Re: [Rdkit-discuss] How to calculate Tanimoto similarity score between reactions
On 10/06/2020 13:11, 丁邵珍 wrote:
Hi, I want to calculate Tanimoto similarity score of two reactions
('CCCO>>CCC=O', 'CC(O)C>>CC(=O)C'), I found all methods of Tanimoto
similarity score calculation are for compounds. Could you please tell
me how to calculate the Tanimoto similarity score of reactions? I am
looking forward to your reply.
I don't know how to do it in rdkit, but if you need some inspiration,
here is how chemaxon does it:
https://docs.chemaxon.com/display/docs/Reaction_fingerprint_RF.html
Yours,
shaozhen
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[Rdkit-discuss] trying to figure out what an rdkit warning means
Hello,
Below I show a smiles string from MOE and the smiles string calculated from
RDKit and the InChI string calculated by RDkit(2020_1).
The error on conversion to inchi string is confusing me after entering both
smiles strings into a viewer I don't see any undefined stereo center.
O=C(/C=C/c1c1)c1ccc(OC/C=C(/CC/C=C(\C)/C)\C)cc1
CC(C)=CCC/C(C)=C/COc1ccc(C(=O)/C=C/c2c2)cc1
[18:10:42] WARNING: Omitted undefined stereo
InChI=1S/C25H28O2/c1-20(2)8-7-9-21(3)18-19-27-24-15-13-23(14-16-24)25(26)17-12-22-10-5-4-6-11-22/h4-6,8,10-18H,7,9,19H2,1-3H3
while len(line) != 0:
fields = line.replace('","',' ').split()
mol1 = fields[0].replace('"','')
mol_name = fields[1]
try:
mol = Chem.MolFromSmiles(mol1,sanitize=False) #, removeHs=False)
except:
mol = None
if mol is None:
print("mol1 failed:",mol1)
output.write("mol1 failes:",mol1)
else:
rkditsmiout.write('\"'+Chem.MolToSmiles(mol,
isomericSmiles=True)+'\"\n')
print(Chem.MolToSmiles(mol, isomericSmiles=True))
rkditsmiout.write('\"'+Chem.inchi.MolToInchi(mol)+'\"\n')
print(Chem.inchi.MolToInchi(mol))
count += 1
print(count)
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Re: [Rdkit-discuss] Scalability of Postgres cartridge
Thank you everyone for the suggestions. For now I don't have immediate plans to adopt the cartridge but it's good to know these things when the time comes. Best, Ivan On Mon, Jun 8, 2020 at 6:49 PM Finnerty, Jim via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > If you have a billion molecule data source and would like to try an > at-scale test, I'd be willing to help out with provisioning the hardware, > looking at the efficiency of the plans, etc., using rdkit with Aurora > PostgreSQL. > > If I understand how the rdkit GIST index filtering mechanism works for a > given similarity metric, a parallel GIST index scan ought to be able to > scale almost linearly scale with the number of cores, provided that the > RDBMS is built on a scalable storage subsystem. > > If so, the largest instance size that's currently supported has 96 cores, > so we can do a fairly high degree of parallelism. > > On 6/5/20, 1:07 PM, "dmaziuk via Rdkit-discuss" < > rdkit-discuss@lists.sourceforge.net> wrote: > > CAUTION: This email originated from outside of the organization. Do > not click links or open attachments unless you can confirm the sender and > know the content is safe. > > > > On 6/5/2020 4:45 AM, Greg Landrum wrote: > > > Having said that, the team behind ZINC used to use the RDKit > cartridge with > > PostgreSQL as the backend for ZINC. They had the database sharded > > across multiple instances and managed to get the fingerprint indices > to > > work there. I don't remember the substructure search performance > being > > terrible, but it wasn't great either. They have since switched to a > > specialized system (Arthor from NextMove software), which offers > > significantly better performance. > > Generally speaking a database of a billion rows needs hardware capable > of running it. Buy a server with 1TB RAM and 64 cores and a couple of > U.2 NVME drives and see how Postgres runs on that. > > Then you need to look at the database, e.g. query in an indexed > billion-row table could be OK but inserting a billion-first row will > not be. > > If you want to scale to these kinds of volumes, you need to do some > work. > > (And much of the point of no-sql hadoop "cloud" workflows is that if > you > can parallelize what you're doing to multiple machines, at some data > size they will start outperforming a centralized fast search engine.) > > Dima > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] SMART reaction for closing rings
Thank you so much! It helps me a lot
On Tue, Jun 9, 2020 at 6:24 PM Greg Landrum wrote:
> Hi Shani,
>
> If you have mapped atoms in the reactants that are not in the products,
> those end up being removed
>
> I'm not sure exactly what reaction you're trying to do, but I think you
> want something like this;
>
> rxn =
> AllChem.ReactionFromSmarts("([C:1]=[C:2].[*:3][*+:4])>>[*:2]-[*:1][*+0:4][*:3]")
> m1 = Chem.MolFromSmiles('C=CC([CH2+])CCC=C(C)C')
> ps = rxn.RunReactants((m1,))
> for p in ps: print(Chem.MolToSmiles(p[0]))
>
> Note that I also explicitly neutralized the carbocation in the products.
> Otherwise the +1 from the reactants would be carried over.
>
> -greg
>
>
> On Tue, Jun 9, 2020 at 4:42 PM Shani Levi wrote:
>
>> Hello,
>> I'm interested in using AllChem.ReactionFromSmarts to predict product for
>> a specific reaction.
>> For example, I want to describe the reaction between double bonds and a
>> carbo-cations.
>>
>> *I tried: *
>> rxn = AllChem.ReactionFromSmarts("([C:1]=[C:2].[*:3][*+:4])>>[*:1][*:4]")
>> m1 = Chem.MolFromSmiles('C=CC([CH2+])CCC=C(C)C')
>> ps = rxn.RunReactants((m1,))
>>
>> *and it gave me four molecules: *
>>
>> [CH2+]C [CH2+]C [CH2+]CCC
>> [CH2+]C(C)C
>>
>> the problem here that it does not describe the ring-closure molecules and
>> it somehow cuts the rest of the molecule, if someone has any suggestions of
>> how to change the SMARTS descriptions that it will define the right
>> reaction.
>>
>> Thank you very much,
>> Shani
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