Re: [Rdkit-discuss] How to draw peptides and let the backbone atoms appear in the most extended form?

2022-07-26 Thread He, Amy 
Hi Paolo,

Thank you so much for your kind advice. Yes that works well for my compounds as 
they are mostly analogs to GC373. Thanks again for your kind help!

Bests,
Amy

--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
[email protected]

From: Paolo Tosco 
Date: Tuesday, July 26, 2022 at 3:05 PM
To: He, Amy 
Cc: [email protected] 
Subject: Re: [Rdkit-discuss] How to draw peptides and let the backbone atoms 
appear in the most extended form?
Hi Amy, the simplest way is probably to use Schroedinger's CoordGen to generate 
coordinates:: from rdkit import Chem from rdkit.Chem.Draw import rdDepictor 
rdDepictor.SetPreferCoordGen(True) peptide = 
Chem.MolFromSmiles("CC(C)C[C@H](NC(=O)OCC1=CC=CC=C1)C(=O)N[C@@H](CC1CCNC1=O)C=O")

Hi Amy,

the simplest way is probably to use Schroedinger's CoordGen to generate 
coordinates::

from rdkit import Chem
from rdkit.Chem.Draw import rdDepictor

rdDepictor.SetPreferCoordGen(True)
peptide = 
Chem.MolFromSmiles("CC(C)C[C@H](NC(=O)OCC1=CC=CC=C1)C(=O)N[C@@H](CC1CCNC1=O)C=O")
rdDepictor.Compute2DCoords(peptide)
0
peptide
[cid:ii_l62jqp9b2]
Should this fail for other peptides, get in touch as there are alternative ways.

Cheers,
p.

On Tue, Jul 26, 2022 at 5:13 PM He, Amy 
mailto:[email protected]>> wrote:
Dear RDKit Experts,

I have a question about drawing peptidomimetic compounds. I wanted to draw the 
peptides and let the backbone atoms appear in the most extended form. Please 
see the following ChemDraw picture as an example for what I was trying to 
achieve:
[cid:1823be2ebef847be2d22]
The molecule shown above is inhibitor 
GC373<https://urldefense.com/v3/__https:/go.drugbank.com/drugs/DB15797__;!!KGKeukY!2ZFin_Fq-pYF9Ui-CxUV2gBcN_Ei7MpmB4sF7eca98u6EtGKnunDGjCKm5JB_w6J6GzPKgP7BazKPpPP7y6YCmoG_9pWszDQb2hjdf0$>.
 The backbone atoms appear in the trans configuration. But this kind of “trans” 
configuration is about the directionality of bonds around the C-N and C-C 
single bonds, so I was unable to use the double bond configuration method (by 
characters ‘\’ and ‘/’) to enforce this type of structure by SMILES… :’(
My RDKit structure from SMILES looks like this:
[VDgAn4ASUVORK5CYII=]

My question is: Is it possible to adjust the drawing method so I can let the 
backbone atoms lay out in the most extended form (the trans configuration as 
shown in the ChemDraw picture)? Thank you for your time and kind advice in 
advance.


Many Thanks,
Amy

--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
[email protected]<mailto:[email protected]>
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Re: [Rdkit-discuss] How to draw peptides and let the backbone atoms appear in the most extended form?

2022-07-26 Thread Paolo Tosco 
Hi Amy,

the simplest way is probably to use Schroedinger's CoordGen to generate
coordinates::

from rdkit import Chem
from rdkit.Chem.Draw import rdDepictor

rdDepictor.SetPreferCoordGen(True)
peptide = Chem.MolFromSmiles("CC(C)C[C@H](NC(=O)OCC1=CC=CC=C1)C(=O)N[C@
@H](CC1CCNC1=O)C=O")
rdDepictor.Compute2DCoords(peptide)
0
peptide
[image: image.png]
Should this fail for other peptides, get in touch as there are alternative
ways.

Cheers,
p.

On Tue, Jul 26, 2022 at 5:13 PM He, Amy  wrote:

> Dear RDKit Experts,
>
>
>
> I have a question about drawing peptidomimetic compounds. I wanted to draw
> the peptides and let the backbone atoms appear in the most extended form.
> Please see the following ChemDraw picture as an example for what I was
> trying to achieve:
>
> The molecule shown above is inhibitor GC373
> . The backbone atoms appear in the
> trans configuration. But this kind of “trans” configuration is about the
> directionality of bonds around the C-N and C-C single bonds, so I was
> unable to use the double bond configuration method (by characters ‘\’ and
> ‘/’) to enforce this type of structure by SMILES… :’(
>
> My RDKit structure from SMILES looks like this:
>
> [image: VDgAn4ASUVORK5CYII=]
>
>
>
> My question is: Is it possible to adjust the drawing method so I can let
> the backbone atoms lay out in the most extended form (the trans
> configuration as shown in the ChemDraw picture)? Thank you for your time
> and kind advice in advance.
>
>
>
>
>
> Many Thanks,
>
> Amy
>
>
>
> --
>
> Amy He
>
> Chemistry Graduate Teaching Assistant
>
> Hadad Research Group
>
> Ohio State University
>
> [email protected]
> ___
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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[Rdkit-discuss] How to draw peptides and let the backbone atoms appear in the most extended form?

2022-07-26 Thread He, Amy 
Dear RDKit Experts,

I have a question about drawing peptidomimetic compounds. I wanted to draw the 
peptides and let the backbone atoms appear in the most extended form. Please 
see the following ChemDraw picture as an example for what I was trying to 
achieve:
[cid:[email protected]]
The molecule shown above is inhibitor 
GC373. The backbone atoms appear in the 
trans configuration. But this kind of “trans” configuration is about the 
directionality of bonds around the C-N and C-C single bonds, so I was unable to 
use the double bond configuration method (by characters ‘\’ and ‘/’) to enforce 
this type of structure by SMILES… :’(
My RDKit structure from SMILES looks like this:
[VDgAn4ASUVORK5CYII=]

My question is: Is it possible to adjust the drawing method so I can let the 
backbone atoms lay out in the most extended form (the trans configuration as 
shown in the ChemDraw picture)? Thank you for your time and kind advice in 
advance.


Many Thanks,
Amy

--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
[email protected]
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