Re: [Rdkit-discuss] how to append conformer number to molecule name in SDF output file?

Sure you can do this by setting the molecule's "_Name" property before each call to SDWriter.write(). Here's a short example: In [15]: sio = StringIO() In [16]: w = Chem.SDWriter(sio) In [17]: basen = m.GetProp('_Name') In [18]: for conf in m.GetConformers(): ...: cid = conf.GetId()

Re: [Rdkit-discuss] AllChem.GetConformerRMSD: this is not RMSD between two conformers but an upper bound of it

The function you want is GetBestRMS, note that you can set the conformer idx for the probe and ref. http://www.rdkit.org/Python_Docs/rdkit.Chem.AllChem-module.html#GetBestRMS Brian Kelley > On Jun 15, 2017, at 5:30 AM, Francois BERENGER > wrote: > >

Re: [Rdkit-discuss] a 2D to 3D (smi to sdf) conformer generator python script using rdkit

Thanks for letting people know about this. If we can get a consensus form that people agree makes sense, this might be a nice addition to either the RDKit/Scripts directory or the cookbook. A couple of smallish comments after a quick skim: - I would really strongly encourage you to use the ETKDG

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

Re: [Rdkit-discuss] AllChem.GetConformerRMSD: this is not RMSD between two conformers but an upper bound of it

On Thu, Jun 15, 2017 at 6:30 AM, Francois BERENGER < beren...@bioreg.kyushu-u.ac.jp> wrote: > > I am afraid that in AllChem.GetConfomerRMSD: one doesn't get the RMSD > between the two conformers but an upper bound of it. > The documentation to this function is misleading: In [21]:

Re: [Rdkit-discuss] a 2D to 3D (smi to sdf) conformer generator python script using rdkit

On 06/15/2017 03:50 PM, Greg Landrum wrote: Thanks for letting people know about this. If we can get a consensus form that people agree makes sense, this might be a nice addition to either the RDKit/Scripts directory or the cookbook. A couple of smallish comments after a quick skim: - I would

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

Hello, If I read a molecule from a .sdf file, will the atom indexes be conserved/preserved? 1st atom in the file will have index 0, 2nd index 1, etc. And, will this always hold in the future? Is this an invariant of rdkit? Thanks, F.

Re: [Rdkit-discuss] AllChem.GetConformerRMSD: this is not RMSD between two conformers but an upper bound of it

Thanks for the documentation fix, I had read the same as Francois. Brian Kelley > On Jun 15, 2017, at 8:02 AM, Greg Landrum wrote: > > > >> On Thu, Jun 15, 2017 at 6:30 AM, Francois BERENGER >> wrote: >> >> I am afraid that in

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