he CIPRanks of the
neighbor atoms. That is why the chirality of the two carbons are different
while their chiral tags are the same.
I am not sure if Lukas had the same question?
Best regards,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
On 10/29/2019 21:14，Alfr
Hi Greg,
Great to know the release!
But the docs for Python API does not work in my browser. It is empty for every
page such as http://rdkit.org/docs/source/rdkit.Chem.AllChem.html
Am I the only one?
Best,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
On 10/25/2019
7;.')
y = mols_from_smiles_list(x) # x is a list of SMILES, and y is a list of
molecule objects
package_results.append(y)
reactants, agents, products = package_results
The code now is not cool enough.
I have no idea with the second question. May I ask where the parameters
threshold_unma
still be checked. (I don't know why)
Finally, I decide to uncheck "Whether to lint python files using pylint" :)
Best,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
On 10/12/2019 14:35，Paolo Tosco wrote：
Hi Hongbin,
Try configuring
extension-pkg-whitel
d and the scripts can run.
I know that it may be caused by the fact that some modules and functions in
RDKit are just wrappers of C++, so pylint may not have recognized these modules
or functions.
But the red wavy line is really offending. Is there any suggestions in addition
to disabling py
'))
product.UpdatePropertyCache()
display(Draw._moltoimg(product, (450, 150), [], legend='mol_1 updated'))
Then you will get the correct products in both aromatic and aliphatic cases.
Best,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
On 10/4/2019 05:04，Sean Str
Hi Sean,
The problem in this case is that in a non-kekulized SMILES, an aromatic
nitrogen atom binding with a hydrogen should be symbolised as “[nH]”. The “H”
is compulsory.
So you can change your reaction into "[#7:1]C(=O)OC(C)(C)C>>[#7H:1]"
Best,
Hongbin Yang 杨弘宾
Hi Axel,
The format like "c11” is implicitly defining the bonds between atoms and
the output of the “canonical” SMILES has redundant ring labels (1 and 2) ,
which I think confused the parser and caused the problem.
I have no idea whether it is a bug or whether it is true reason.
But try th
Hi Tim,
Greg posted a gist on how to generate R-group matrices shortly before.
https://sourceforge.net/p/rdkit/mailman/message/36744886/
Does it help?
Hongbin Yang
发件人: Tim Dudgeon
发送时间: 2019年8月26日 21:08
收件人: rdkit-discuss@lists.sourceforge.net
主题: [Rdkit-discuss] Generating R-group
you
should consider this to “draw” such R-group tables.
Best,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology
On 08/20/2019 17:36，Greg Landrum wrote：
I actually had a bit of
.
Best regards,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
On 08/18/2019 20:23，ken wrote：
Hello,
I am trying to build a 2-D R-group grid (or table, or spreadsheet), where the
row headers contain R1 values and the column headers contain R2 values (or vice
versa
allic compounds ?)
Best regards,
Hongbin Yang 杨弘宾, Ph.D.
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology
___
Rdkit-discuss mailing list
Rdkit-di
Hi, Chris,
? ? Thank you very much for the suggestion. But I tend to tell my fellows to
use?Lipinski' HBA in PP :).
? ? (BTW,?http://www.macinchem.org?is pretty good. I like the website and
thanks for the "advertisement")
Cheers,
Hongbin Yang?
?From:?Chris SwainDate
DKit::getDrawCoordsViaId, "a")
.def("getAtomCoords", RDKit::getAtomCoordsViaId,"b")
;...
(I don't know why I added "a" and "b" and they may not necessary. I am not good
at C++ and boost-python) BTW, I wonder is it possible to
I made a test.?Abacavir have 7 (current edition) and 6 (old)
respectively. And in PP, it also returned these two results).
reference:?http://www.rdkit.org/docs/api/rdkit.Chem.Lipinski-pysrc.html#NumHAcceptors?
Hongbin Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, S
le are using it...
I tried installing cairocffi but nothing worked. Then I installed pycairo
and really, it can anti-aliasing.
Hongbin Yang
From: Paul EmsleyDate: 2017-05-09 19:05To: rdkit-discussSubject: Re:
[Rdkit-discuss] Which package should be used to improve the drawing quality in
win64O
ality?
(rdMolDraw is good, but its not as easy to use as DrawMolecule).
Hongbin Yang?
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http:
Smiles('c1ccc(cc1)-c1nnc(n1)-c1c1',False)` (reference:
http://www.rdkit.org/docs/api/rdkit.Chem.rdmolfiles-module.html#MolFromSmiles)
2. Manually Kekulize it:
`Chem.MolFromSmiles('c1ccc(cc1)-C1=NN=C(N1)-c1c1')` . This indicate the H
is on the 4'N.
Hongbin Yang
So I added the channel via `conda config --add channels bioconda` ,
installed rdkit by `conda install rdkit` and it worked. I found that it
requires boost 1.57.0-4 and thus I guess that 1.56.0 is not well compatible
with rhel5. The cost is that I can not use the lastest version, but it'
](https://github.com/rdkit/rdkit/issues/762 )
user-agent conda/4.3.4 requests/2.12.4 CPython/2.7.12 Linux/2.6.18-308.el5
CentOS/5.8 glibc/2.5
Hongbin Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology
Fr
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