Hello again, I browsed through the sources and I found the answer to my question: the atom at index 0 from the replacement is used for the new bond. It would be nice to be able to specify the index of this bonding atom as a parameter in AllChem.ReplaceSubstructs.
Is it possible to reorder atoms in a molecule (i.e. to have a chosen atom at index 0)? Best wishes, Michal On 7 November 2013 11:38, Michal Krompiec <michal.kromp...@gmail.com> wrote: > Hello, > I have a question about AllChem.ReplaceSubstructs(mol, > query,replacement). As I understand, it replaces 'query' pattern in > 'mol' by 'replacement' fragment. It is clear which atom from 'mol' is > the joining atom, but which is the joining atom in 'replacement'? The > atom with index=0? Is it possible to specify which atom in the > 'replacement' should be bonded to 'mol'? It would be lovely to be able > to do so, because the only alternative (using reaction SMARTS) is > much, much slower. > If not, is it possible to generate (from a given Mol object) a SMILES > string starting from the specified atom index? > > Thanks, > Michal ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
