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, <[email protected]> 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) > > > _______________________________________________ > 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
