Re: [Rdkit-discuss] delete a substructure

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

Re: [Rdkit-discuss] delete a substructure

olFromSmiles('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

[Rdkit-discuss] delete a substructure

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 =

Re: [Rdkit-discuss] delete a substructure

all 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 > > >

Re: [Rdkit-discuss] delete a substructure

OH) >> >> ((1, 3, 2),) >> >> Since atom "3" has been already matched, it should be ignored. >> So you can create a "set" to record the matched atoms to avoid >> repetitive count. >> >> -- >> Hongb

Re: [Rdkit-discuss] SMARTS for Joback and Reid method

lAcyclic", ">C=O", "[$([CX3H0](=[OX1]));!$([CX3]( >> =[OX1])-[OX2]);!R]=O"}, >> >> {"CarbonylCyclic", ">C=O (ring)","[$([#6X3H0](=[OX1])); >> !$([#6X3](=[#8X1])~[#8X2]);R]=O"}, >> >> {"Aldehyde&quo

[Rdkit-discuss] SMARTS for =C=, #CH, #C-

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- :

Re: [Rdkit-discuss] SMARTS for =C=, #CH, #C-

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 <da...@dalkescientific.com> wrote: > On Nov 8, 2017, at 21:00, Chenyang

Re: [Rdkit-discuss] convert a smiles file to a xyz file

put_files.py > > The xtb input 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 <cs3...@columbia.edu> wrote: > > Hi Everyone, > &g

[Rdkit-discuss] convert a smiles file to a xyz file

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.

Re: [Rdkit-discuss] convert a smiles file to a xyz file

es/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 < > rdkit-discuss@lists.sourcefor

Re: [Rdkit-discuss] segmentation fault 11

> Hi Chenyang, > > This 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, Chenyan

[Rdkit-discuss] GETAWAY descriptors

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

Re: [Rdkit-discuss] [*External*] GETAWAY descriptors

"HATS8p","HATSp","H0i","H1i","H2i","H3i","H4i","H5i","H6i","H7i","H8i","HTi","HATS0i","HATS1i","HATS2i", > > > "HATS3i","HATS4