Re: [Rdkit-discuss] atom indexing

Great to know, many thanks Greg! Ling Greg Landrum 於 2023年6月19日週一 下午9:53寫道： > Hi Ling, > > On Mon, Jun 19, 2023 at 3:03 AM Ling Chan wrote: > >> >> I got some questions about atom indexing. Just wonder if you could help >> me? >> >>1. In m3=Chem.CombineMols(m1,m2) , is it guaranteed that

Re: [Rdkit-discuss] atom indexing

Hi Ling, On Mon, Jun 19, 2023 at 3:03 AM Ling Chan wrote: > > I got some questions about atom indexing. Just wonder if you could help me? > >1. In m3=Chem.CombineMols(m1,m2) , is it guaranteed that the atom >indices in m3 is equivalent to the indices in m1 followed by the indices in >

[Rdkit-discuss] atom indexing

Dear colleagues, I got some questions about atom indexing. Just wonder if you could help me? 1. In m3=Chem.CombineMols(m1,m2) , is it guaranteed that the atom indices in m3 is equivalent to the indices in m1 followed by the indices in m2? 2. If I construct an editable mol from m1, is

Re: [Rdkit-discuss] Atom indexing with AssignBondOrdersFromTemplate

-- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1...@osu.edu From: Bennion, Brian Date: Sunday, July 17, 2022 at 8:20 PM To: He, Amy , rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Atom indexing with AssignBondOrdersFromTemplate I

Re: [Rdkit-discuss] Atom indexing with AssignBondOrdersFromTemplate

I don’t know if this is the issue but Are the order of atoms the same between the pdb file and the smiles string? --- Sent from Workspace ONE Boxer On July 16, 2022 at 8:14:51 PM PDT, He, Amy wrote: Dear RDKit experts, I am new to RDKit and I have a

[Rdkit-discuss] Atom indexing with AssignBondOrdersFromTemplate

Dear RDKit experts, I am new to RDKit and I have a simple question about atom indexing with RDKit. I am using RDKit in Python to process a collection of small molecule, for each I have the SMILES and a pdb file without explicit hydrogens. To draw the 2D images of the molecules, I used

Re: [Rdkit-discuss] atom indexing in mol and conformer

Good, thank you Sereina! Ling Sereina Riniker 於 2022年6月19日週日 上午1:48寫道： > Dear Ling, > > Yes, the atom indexing is the same for all conformers of a molecule. > > Best regards, > Sereina > > > > > On 19 Jun 2022, at 00:04, Ling Chan wrote: > > > > Dear colleagues, > > > > Just wonder if the atom

Re: [Rdkit-discuss] atom indexing in mol and conformer

Dear Ling, Yes, the atom indexing is the same for all conformers of a molecule. Best regards, Sereina > On 19 Jun 2022, at 00:04, Ling Chan wrote: > > Dear colleagues, > > Just wonder if the atom indexing in a conformer is always identical to that > of the parent molecule? I suspect it is

[Rdkit-discuss] atom indexing in mol and conformer

Dear colleagues, Just wonder if the atom indexing in a conformer is always identical to that of the parent molecule? I suspect it is but would like to confirm. Specifically, I would like to confirm that for conf in mol.GetConformers(): conf.GetAtomPosition(idx) always corresponds to the

[Rdkit-discuss] atom indexing

Hello folks, In a way this is a continuation of a previous discussion. My question is: so is there a simple way to obtain the original indexing with all hydrogen atoms included? Do I have to write my own function? Thank you. Ling Re: [Rdkit-discuss] SMILES and atom indexing greg landrum 

Re: [Rdkit-discuss] atom indexing

Hi Ling, On Thu, Aug 1, 2013 at 2:56 AM, S.L. Chan slch...@yahoo.com wrote: Hello folks, In a way this is a continuation of a previous discussion. My question is: so is there a simple way to obtain the original indexing with all hydrogen atoms included? Do I have to write my own function?