[Rdkit-discuss] Canonicalisation with reaction labels

Hi With a 2013 RDkit install we get consistent canonicalization between reaction labelled and unlabelled atoms. >>> mol = Chem.MolFromSmiles('C1CC([*])CCN1') >>> Chem.MolToSmiles(mol) '[*]C1CCNCC1' >>> mol = Chem.MolFromSmiles('C1CC([*:1])CCN1') >>> Chem.MolToSmiles(mol) '[*:1]C1CCNCC1' In

Re: [Rdkit-discuss] Canonicalisation with reaction labels

On Dec 16, 2016, at 1:55 PM, Stephen Pickett wrote: > With a 2013 RDkit install we get consistent canonicalization between reaction > labelled and unlabelled atoms. > >>> mol = Chem.MolFromSmiles('C1CC([*])CCN1') > >>> Chem.MolToSmiles(mol) > '[*]C1CCNCC1' > >>> mol =

Re: [Rdkit-discuss] Canonicalisation with reaction labels

Hi Stephen, The new canonicalization algorithm intentionally takes the atom-mapping information into account. The logic is that the entire SMILES provided should be canonical, so if the SMILES includes atom maps, those atom maps should be considered while canonicalizing. If you have a molecule

Re: [Rdkit-discuss] Canonicalisation with reaction labels

Interesting question. Not sure if it's relevant but in ECBlast we do provide Canonicalised reaction labels. I agree with Greg that AAM is important. https://github.com/asad/ReactionDecoder http://www.ebi.ac.uk/thornton-srv/software/rbl/ Regards, Asad Sent from my iPhone > On 16 Dec 2016, at

[Rdkit-discuss] SetAtomAlias

Hi all, I try add labels to atoms in a molecule, so that lines like A1 C12 A2 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

Re: [Rdkit-discuss] SetAtomAlias

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,

Re: [Rdkit-discuss] SetAtomAlias

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

Re: [Rdkit-discuss] SDwriter

It's easy enough to make this an option, but given that it is part of the SDF spec (as Andrew has pointed out) the only reason I can think of to do so would be because it causes problems for some other piece of (likely commonly used) software. Are the sequence numbers causing a problem for you?

Re: [Rdkit-discuss] SDwriter

This SD file is then used as an input for another program, that program is having problems reading the sequence numbers. Thanks, MAK On Fri, Dec 16, 2016 at 10:43 PM, Greg Landrum wrote: > It's easy enough to make this an option, but given that it is part of the > SDF