Re: r13417 - /branches/xyz/generic_fns/structure/internal.py -- July 05, 2011 - 16:53

Hi Han,

I've finally have my temporary replacement computer installed and set
up!  The idea behind this code looks good.  One problem that might
arise though is that the spin_loop() method loops over loaded spins,
and not over the atomic data of the loaded structures.  I don't know
if this will fail, but I would suggest looking at the internal
structural object atom_loop() method.  The atom_loop() will take a
spin ID string (i.e. '#a:6@156') and loop over the atoms matching the
ID.  An alternative idea would be to add a method to the internal
structure object called get_atom() which takes the ID string and
returns the atom.  This function could then check that the ID only
matches a single atom, throwing a RelaxError if not the case.  It
could be a simple wrapper around atom_loop().  What do you think?

Regards,

Edward


On 4 July 2011 14:43,  <hasu@xxxxxxxxxxxxxxxxx> wrote:
> Author: han87
> Date: Mon Jul  4 14:43:10 2011
> New Revision: 13417
>
> URL: http://svn.gna.org/viewcvs/relax?rev=13417&view=rev
> Log:
> Adding code for extracting a vector of a xyz file.
>
> Code for extracting a vector between specified spins in a xyz file has been 
> included in the '/generic_fns/structure/internal.py'.
>
> Modified:
>    branches/xyz/generic_fns/structure/internal.py
>
> Modified: branches/xyz/generic_fns/structure/internal.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/structure/internal.py?rev=13417&r1=13416&r2=13417&view=diff
> ==============================================================================
> --- branches/xyz/generic_fns/structure/internal.py (original)
> +++ branches/xyz/generic_fns/structure/internal.py Mon Jul  4 14:43:10 2011
> @@ -35,6 +35,7 @@
>  from api_base import Base_struct_API, ModelList
>  from data.relax_xml import fill_object_contents, xml_to_object
>  from generic_fns import pipes, relax_re
> +from generic_fns.mol_res_spin import spin_loop
>  from generic_fns.mol_res_spin import Selection
>  from relax_errors import RelaxError, RelaxNoPdbError
>  from relax_io import file_root, open_read_file
> @@ -107,7 +108,27 @@
>
>         # No attached atoms.
>         if num_attached == 0:
> -            return None, None, None, None, None, "No attached atom could 
> be found"
> +            if relax_re.search('@*', attached_atom):
> +                matching_list = []
> +                bonded_num=[]
> +                bonded_name=[]
> +                element=[]
> +                pos=[]
> +                for spin, mol_name, res_num, res_name in 
> spin_loop(selection=attached_atom, full_info=True):
> +                    bonded_num.append(spin.num)
> +                    bonded_name.append(spin.name)
> +                    element.append(spin.element)
> +                    pos.append(spin.pos)
> +                if len(bonded_num) == 1:
> +                    return bonded_num[0], bonded_name[0], element[0], 
> pos[0], attached_atom, None
> +                elif len(bonded_num) > 1:
> +                    # Return nothing but a warning.
> +                    return None, None, None, None, None, 'More than one 
> attached atom found: ' + repr(matching_names)
> +                elif len(bonded_num) > 1:
> +                    # Return nothing but a warning.
> +                    return None, None, None, None, None, "No attached atom 
> could be found"
> +            else:
> +                return None, None, None, None, None, "No attached atom 
> could be found"
>
>         # The bonded atom info.
>         index = matching_list[0]
> @@ -634,7 +655,7 @@
>                 if index != None:
>                     # Get the atom bonded to this 
> model/molecule/residue/atom.
>                     bonded_num, bonded_name, element, pos, attached_name, 
> warnings = self.__bonded_atom(attached_atom, index, mol)
> -
> +
>                     # No bonded atom.
>                     if (bonded_num, bonded_name, element) == (None, None, 
> None):
>                         continue
> @@ -1596,7 +1617,7 @@
>         @keyword index2:        The index of the second atom.
>         @type index2:           int
>         """
> -
> +
>         # Update the bonded array structure, if necessary.
>         if index2 not in self.bonded[index1]:
>             self.bonded[index1].append(index2)
>
>
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