Re: [Rdkit-discuss] Question about WedgeMolBonds
(or by means of an optional argument :-) ) -P. Sent from a cell phone. Please forgive brvty and m1St@kes. On Feb 26, 2017 00:36, "Greg Landrum" wrote: > > > On Sat, Feb 25, 2017 at 7:23 PM, John Mayfield < > john.wilkinson...@gmail.com> wrote: > >> Is there something that the compute2DCoords() is doing that makes it a >>> dependency for WedgeMolBonds() >> >> >> Yes, calculating 2D coordinates. Look at these two molecules, they are >> the same but the atoms have been positioned differently in 2D and hence the >> wedging needs to be different. Therefore you need 2D coordinates before you >> can (re)assign wedges. >> [image: Inline images 3] >> > > John is exactly right here. > > >> In truth since the two (2D layout and wedging) are dependant I'd probably >> make the layout call the wedging automatically >> > > Not a bad idea, but the RDKit doesn't do it since you don't always need > the bond wedging information. > > -greg > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Question about WedgeMolBonds
On Sat, Feb 25, 2017 at 7:23 PM, John Mayfield wrote: > Is there something that the compute2DCoords() is doing that makes it a >> dependency for WedgeMolBonds() > > > Yes, calculating 2D coordinates. Look at these two molecules, they are the > same but the atoms have been positioned differently in 2D and hence the > wedging needs to be different. Therefore you need 2D coordinates before you > can (re)assign wedges. > [image: Inline images 3] > John is exactly right here. > In truth since the two (2D layout and wedging) are dependant I'd probably > make the layout call the wedging automatically > Not a bad idea, but the RDKit doesn't do it since you don't always need the bond wedging information. -greg -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Question about WedgeMolBonds
> > Is there something that the compute2DCoords() is doing that makes it a > dependency for WedgeMolBonds() Yes, calculating 2D coordinates. Look at these two molecules, they are the same but the atoms have been positioned differently in 2D and hence the wedging needs to be different. Therefore you need 2D coordinates before you can (re)assign wedges. [image: Inline images 3] In truth since the two (2D layout and wedging) are dependant I'd probably make the layout call the wedging automatically John On 25 February 2017 at 03:39, Shubbey McBean wrote: > Hi, I am using WedgeMolBonds() to label converted 3D->2D conformations, > roughly: > > // ... read in 3D mol > assignChiralTypesFrom3D(mol); > assignStereochemistry(mol,true,true); > WedgeMolBonds(mol,&mol.getConformer()); > compute2DCoords(...) > > However, this does not produce an accurate result. In order to "fix" > this, I need to reverse the last two calls (calling the 3D->2D _before_ > WedgeMolBonds). This seems counter-intuitive to me. Is there something > that the compute2DCoords() is doing that makes it a dependency for > WedgeMolBonds()? Or am I going about this the wrong way? The specifics of > my situation make it preferable to order things as stated, but it's not a > deal-breaker. Mostly I am just a bit stuck as to what is going on here. > > Thanks! > > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Question about WedgeMolBonds
Hi, I am using WedgeMolBonds() to label converted 3D->2D conformations, roughly: // ... read in 3D mol assignChiralTypesFrom3D(mol); assignStereochemistry(mol,true,true); WedgeMolBonds(mol,&mol.getConformer()); compute2DCoords(...) However, this does not produce an accurate result. In order to "fix" this, I need to reverse the last two calls (calling the 3D->2D _before_ WedgeMolBonds). This seems counter-intuitive to me. Is there something that the compute2DCoords() is doing that makes it a dependency for WedgeMolBonds()? Or am I going about this the wrong way? The specifics of my situation make it preferable to order things as stated, but it's not a deal-breaker. Mostly I am just a bit stuck as to what is going on here. Thanks! -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss