Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.
Hi Markus, I think the problem should be fixed now. The recipes were building the cartridge using the earlier release tag, and therefore executing tests that were not fully up-to-date. Please try again and let me know in case the problem persisted. Best, Riccardo -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDkit Ruby binding /gem
On Thu, Jun 30, 2016 at 7:19 PM, Yannick .Djoumbou wrote: > > Thanks for the suggestion. I will try that. > I really think a native ruby gem would be really awesome, especially for > all those Ruby on rails users, such as me :-D. > It is certainly possible to produce such a thing. SWIG, the tool that we use to create the Java and C# wrappers for the RDKit, can also generate ruby wrappers. It would require someone with some pretty solid knowledge of Ruby and a basic level of comfort with C++ to do the work. It's probably not a huge amount of work, but it's also not a minor project. Someone would really need to invest some time in this to make it happen. -greg -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDkit Ruby binding /gem
Hi Michal, Thanks for the suggestion. I will try that. I really think a native ruby gem would be really awesome, especially for all those Ruby on rails users, such as me :-D. Regards, On Wed, Jun 29, 2016 at 2:42 AM, Michał Nowotka wrote: > Hi, > > I'm not aware of any native Ruby bindings. However I would say, the > best solution is to use some kind of remote API. > A while ago I created a project called Braker, which exposes most of > the RDKit methods as a RESTful API. > > The code is here: https://github.com/chembl/chembl_beaker > The live endpoint is here: https://www.ebi.ac.uk/chembl/api/utils/docs > (is uses older version of rdkit, so the best is to set up your own > local endpoint). > This tool is also included in this Docker image: > > http://ftp.ebi.ac.uk/pub/databases/chembl/VM/Docker/mychembl_20_ubuntu_docker.tar.gz > > I'm happy to answer any further questions if you are interested. > > Kind regards, > > Michał Nowotka > > On Wed, Jun 29, 2016 at 9:31 AM, Yannick .Djoumbou > wrote: > > Hi all, > > > > I would like to use RDKit from a Ruby API.Is anyone aware of a well > > maintained rdkit gem for ruby? > > > > Regards, > > > > > -- > > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > > present their vision of the future. This family event has something for > > everyone, including kids. Get more information and register today. > > http://sdm.link/attshape > > ___ > > Rdkit-discuss mailing list > > Rdkit-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.
Hi Riccardo, Thanks for your efforts and sorry that I didn't reply earlier. I am not sure about all the side conditions in order this error to occur but I am glad you can reproduce it. Markus - | Markus Sitzmann | markus.sitzm...@gmail.com > On 30.06.2016, at 08:30, Riccardo Vianello > wrote: > >> On Tue, Jun 28, 2016 at 11:40 PM, Markus Sitzmann >> wrote: >> unfortunately I have another problem - rdkit-postgres isn't building for me >> since the change to Release_2016_03_2. Is that a known problem? > > I tested a couple of full builds and the master branch looks ok, but I could > reproduce this error with the tagged release. I will try to identify the > exact cause. > > Best, > Riccardo > -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Conformer generation does not sample well?
Hi Sereina
Many thanks for investigating this.
Tim
On 29/06/2016 09:29, Sereina wrote:
Hi Tim,
I had a look at the 1DWD example and I detail in the following the
analysis I did as it may be useful to other users.
The conformer generation function has the option to print the
experimental torsion preferences that were used in the generation:
printExpTorsionAngles=True
For 1DWD, it gives the following output:
> ref =
Chem.MolFromSmiles('NC(=[NH2+])c1ccc(C[C@@H](NC(=O)CNS(=O)(=O)c2ccc3c3c2)C(=O)N2C2)cc1’)
> mol1 =
Chem.MolFromPDBFile(RDConfig.RDBaseDir+'/rdkit/Chem/test_data/1DWD_ligand.pdb')
> mol1 = AllChem.AssignBondOrdersFromTemplate(ref, mol1)
> mol1 = Chem.AddHs(mol1)
> numConfs = 100
> cids = AllChem.EmbedMultipleConfs(mol1, numConfs=numConfs,
useExpTorsionAnglePrefs=True, useBasicKnowledge=True,
printExpTorsionAngles=True)
O=[S:1](=O)[NX3H1:2]!@;-[CX4H2:3][!#1:4]: 0 13 14 15, (17.9, -13.3,
9.2, 4.7, -2.3, -0.9)
O=[C:1][NX3H1:2]!@;-[CX4H1:3][H:4]: 15 17 18 48, (5, 0, 0, 0, 0, 0)
[O:1]=[CX3:2]!@;-[NX3H0:3][!#1:4]: 20 19 31 32, (0, 8, 0, 0, 0, 0)
[O:1]=[CX3:2]!@;-[NX3H1:3][!#1:4]: 16 15 17 18, (100, 0, 0, 0, 0, 0)
[c:1][S:2](=O)(=O)!@;-[NX3H1:3][C:4]: 4 0 13 14, (0, 16, 5, 7, 0, 0)
[aH1:1][c:2]([aH1])!@;-[SX4:3][!#1:4]: 3 4 0 13, (0, 1.5, 0, 0, 0, 0)
N[C:2](=[O:1])!@;-[CH2:3][N:4]: 16 15 14 13, (0, 10, 0, 0, 0, 0)
[!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 17 18 21 22, (0, 0, 7, 0, 0, 0)
[NH1:1][CX4:2]!@;-[CX3:3]=[O:4]: 17 18 19 20, (0, 2.1, -0.1, -1, -0.4,
-0.1)
[cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 23 22 21 18, (0, 3.6, 0, 0,
0, 0)
[a:1][c:2]!@;-[C:3](=[N:4]): 25 27 28 30, (0, 5, 0, 0, 0, 0)
[*:1][X3,X2:2]=[X3,X2:3][*:4]: 27 28 30 57, (0, 100, 0, 0, 0, 0)
The output is structured as follows: First comes the SMARTS pattern,
then the indices of the four atoms involved and finally the six force
constants K_1, K_2, K_3, K_4, K_5, K_6 for the torsion potential (see
Eq. (2) in JCIM, 55, 2562, 2015).
The position of the non-zero force constant tells you the multiplicity
i of the cosine. E.g. for the torsion between atoms 18 and 21 the
third force constant is 7.0 and all others are zero, thus the torsion
potential for this bond has a multiplicity i = 3 (i.e. three maxima).
The information about the phase shift is not exposed, but we can
change that if people find it useful.
Currently to get the full information about the torsion potential, you
need to search for the SMARTS pattern in
Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp
There you find the line: "[!#1:1][CX4:2]!@;-[CX4:3][!#1:4] 1 0.0 1 0.0
1 7.0 1 0.0 1 0.0 1 0.0\n"
Here we have twelve parameters, always two for a given multiplicity:
first the phase shift (can be 1 or -1) and second the force constant.
For this particular torsion pattern we have a multiplicity of 3, a
phase shift of cos(d) = 1 and a force constant K_3 = 7.0, which
corresponds to three peaks at 60°, 180° and 300° in the range [0°,
360°] (or -60°, 60° and 180° in the range [-180°, 180°]).
The two bonds connecting the benzamidine ring to the rest of the
molecule are between atoms 22/21 and 21/18.
I calculated the signed dihedral angle for these two bonds, here is
the code for the second one:
> angles = []
> for cid in cids:
>conf = mol1.GetConformer(id=cid)
># torsion of atoms 17 18 21 22
>p1 = conf.GetAtomPosition(17)
>p2 = conf.GetAtomPosition(18)
>p3 = conf.GetAtomPosition(21)
>p4 = conf.GetAtomPosition(22)
>a = Geometry.ComputeSignedDihedralAngle(p1, p2, p3, p4)/math.pi *
180.0
>angles.append(a)
For 100 confs, this gives the following distribution:
So, the torsion potential is sampled as it is supposed to do.
For the other bond between atmos 22/21, we have the following line in
TorsionPreferences.cpp:
"[cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4] 1 0.0 1 3.6 1 0.0 1 0.0 1 0.0
1 0.0\n”
This means, we have a multiplicity of 2, a phase shift cos(d) = 1 and
a force constant of 3.6, which corresponds to two peaks at -120° and
120° in the range [-180°, 180°].
The histogram looks like:
Again, the potential is largely sampled as it’s supposed to be.
Now, let’s have a look at the two bonds connecting atom 18 to the
other two branches.
For the bond between atoms 18/17, we should have a single peak at 0°,
which we get most of the time
The bond between atoms 18/19 has a multi-term potential, which is a
bit more difficult to interpret from the numbers alone.
"[NH1:1][CX4:2]!@;-[CX3:3]=[O:4] 1 0.0 -1 2.1 -1 -0.1 -1 -1.0 1 -0.4 1
-0.1\n"
It has three peaks at -150°, 0° and 150° in the range [-180°, 180°].
The peak at 0° is broad.
The histogram looks like:
For the 100 conformers, the peaks at -150° and 150° are not sampled. I
therefore generated 1000 conformers, but the sampling does not really
improve:
The algorithm of ETKDG takes a randomly generated conformer from
standard distance geometry and minimizes it with the ET and K terms.
For each bond with an exp. torsion term, the tors
