Re: [Rdkit-discuss] SDF and FindMolChiralCenters()

If your file has 3D coordinates, AssignAtomChrialTagsFromStructure may help you. Ling On Fri, Sep 9, 2016 at 3:40 PM, Paolo Tosco wrote: > Dear Dimitri, > > the MOL reader perceives chirality based on the bond stereo field of the > bond block. Instead the atom stereo

Re: [Rdkit-discuss] SDF and FindMolChiralCenters()

Dear Dimitri, the MOL reader perceives chirality based on the bond stereo field of the bond block. Instead the atom stereo parity value of the atom block is read and stored in the "molParity" atom property, but it is ignored for the purpose of chirality perception, as per the MOL file specs:

[Rdkit-discuss] SDF and FindMolChiralCenters()

Hi everyone, m = rdkit.Chem.SupplierFromFilename( filename, removeHs = False ).next() sts = rdkit.Chem.FindMolChiralCenters( m, includeUnassigned = True ) for s in sts : lbl = m.GetAtomWithIdx( s[0] ).GetSymbol() + str( s[0] + 1 ) print lbl, ":", s[1] For L-ALA 3D SDF the output is C4 :

Re: [Rdkit-discuss] AddHs()

How about "explicit", rather than "physical", hydrogens? -P. Sent from a cell phone. Please forgive brvty and m1St@kes. On Sep 9, 2016 1:57 AM, "Greg Landrum" wrote: > > > On Thu, Sep 8, 2016 at 10:35 PM, Dimitri Maziuk > wrote: > >> On

Re: [Rdkit-discuss] AddHs()

On 09/09/2016 12:56 AM, Greg Landrum wrote: > This is absolutely correct: if you remove the Hs and then later re-add them > it is extremely unlikely that you will end up with the same H indices > before and after the change. It makes much more sense to just use > removeHs=False That's what I

Re: [Rdkit-discuss] embedMolecule - optimal bond and angle values

[adding the mailing list back in] On Thu, Sep 8, 2016 at 10:26 PM, Rafal Roszak wrote: > On Thu, 8 Sep 2016 17:32:40 +0200 > Greg Landrum wrote: > > > What are you trying to accomplish? There may be a better approach. > > I have big molecules which