Hi, Yes, this would be a problem. The code is a temporary work around, and is avoided if you specify a unique proton name (assuming the protons have different names). The problem here is if you have RDCs for both of the CH bonds in a CH2 group, how are we going to specify which RDC belongs to which atom from the XYZ file? How do we differentiate the different values? We will need to think about that one for a bit. How did we previously do this?
Regards, Edward On 28 June 2011 12:09, Han Sun <[email protected]> wrote: > 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, <[email protected]> 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. >>> >>> >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ 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
