Re: [Rdkit-discuss] atom indexes and order of atoms in the input file

On 06/15/2017 01:14 PM, Brian Kelley wrote: > Sorry to hear about the flooding. >> Unfortunately we got flooded day before yesterday and the servers doing >> the crunching are currently down. I should have mentioned that the server (URL is in the article), which I'll hopefully get back up today,

Re: [Rdkit-discuss] atom indexes and order of atoms in the input file

Sorry to hear about the flooding. As an aside if you want to get they smiles atom output order, it is saved as a property on the molecule after a call to MolToSmiles, To get to the property, use mol.GetPropsAsDict(True,True) and it will be there with the key named something like

Re: [Rdkit-discuss] atom indexes and order of atoms in the input file

On 06/15/2017 10:13 AM, Maciek Wójcikowski wrote: > Hi, > > If you really want to rely on the order of atom you can renumber them > anyhow you like with Chem.RenumberAtoms() > http://rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#RenumberAtoms > There is also a function which returns

Re: [Rdkit-discuss] atom indexes and order of atoms in the input file

Hi, If you really want to rely on the order of atom you can renumber them anyhow you like with Chem.RenumberAtoms() http://rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#RenumberAtoms There is also a function which returns canonical order of atoms for you: Chem.CanonicalRankAtoms() As I

Re: [Rdkit-discuss] atom indexes and order of atoms in the input file

Yes, atoms are always added in file order. It would take a major change in rdkit to change/violate this. Brian Kelley > On Jun 15, 2017, at 7:52 AM, Francois BERENGER > wrote: > > Hello, > > If I read a molecule from a .sdf file, will the atom indexes