Re: r13246 - /branches/xyz/prompt/structure.py -- June 28, 2011 - 12:07

Hi Edward,

in the function __bonded_atom() I found following code:

        # Problem.
        if num_attached > 1:
            # Get the atom names.
            matching_names = []
            for i in matching_list:
                matching_names.append(mol.atom_name[i])

            # Return nothing but a warning.
            return None, None, None, None, None, 'More than one  
attached atom found: ' + repr(matching_names)

This means that it can only load one atom. But this is often not the  
case for small molecule. For example if I have a CH3 group and I  
asked it to load protons, all three protons should be loaded.

Best,
Han


On Jun 27, 2011, at 7:26 PM, Edward d'Auvergne wrote:

> Hi Han,
>
> This is another case were the current code can be used, and if it
> doesn't work then it should be fixed rather than a new function added.
>  The structure.vectors() method is independent of the format of the
> structural file.  Normally when I use it, the PDB file has been read
> in and is in the internal structure format.  After reading the XYZ
> file, it should also be in the internal format.  So the
> structure.vectors() user function should work on both.  So if you load
> all the carbons as spins from the organic molecule, the CH vectors
> should be extractable with:
>
> relax> structure.vectors(attached='H', spin_id='@C')
>
> The 'H' needs no '*' characters as all protons in the XYZ file are
> called 'H'.  The internal structural object will then determine which
> 'H' atoms are attached to the C atoms.  This is either taken from the
> structural file, or it uses a very basic distance based algorithm in
> __bonded_atom() and __find_bonded_atoms().  I have a feeling that this
> will work automatically.
>
> Regards,
>
> Edward
>
>
>
> On 27 June 2011 18:55,  <hasu@xxxxxxxxxxxxxxxxx> wrote:
> > Author: han87
> > Date: Mon Jun 27 18:55:51 2011
> > New Revision: 13246
> >
> > URL: http://svn.gna.org/viewcvs/relax?rev=13246&view=rev
> > Log:
> > A new function vector_xyz() was generated.
> >
> > A new function vector_xyz() was generated in '/prompt/ 
> > structure.py' for extracting a vector of two given atoms in a xyz  
> > file.
> >
> > Modified:
> >    branches/xyz/prompt/structure.py
> >
> > Modified: branches/xyz/prompt/structure.py
> > URL: http://svn.gna.org/viewcvs/relax/branches/xyz/prompt/ 
> > structure.py?rev=13246&r1=13245&r2=13246&view=diff
> > ===================================================================== 
> > =========
> > --- branches/xyz/prompt/structure.py (original)
> > +++ branches/xyz/prompt/structure.py Mon Jun 27 18:55:51 2011
> > @@ -686,6 +686,76 @@
> >         generic_fns.structure.main.vectors(attached=attached,  
> > spin_id=spin_id, model=model, verbosity=verbosity, ave=ave,  
> > unit=unit)
> >
> >
> > +    def vectors_xyz(self, spin_id1=None, spin_id2=None,  
> > model=None, verbosity=1, ave=True, unit=True):
> > +        """Extract and store the bond vectors from the loaded  
> > structures in the spin container.
> > +
> > +        Keyword arguments
> > +        ~~~~~~~~~~~~~~~~~
> > +
> > +        spin_id1:  The spin identification string of the spin 1.
> > +
> > +        spin_id2:  The spin identification string of the spin 2.
> > +
> > +        model:  The model to extract bond vectors from (which if  
> > set to None will cause the vectors
> > +        of all models to be extracted).
> > +
> > +        verbosity:  The amount of information to print to  
> > screen.  Zero corresponds to minimal
> > +        output while higher values increase the amount of  
> > output.  The default value is 1.
> > +
> > +        ave:  A flag which if True will cause the bond vectors  
> > from all models to be averaged.  If
> > +        vectors from only one model is extracted, this argument  
> > will have no effect.
> > +
> > +        unit:  A flag which if True will cause the unit vector to  
> > calculated rather than the full
> > +        length bond vector.
> > +
> > +
> > +        Description
> > +        ~~~~~~~~~~~
> > +
> > +        For a number of types of analysis, bond vectors or unit  
> > bond vectors are required for the
> > +        calculations.  This user function allows these vectors to  
> > be extracted from the loaded
> > +        structures. The bond vector will be that from the two  
> > atoms of a xyz file loaded in relax.
> > +
> > +        The extraction of vectors can occur in a number of ways.   
> > For example if an NMR structure
> > +        with N models is loaded or if multiple molecules, from  
> > any source, of the same compound are
> > +        loaded as different models, there are three options for  
> > extracting the bond vector.  Firstly
> > +        the bond vector of a single model can be extracted by  
> > setting the 'model' argument.
> > +        Secondly the bond vectors from all models can be  
> > extracted if 'model' is None and 'ave' is
> > +        set to False.  Thirdly, if 'model' is None and 'ave' is  
> > set to True, then a single vector
> > +        which is the average for all models will be calculated.
> > +
> > +
> > +        Example
> > +        ~~~~~~~
> > +
> > +        To extract a vector of two atoms from xyz file, type:
> > +
> > +        relax> structure.vectors(spin_id1='#SSS-cluster4-new- 
> > test_mol1@2', spin_id1='#SSS-cluster4-new-test_mol1@1')
> > +        """
> > +
> > +        # Function intro text.
> > +        if self._exec_info.intro:
> > +            text = self._exec_info.ps3 + "structure.vectors("
> > +            text = text + "spin_id1=" + repr(spin_id1)
> > +            text = text + ", spin_id2=" + repr(spin_id2)
> > +            text = text + ", model=" + repr(model)
> > +            text = text + ", verbosity=" + repr(verbosity)
> > +            text = text + ", ave=" + repr(ave)
> > +            text = text + ", unit=" + repr(unit) + ")"
> > +            print(text)
> > +
> > +        # The argument checks.
> > +        arg_check.is_str(spin_id1, 'spin_identification_string',  
> > can_be_none=True)
> > +        arg_check.is_str(spin_id2, 'spin identification string',  
> > can_be_none=True)
> > +        arg_check.is_int(model, 'model', can_be_none=True)
> > +        arg_check.is_int(verbosity, 'verbosity level')
> > +        arg_check.is_bool(ave, 'average vector flag')
> > +        arg_check.is_bool(unit, 'unit vector flag')
> > +
> > +        # Execute the functional code.
> > +        generic_fns.structure.main.vectors_xyz(spin_id1=spin_id1,  
> > spin_id2=spin_id2, model=model, verbosity=verbosity, ave=ave,  
> > unit=unit)
> > +
> > +
> >     def write_pdb(self, file=None, dir=None, model_num=None,  
> > force=False):
> >         """The PDB writing function.
> >
> >
> >
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