Dear Peter, I got:
AttributeError: 'module' object has no attribute 'SetAtomAlias' with your example code, below. Best regards, Jean-Marc Le 17/12/2016 à 00:44, Peter Gedeck a écrit :
Hello,SetMolAlias is available in Python as a function and not as an Atom method:from rdkit import Chem import sys m = Chem.MolFromSmiles('CCC') for i, atom in enumerate(m.GetAtoms()): Chem.SetAtomAlias(atom, 'C' + str(i + 1)) w = Chem.SDWriter(sys.stdout) w.write(m) w.close() Best, PeterOn Fri, Dec 16, 2016 at 5:31 PM Paolo Tosco <[email protected] <mailto:[email protected]>> wrote:Dear Jean-Marc, here: https://gist.github.com/ptosco/6e4468350f0fff183e4507ef24f092a1#file-pdb_atom_names-ipynb there's an example how to use the atom aliases in RDKit. Cheers, p. On 12/16/2016 10:26 PM, Jean-Marc Nuzillard wrote: > Hi all, > > I try add labels to atoms in a molecule, so that lines like > > A 1 > C12 > A 2 > C3 > > are written when the molecule is written in a SD file. > > Considering atom a and alias text txt, > I expected the function call SetAtomAlias(a, txt) to do the job. > I found this function in a documentation page about the rdchem module. > So, my script started with > > from rdkit import Chem > from rdkit.Chem import rdchem > > I got: > > NameError: name 'SetAtomAlias' is not defined. > > I guess the solution is trivial. > Forgive my ignorance. > > All the best, > > Jean-Marc > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list [email protected] <mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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