Re: r13121 - in /branches/xyz: generic_fns/structure/internal.py test_suite/system_tests/structure.py -- June 20, 2011 - 11:25

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 <hasu@xxxxxxxxxxxxxxxxx> 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,  <hasu@xxxxxxxxxxxxxxxxx> 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.
> > > >
> > > >
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