[Rdkit-discuss] How to perform a "mild" 2D Clean
In many chemical drawing programs, there exists a "2D Clean" function. This function usually has two tiers of cleaning. The first tier clean is mild: standardizing bond lengths and bond angles, but leaving the general conformation intact. The second tier is stronger: completely recomputing the 2D coordinates from scratch. In RDKit, Generate2DCoords() does an admirable job at performing the strong version of the above. However, I haven't found anything that can perform the mild 2D Clean. What I've examined so far: 1. TransformMol(): this can scale the structure to get bond lengths close to the desired length, but doesn't help for molecules with bonds that have different lengths -- the asymmetry is preserved after the scaling. 2. Iterating through all bonds and calling SetBondLength() to a constant value: this fails for bonds that are in rings. 3. Iterating through atoms and calling SetAngleDeg() to standardize bond angles: I haven't tried this yet -- it is next on my list. However, even if this works, it won't fix the bond length part of the clean. Any other suggestions? ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Plotting values next to atoms
Hi Eric, On Fri, Nov 2, 2018 at 2:00 PM Eric Jonas wrote: > Hello! I'm trying to figure out if there's any known or sane way to > automatically plot numerical values adjacent to atoms using the rdkit > drawing machinery. Ideally I'd like to annotate certain atoms > programmatically with values. I think the conventional way this is done for > publication is post-hoc editing in illustrator but it would be great if > there was an automatic or supported mechanism. > Doing this correctly is on the list of high-priority things to do, and I really hope to have something done for the 2019.03 release, but there's no way I can guarantee that (it's a hard problem). In the meantime, there's a way to at least do something that is, hopefully, better than nothing: https://gist.github.com/greglandrum/8cf8ecc3253abf0a5139a776a5095163 displayed here: https://nbviewer.jupyter.org/gist/greglandrum/8cf8ecc3253abf0a5139a776a5095163 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] svg: next question
On 11/02/2018 12:19 AM, Greg Landrum wrote: > On Fri, Nov 2, 2018 at 12:32 AM Dimitri Maziuk via Rdkit-discuss < > rdkit-discuss@lists.sourceforge.net> wrote: > >> Does anyone know where TH does >> >> >> >> come from? -- > > > assuming you're using the RDKit's MolDraw2DSVG class, that comes from here: > https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp#L53 Should it be changed to utf-8? I suspect any system where RDKit builds at this point is using that, and I believe technically element can contain unicode. E.g. you should be able to render your amino-acids with atoms labeled w/ Greek alphas, betas, etc. as per IUPAC. >> I have two SVGs generated by the same container running on >> the same linux host and one has the above, the other has >> >> >> > > No idea where that might have come from, but it's not MolDraw2DSVG Weird. I'll see if I get any more of those... -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Plotting values next to atoms
On 11/02/2018 07:59 AM, Eric Jonas wrote: > Hello! I'm trying to figure out if there's any known or sane way to > automatically plot numerical values adjacent to atoms using the rdkit > drawing machinery. Ideally I'd like to annotate certain atoms > programmatically with values. This draws atom labels: op = dr.drawOptions() for i in range( self._mol.GetNumAtoms() ) : op.atomLabels[i] = self._mol.GetAtomWithIdx( i ).GetSymbol() + str( (i + 1) ) HTH, -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Fail one case adding functional groups to certain atomic index of core
Thanks for the tip!
Hi, Greg
I will check it another for cases. SetNoImplicit and SetNoExplicit are
very confused ones. What this makes it soluble?
Best,
Noki.
On Fri, Nov 2, 2018 at 1:01 PM Greg Landrum wrote:
> You're going to reach the limit of what this simple approach can do can do
> very quickly. :-)
> When you express the sulfur atom as [SH] in the SMILES, you tell the RDKit
> that it must have an H attached. That information is preserved when you
> connect the S to the other molecule, so you end up with a valence that's
> too high.
>
> I added a function combine2 to the gist (
> https://gist.github.com/greglandrum/fd488309268cb085be218f26178e13b8)
> that can handle this case,
>
> On Thu, Nov 1, 2018 at 9:33 AM Noki Lee wrote:
>
>> Hi, Greg
>>
>> Recently, I got the code producing a combined molecule from one core and
>> several functional groups:
>> https://gist.github.com/greglandrum/fd488309268cb085be218f26178e13b8
>>
>> Here is the exception case that I encountered.
>>
>> core = Chem.MolFromSmiles('N(=N/c1c1)\c2c2')
>> pieces = [Chem.MolFromSmiles(x) for x in ('C(=O)O','O=[SH](=O)O')]
>> connections = ((7,0),(4,1))
>> newMol = combine(core,pieces,connections)
>> Draw.MolToImage(core).show()
>> Draw.MolToImage(pieces[0]).show()
>> Draw.MolToImage(pieces[1]).show()
>> Draw.MolToImage(newMol).show()
>> print(Chem.MolToSmiles(newMol))
>>
>> I tried using all canonicalized smiles. I worked for 'O=S(=O)O' which is
>> not canonicalized one.
>> If I put 'O=[SH](=O)O', it works. But it's not what I wanted. The tail of
>> H(hydrogen) tags along the S atom.
>> I tried [S-] instead [SH], but it is also not what I expected. S in the
>> result of 'combine' function has a negative charge. Can you suggest
>> something?
>>
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