Re: [Rdkit-discuss] Strange MMFF94 Optimization Results?

[Patrick Avery]

I started using the SD format instead, and it fixed my problems (the
molecules now have correct bond orders and they are MMFF94 optimized
properly).

Thanks for the help!

On Thu, Nov 2, 2017 at 3:21 PM, Paolo Tosco <paolo.to...@unito.it> wrote:

> Hi Patrick,
>
> I don't know Avogadro in detail, but as it is based on OpenBabel I can
> imagine it uses an algorithm to guess bond orders from bond distances,
> angles, etc., whereas the RDKit does not. In fact, if I convert a benzene
> ring from SMILES to SDF through PDB format (which does not contain any bond
> information once CONECT records are removed), I still get correct bond
> orders; this does not happen with RDKit (which is expected):
>
> echo 'c1c1' | babel --gen3d -i smi -o pdb | grep -v CONECT | babel -i
> pdb -o sdf
>
> yields
>
>
>  OpenBabel11021718533D
>
>  12 12  0  0  0  0  0  0  0  0999 V2000
>-0.76001.1690   -0.0010 C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.63301.2450   -0.0010 C   0  0  0  0  0  0  0  0  0  0  0  0
> 1.39500.07700. C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.7640   -1.16800.0030 C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.6290   -1.24300. C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.3910   -0.0750   -0.0020 C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.35402.07900.0010 H   0  0  0  0  0  0  0  0  0  0  0  0
> 1.12402.2140   -0.0030 H   0  0  0  0  0  0  0  0  0  0  0  0
> 2.48000.1350   -0. H   0  0  0  0  0  0  0  0  0  0  0  0
> 1.3580   -2.07800.0060 H   0  0  0  0  0  0  0  0  0  0  0  0
>-1.1200   -2.2130   -0. H   0  0  0  0  0  0  0  0  0  0  0  0
>-2.4760   -0.1340   -0.0030 H   0  0  0  0  0  0  0  0  0  0  0  0
>   1  2  1  0  0  0  0
>   1  7  1  0  0  0  0
>   2  3  2  0  0  0  0
>   3  9  1  0  0  0  0
>   3  4  1  0  0  0  0
>   4 10  1  0  0  0  0
>   5 11  1  0  0  0  0
>   5  4  2  0  0  0  0
>   6  1  2  0  0  0  0
>   6  5  1  0  0  0  0
>   8  2  1  0  0  0  0
>  12  6  1  0  0  0  0
> M  END
>
> whereas:
>
> mol = Chem.AddHs(Chem.MolFromSmiles('c1c1'))
> rdDistGeom.EmbedMolecule(mol)
> molFromPDB = Chem.MolFromPDBBlock(re.sub('CONECT.*\n', '',
> Chem.MolToPDBBlock(mol), flags=re.MULTILINE), removeHs = False)
> print (Chem.MolToMolBlock(molFromPDB))
>
> yields
>
>
>  RDKit  3D
>
>  12 12  0  0  0  0  0  0  0  0999 V2000
>-0.0060   -1.36200.0590 C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.2180   -0.70800.0690 C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.20900.6740   -0.0030 C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.00301.36200.0280 C   0  0  0  0  0  0  0  0  0  0  0  0
> 1.22100.70900.0760 C   0  0  0  0  0  0  0  0  0  0  0  0
> 1.1960   -0.67800. C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.0250   -2.4100   -0.2260 H   0  0  0  0  0  0  0  0  0  0  0  0
>-2.1060   -1.17600.4870 H   0  0  0  0  0  0  0  0  0  0  0  0
>-2.09101.1950   -0.3790 H   0  0  0  0  0  0  0  0  0  0  0  0
> 0.04202.4080   -0.2780 H   0  0  0  0  0  0  0  0  0  0  0  0
> 2.10301.18300.5000 H   0  0  0  0  0  0  0  0  0  0  0  0
> 2.0960   -1.1980   -0.3330 H   0  0  0  0  0  0  0  0  0  0  0  0
>   2  1  1  0
>   3  2  1  0
>   4  3  1  0
>   5  4  1  0
>   6  5  1  0
>   6  1  1  0
>   7  1  1  0
>   8  2  1  0
>   9  3  1  0
>  10  4  1  0
>  11  5  1  0
>  12  6  1  0
> M  END
>
> Note that the RDKit gets the correct bond orders if the PDB file contains
> CONECT records with duplicate (or triplicate) entries for the relevant atom
> indices, which is the widely accepted (though non official) way to encode
> bond orders in PDB files.
>
> Cheers,
> p.
>
> On 11/02/17 18:45, Patrick Avery wrote:
>
> Yes, that is probably correct. I am loading a pdb file for the initial
> conformer, so bond orders are not specified.
>
> But I find it strange, still, that when I use MMFF94 in Avogadro to
> optimize it, it results in a planar shape even though all the bonds are
> still single.
>
> On Thu, Nov 2, 2017 at 2:38 PM, Paolo Tosco <paolo.to...@unito.it> wrote:
>
>> Dear Patrick,
>>
>> my guess is that you loaded the caffeine coordinates from PDB, or anyway
>> from a format where bond orders were not specified. All atoms appear to be
>> sp3-hybridized, which results in the wrong geometry being generated.
>>
>> Hope that helps,
>> Paolo
>>
>> On 11/02/17 18:20, Patrick Avery wrote:
>>
>> Hey there RDKitters,
>>
>> I have been generating conformers in RDKit, optimizing them using MMFF94,
>> and sorting them by thei

Re: [Rdkit-discuss] Strange MMFF94 Optimization Results?

[Patrick Avery]

Yes, that is probably correct. I am loading a pdb file for the initial
conformer, so bond orders are not specified.

But I find it strange, still, that when I use MMFF94 in Avogadro to
optimize it, it results in a planar shape even though all the bonds are
still single.

On Thu, Nov 2, 2017 at 2:38 PM, Paolo Tosco <paolo.to...@unito.it> wrote:

> Dear Patrick,
>
> my guess is that you loaded the caffeine coordinates from PDB, or anyway
> from a format where bond orders were not specified. All atoms appear to be
> sp3-hybridized, which results in the wrong geometry being generated.
>
> Hope that helps,
> Paolo
>
> On 11/02/17 18:20, Patrick Avery wrote:
>
> Hey there RDKitters,
>
> I have been generating conformers in RDKit, optimizing them using MMFF94,
> and sorting them by their energies. For some tests, I have been using
> caffeine. But I seem to have some strange results, and I wonder if anyone
> knows why.
>
> I have attached two images of an MMFF94 optimized caffeine conformer. In
> them, the oxygen in the top right corner is the primary strange thing I see
> (although it doesn't seem to be very planar either, which may be somewhat
> strange).
>
> Note that the oxygen is sticking out of the plane of the molecule. This is
> the lowest energy conformer generated and optimized by RDKit (and other
> conformers low in energy are similar to it - with the oxygen sticking out).
>
> If I take that exact molecule and MMFF94 optimize it in Avogadro, all the
> atoms move to be in the same plane (including the oxygen that was sticking
> out). So the problem goes away if I MMFF94 optimize it with Avogadro.
>
> So the question is: why are RDKit and Avogadro giving different results
> for the MMFF94 optimization? And why does RDKit's MMFF94 push the oxygen
> out of the plane so much?
>
> In RDKit, I am using the C++ function RDKit::MMFF::
> MMFFOptimizeMoleculeConfs().
>
> My parameters are the mol (with all the conformers in it), an empty result
> vector, 1 thread, 1000 maximum optimization iterations, "MMFF94" for the
> mmffVariant, 100.0 for the nonbonded threshold, and true for
> ignoreInterfragInteractions.
>
> Let me know if anyone knows why.
>
> Thanks,
> Patrick
>
>
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>
>
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[Rdkit-discuss] Strange MMFF94 Optimization Results?

[Patrick Avery]

Hey there RDKitters,

I have been generating conformers in RDKit, optimizing them using MMFF94,
and sorting them by their energies. For some tests, I have been using
caffeine. But I seem to have some strange results, and I wonder if anyone
knows why.

I have attached two images of an MMFF94 optimized caffeine conformer. In
them, the oxygen in the top right corner is the primary strange thing I see
(although it doesn't seem to be very planar either, which may be somewhat
strange).

Note that the oxygen is sticking out of the plane of the molecule. This is
the lowest energy conformer generated and optimized by RDKit (and other
conformers low in energy are similar to it - with the oxygen sticking out).

If I take that exact molecule and MMFF94 optimize it in Avogadro, all the
atoms move to be in the same plane (including the oxygen that was sticking
out). So the problem goes away if I MMFF94 optimize it with Avogadro.

So the question is: why are RDKit and Avogadro giving different results for
the MMFF94 optimization? And why does RDKit's MMFF94 push the oxygen out of
the plane so much?

In RDKit, I am using the C++ function
RDKit::MMFF::MMFFOptimizeMoleculeConfs().

My parameters are the mol (with all the conformers in it), an empty result
vector, 1 thread, 1000 maximum optimization iterations, "MMFF94" for the
mmffVariant, 100.0 for the nonbonded threshold, and true for
ignoreInterfragInteractions.

Let me know if anyone knows why.

Thanks,
Patrick
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Re: [Rdkit-discuss] recent packages for Ubuntu

[Patrick Avery]

I'm in support of upgrading the RDKit binary package on ubuntu, and I'm
willing to help some if it is needed.

On Wed, Sep 6, 2017 at 2:10 AM Greg Landrum  wrote:

> Michael Banck, who did the work to make the RDKit part of debichem, would
> be the person I'd think is best qualified to comment on this.
>
> Aside from this github issue (https://github.com/rdkit/rdkit/issues/911)
> I haven't seen much here.
>
> -greg
>
>
> On Wed, Sep 6, 2017 at 2:59 AM, Francois BERENGER <
> beren...@bioreg.kyushu-u.ac.jp> wrote:
>
>> Hello,
>>
>> If the update of the binary packages for Ubuntu/Debian
>> is documented somewhere, it would help people who
>> want to make available binary packages of rdkit as soon as there
>> is a new rdkit release.
>>
>> I think we should have a ppa for people who want to use
>> the bleeding edge version of rdkit.
>>
>> Regards,
>> F.
>>
>>
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>
>
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[Rdkit-discuss] Periodic RMSD and C++ API Ubuntu Repo Updates?

[Patrick Avery]

Hi Greg,

I know proteins are sometimes used within periodic boundaries. We aren't
using proteins, but we will be using molecules within crystals. I was
wondering if there is a way in RDKit to calculate RMSD between two periodic
systems (such as two crystals, each containing molecules), and if not, if
there is a way to generate some kind of fingerprint? I know the RMSD and
fingerprinting methods exist for molecules, but I'm not sure if there are
ones for periodic conditions. Note that we may have multiple "molecules"
inside each crystal.

Also, we were running tests with RDKit using Python, but since our program
is written in C++, I think it is easier to integrate it with the C++ API. I
already have an integration set-up that includes the proper headers and
links the proper libraries for our needs. But I had to compile RDKit myself
to do so. I noticed there are repositories for RDKit (like on Ubuntu), but
it looks like they are not up-to-date (some of the functions I need are not
yet present). I was wondering if those will get updated sometime in the
future?

The updated repositories aren't necessary (because I can always have others
compile RDKit themselves if they need to compile our program), but they're
nice to have because they speed up the process.

Thanks,
Patrick
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