Re: [Rdkit-discuss] Using DrawAttachmentLine for bidentate ligands
Yep, I’m aware .. but it wouldn’t take too much work to at least ignore
“<“ and “>” in the Open Babel parser.
In the meantime, my Python scripts will strip them from the SMILES strings
before passing them to Open Babel.
-Geoff
On Aug 14, 2022 at 4:42:25 AM, David Cosgrove
wrote:
> Hi Geoff,
> You should bear in mind that the dative bond syntax is an RDKIt extension
> to SMILES so is not guaranteed to be parsed correctly by other
> cheminformatics toolkits.
> Dave
>
>
> On Sun, 14 Aug 2022 at 00:42, Geoffrey Hutchison <
> geoff.hutchi...@gmail.com> wrote:
>
>> mol = Chem.MolFromSmiles("C12=CC=CC=[N]1->[*]<-[N]3=C2C=CC=C3")
>>
>>
>> Hmm. I forgot the SMILES syntax of dative bonds. That's a nice idea.
>>
>> I actually decided to use the noFreeType=True option, add a highlight as
>> the "metal" and remove the * from the depiction.
>>
>> The initial set is at:
>> https://github.com/OpenChemistry/fragments/tree/main/ligands
>>
>> Thanks!
>> -Geoff
>>
>>
>>
>>
>> ___
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>>
> --
> David Cosgrove
> Freelance computational chemistry and chemoinformatics developer
> http://cozchemix.co.uk
>
>
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Re: [Rdkit-discuss] Using DrawAttachmentLine for bidentate ligands
Hi Geoff,
You should bear in mind that the dative bond syntax is an RDKIt extension
to SMILES so is not guaranteed to be parsed correctly by other
cheminformatics toolkits.
Dave
On Sun, 14 Aug 2022 at 00:42, Geoffrey Hutchison
wrote:
> mol = Chem.MolFromSmiles("C12=CC=CC=[N]1->[*]<-[N]3=C2C=CC=C3")
>
>
> Hmm. I forgot the SMILES syntax of dative bonds. That's a nice idea.
>
> I actually decided to use the noFreeType=True option, add a highlight as
> the "metal" and remove the * from the depiction.
>
> The initial set is at:
> https://github.com/OpenChemistry/fragments/tree/main/ligands
>
> Thanks!
> -Geoff
>
>
>
>
> ___
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> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
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Re: [Rdkit-discuss] Using DrawAttachmentLine for bidentate ligands
> mol = Chem.MolFromSmiles("C12=CC=CC=[N]1->[*]<-[N]3=C2C=CC=C3")
Hmm. I forgot the SMILES syntax of dative bonds. That's a nice idea.
I actually decided to use the noFreeType=True option, add a highlight as the
"metal" and remove the * from the depiction.
The initial set is at:
https://github.com/OpenChemistry/fragments/tree/main/ligands
Thanks!
-Geoff
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Re: [Rdkit-discuss] Using DrawAttachmentLine for bidentate ligands
Hi Geoff,
you can indeed use DrawWavyLine() coupled to some basic 2D geometry as in
the example below:
from rdkit import Chem
from rdkit.Geometry import Point3D, Point2D
from rdkit.Chem.Draw import rdDepictor, rdMolDraw2D
from IPython.display import SVG
mol = Chem.MolFromSmiles("C12=CC=CC=[N]1->[*]<-[N]3=C2C=CC=C3")
rdDepictor.Compute2DCoords(mol)
0
dative_bonds = [b for b in mol.GetBonds() if b.GetBondType() ==
Chem.BondType.DATIVE]
def draw_attachment_line(mol, drawer, bond, wavy_color=(0.0, 0.0, 0.0),
n_segments=12, offset=0.07, wavy_len=0.8):
bi = bond.GetBeginAtomIdx()
ei = bond.GetEndAtomIdx()
bc = mol.GetConformer().GetAtomPosition(bi)
ec = mol.GetConformer().GetAtomPosition(ei)
bv = bc - ec
bv.Normalize()
midpoint = (bc + ec) * 0.5
ba = midpoint + Point3D(bv.y, -bv.x, 0.0) * (wavy_len * 0.5)
ea = midpoint + Point3D(-bv.y, bv.x, 0.0) * (wavy_len * 0.5)
drawer.DrawWavyLine(Point2D(ba.x, ba.y), Point2D(ea.x, ea.y),
wavy_color, wavy_color, n_segments, offset)
drawer = rdMolDraw2D.MolDraw2DSVG(500, 300)
drawer.DrawMolecule(mol)
for bond in dative_bonds:
draw_attachment_line(mol, drawer, bond)
drawer.FinishDrawing()
SVG(drawer.GetDrawingText())
[image: image.png]
You can tweak the default offset of waves, the number of waves and the
length of the wavy bond through the relevant parameters in
draw_attachment_line().
Cheers,
p.
On Wed, Aug 10, 2022 at 5:22 PM Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> I've been using RDKit for depicting sets of ligands from SMILES, which has
> been great.
>
> I'd like to add some bidentate and tridentate ligands. Let's stick to
> bipyridine at first (see image)
>
>
> I have the appropriate SMILES, leaving * as part of a 5 atom ring
> involving the nitrogen atoms (and sanitize = False)
> C12=CC=CC=[N]1[*][N]3=C2C=CC=C3
>
> The resulting depiction is great .. except I'd like to add the attachment
> "squiggles" across the N-* bonds.
>
> I see there are DrawAttachmentLine and DrawWavyLine methods, but I'd need
> to get the positions of the N and * atoms.
>
> What's the best way to do that and / or automate adding wavy lines across
> arbitrary bonds?
>
> Thanks,
> -Geoff
>
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Re: [Rdkit-discuss] Using DrawAttachmentLine for bidentate ligands
Hi Geoff, The drawer has the GetDrawCoords() method. There are 2 overloads, one takes a Point2D, the other an atom index, and both return the coordinates in the drawers reference frame. Assuming you're working in Python. In C++, they're getDrawCoords(). https://www.rdkit.org/docs/source/rdkit.Chem.Draw.rdMolDraw2D.html Dave On Wed, Aug 10, 2022 at 4:22 PM Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > I've been using RDKit for depicting sets of ligands from SMILES, which has > been great. > > I'd like to add some bidentate and tridentate ligands. Let's stick to > bipyridine at first (see image) > > > I have the appropriate SMILES, leaving * as part of a 5 atom ring > involving the nitrogen atoms (and sanitize = False) > C12=CC=CC=[N]1[*][N]3=C2C=CC=C3 > > The resulting depiction is great .. except I'd like to add the attachment > "squiggles" across the N-* bonds. > > I see there are DrawAttachmentLine and DrawWavyLine methods, but I'd need > to get the positions of the N and * atoms. > > What's the best way to do that and / or automate adding wavy lines across > arbitrary bonds? > > Thanks, > -Geoff > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- David Cosgrove Freelance computational chemistry and chemoinformatics developer http://cozchemix.co.uk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Using DrawAttachmentLine for bidentate ligands
I've been using RDKit for depicting sets of ligands from SMILES, which has been great. I'd like to add some bidentate and tridentate ligands. Let's stick to bipyridine at first (see image) I have the appropriate SMILES, leaving * as part of a 5 atom ring involving the nitrogen atoms (and sanitize = False) C12=CC=CC=[N]1[*][N]3=C2C=CC=C3 The resulting depiction is great .. except I'd like to add the attachment "squiggles" across the N-* bonds. I see there are DrawAttachmentLine and DrawWavyLine methods, but I'd need to get the positions of the N and * atoms. What's the best way to do that and / or automate adding wavy lines across arbitrary bonds? Thanks, -Geoff ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
