Re: r13121 - in /branches/xyz: generic_fns/structure/internal.py test_suite/system_tests/structure.py -- June 20, 2011 - 11:37

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 <hasu@xxxxxxxxxxxxxxxxx> 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 <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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