"HATS8p","HATSp","H0i","H1i","H2i","H3i","H4i","H5i","H6i","H7i","H8i","HTi","HATS0i","HATS1i","HATS2i",
>
>
> "HATS3i","HATS4
Hi everyone,
I hope to calculate the R3m descriptor which is among a family of GETAWAY
descriptors originally proposed by this paper
https://pubs.acs.org/doi/pdf/10.1021/ci015504a .
I tried writing some code as below to calculate it but obtained with a
Python list of a length of 273. I also teste
ut is simple an xyz file with some additional lines below if
> the molecule is charged. You can simply those lines in the code.
>
> Best regards, Jan
>
> On 23 May 2018, at 17:23, Chenyang Shi wrote:
>
> Hi Everyone,
>
> I am seeking helps about how to convert a SMILES fi
several challenges/nonuniqueness in going from
> SMILES to 3D. Some of the conformer search tools in the link can help a
> little bit, but in general it's a tricky problem.
>
> Best,
> Ben
>
> On Wed, May 23, 2018 at 10:30 AM, Dimitri Maziuk via Rdkit-discuss <
> rdki
Hi Everyone,
I am seeking helps about how to convert a SMILES file to a series of
coordinates for the molecule, in the format of xyz.
I saw some online service that can do the job (e.g.
http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html),
but it is not convenient to use.
;>
>> {"EtherAcyclic", "-O-", "[OX2H0;!R;!$([OX2H0]-[#6]=[#8])]"},
>>
>> {"EtherCyclic", "-O- (ring)", "[#8X2H0;R;!$([#8X2H0]~[#6]=[#8])]"},
>>
>> {"CarbonylAcyclic", ">C=O", "[$([C
Hi everyone,
I have been recently working on a project that implements Joback method
using RDKit (https://en.wikipedia.org/wiki/Joback_method).
I believe the core to the success of this project is to make the 41
functional groups correctly represented by SMARTS code. I have compiled my
own codes,
Dear Andy,
Thank you for a quick and thorough email. I find it very instructional,
although I need to read it a couple times more to digest it.
Cheers,
Chenyang
On Wed, Nov 8, 2017 at 2:27 PM, Andrew Dalke
wrote:
> On Nov 8, 2017, at 21:00, Chenyang Shi wrote:
> > =C= : [CH
Dear RDKitters,
I have a question regarding SMARTS codes for three simple functional
groups, these are =C=, #CH and #C-. I am new to SMARTS/SMILES. I indeed
tried to guess their codes. Here are my guesses:
=C= : [CH0;A;X2;!R](=[$(*)])=[$(*)]
#CH : [CH1;A;X2;!R]#[$(*)]
#C- : [CH0;A;X2;!R]#[$(*)
his looks like the breakage caused by conda v4.3.27. There's some more
> information here:
> https://www.mail-archive.com/rdkit-discuss@lists.
> sourceforge.net/msg07325.html
>
> Best,
> -greg
>
>
> On Sat, Oct 28, 2017 at 5:27 AM, Chenyang Shi wrote:
>
>> Hi
Thank you Chris. I found that one too; it is quite convenient to visualize
both SMARTS and SMILES strings.
On Thu, Mar 9, 2017 at 11:28 AM, Chris Swain wrote:
> I use SMARTSviewer at Univ of Hamburg
>
> http://www.zbh.uni-hamburg.de/en/bioinformatics-server.html
>
> Chris
>
> On 9 Mar 2017, at 1
'CC1=CC(=C(C=C1)C(=O)O)O')
> m.GetSubstructMatches(Chem.MolFromSmiles('[$(Oc)]'))
> >>> ((10,),)
>
> Then only atom *10* will be matched and it won't interfere with other
> counts.
>
> Reference: http://www.daylight.com/dayhtml/doc/theory/theory.
; has been already matched, it should be ignored.
>> So you can create a "set" to record the matched atoms to avoid
>> repetitive count.
>>
>> --
>> Hongbin Yang 杨弘宾
>>
>>
>> *From:* Chenyang Shi
>>
>> *D
of
> the groups in your list?
>
> If you actually want to remove them, you are probably better off using the
> chemical reaction functionality instead of DeleteSubstructs(), which
> recalculates the number of implicit Hs on atoms after each call.
>
> -greg
>
>
> On Mon, M
Hi everyone,
I am new to rdkit but I am already impressed by its vibrant community. I
have a question regarding deleting substructure. In the RDKIT
documentation, this is a snippet of code describing how to delete
substructure:
>>>m = Chem.MolFromSmiles("CC(=O)O")
>>>patt = Chem.MolFromSmarts("C(
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