/structure.py (original) >>>>>>> +++ branches/xyz/test_suite/system_tests/structure.py Mon Jun 20 >>>>>>> 10:07:35 >>>>>>> 2011 >>>>>>> @@ -659,10 +659,10 @@ >>>>>>> >>>>>>> >>>>>>> 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') >>>>>>> + >>>>>>> self.assertEqual(cdp.structure.structural_data[0].mol[0].mol_name, >>>>>>> 'SSS-cluster4-new-test_mol1') >>>>>>> >>>>>>> # Load a single atom and test it. >>>>>>> - >>>>>>> self.interpreter.structure.load_spins('SSS-cluster4-new-test:3@C') >>>>>>> + >>>>>>> >>>>>>> self.interpreter.structure.load_spins('SSS-cluster4-new-test_mol1:@C') >>>>>>> self.assertEqual(count_spins(), 1) >>>>>>> >>>>>>> # Try loading a few protons. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>> >>>>> >>> >>> > > _______________________________________________ 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
