Re: [Rdkit-discuss] explicit H atoms

On Tue, Mar 9, 2021 at 6:15 PM Jason Biggs wrote: > > On Tue, Mar 9, 2021 at 10:49 AM Maciek Wójcikowski > wrote: > >> Hi Jean-Marc, >> >> I know you can draw them, but both SMILES and RDKit internally use two >> bonds (up/down) directions to assign the bond stereo, which means that >> there

[Rdkit-discuss] Can't load mol2 file.

Hi RDKiters, Hope you are well. I'm having trouble loading these molecules. Do you know any walk around?? Bests, Eduardo In: rdkit.__version__ Out: '2020.09.5' In: Chem.MolFromMOL2File('file.mol2') Out: None In:Chem.MolFromPDBBlock(pdb_block) Out: (Molecule successfully loaded but missing

Re: [Rdkit-discuss] explicit H atoms

This is the continuation of the previous reply, to elaborate on "the stripped structure can always be represented using wedged bonds". One potential problem is that a bond is required to be wedged from both ends. But this should not happen. For an atom to be chiral, it needs to be attached to at

Re: [Rdkit-discuss] explicit H atoms

Hello Jean-Marc, This is a very interesting question. Given any molecule, consider its structure stripped of all H's. There is no reason why this stripped structure cannot be represented using wedged bonds etc. (Will continue on the next reply.) Hence potential problems can only arise when the

Re: [Rdkit-discuss] explicit H atoms

Jason Biggs On Tue, Mar 9, 2021 at 10:49 AM Maciek Wójcikowski wrote: > Hi Jean-Marc, > > I know you can draw them, but both SMILES and RDKit internally use two > bonds (up/down) directions to assign the bond stereo, which means that > there are not > Fortunately the RDKit also allows you to

Re: [Rdkit-discuss] explicit H atoms

Hi Jean-Marc, I know you can draw them, but both SMILES and RDKit internally use two bonds (up/down) directions to assign the bond stereo, which means that there are not enough bonds to define both double bonds configuration and have the middle one undefined at the same time. Pozdrawiam, |

Re: [Rdkit-discuss] explicit H atoms

Hi Maciek, I would find your example rather readable even without explicit H atoms. I drew it like that because I do not have the wavy wedge at hand. Thanks for your proposal, Best, Jean-Marc Le 09/03/2021 à 11:26, Maciek Wójcikowski a écrit : Hi, I'd say that for a tetrahedral stereo

Re: [Rdkit-discuss] explicit H atoms

The structure I posted was drawn with ChemDraw (now sold by PerkinElmer). Best, Jean-Marc Le 09/03/2021 à 10:44, Paul Emsley a écrit : On 09/03/2021 09:01, Jean-Marc Nuzillard wrote: Sure, testosterone may be drawn as [snip] OK :-) That's a top quality rendering by the way. How did you

Re: [Rdkit-discuss] explicit H atoms

Hi, I'd say that for a tetrahedral stereo that is possible to remove all of Hs. But for double bonds it might not be as easy, or impossible for some edge cases - conjugated double bonds in particular. Here is one: [image: image.png] [H]\C(=C/C)C=C\C([H])=C\C Pozdrawiam, | Best regards,

Re: [Rdkit-discuss] explicit H atoms

On 09/03/2021 09:01, Jean-Marc Nuzillard wrote: Sure, testosterone may be drawn as [snip] OK :-) That's a top quality rendering by the way. How did you make it? Paul. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net

Re: [Rdkit-discuss] explicit H atoms

Sure, testosterone may be drawn as Jean-Marc Le 08/03/2021 à 18:26, Rocco Moretti a écrit : On Mon, Mar 8, 2021 at 11:17 AM Paul Emsley > wrote: On 08/03/2021 13:55, Jean-Marc Nuzillard wrote: > > Is it always possible to represent an organic