[Rdkit-discuss] serialization of EditableMol objects ?

Hi all, I use rdkit through its Python API. As part of an iterative computation on a molecule, I have to repeatedly remove different combinations of bonds from it. I noticed that the calls to Chem.EditableMol() to create the em, to em.GetMol() to get back the new molecule, and to

[Rdkit-discuss] Fwd: Possible stereo centers incorrectly assigned?

Hi John, Michal, and everyone, I've been following this discussion with interest and wrote a code snippet to test out John M.'s idea to access the '_CIPCode' property of atoms. The results of doing are opposite to the result of the original getStereoInfo() function, and thus are in accord with

[Rdkit-discuss] Fwd: Chem.Descriptors.ExactMolWt

Hi RDKit users, Should we expect the ExactMolWt() function from the Descriptors module to know about the mass of electrons? I initially expected that it would, and thus was surprised by this behavior: > > > > > > > > > > *proton_smiles = '[H+]'proton = >

[Rdkit-discuss] isotopic SMILES

Hellow rdkit users, What behavior should we expect for Chem.MolToSmiles() when dealing with isotopically substituted molecules? I am confused by this behavior: >>> labeled_etoh = Chem.MolFromSmiles('C[13C]O') >>> print(Chem.MolToSmiles(labeled_etoh)) C[C]O >>>

Re: [Rdkit-discuss] isotopic SMILES

I think you've persuaded me that .SetIsotope() is the way to go... I don't understand how that avoids any problem. How do you specify the > target atom for that case? > In any case, won't the InChI normalization affect some of your structures > (e.g., detaching metals) and make it even harder to

Re: [Rdkit-discuss] isotopic SMILES

I replied to Andrew's very nice discussion of implicit hydrogens in SMILES but forgot to include the whole list. Wow, thank you, that was very useful. I didn't realize those nuances of > SMILES. > > On the rdkit "side", the distinction made in Smiles between implicit and > explicit hydrogens

Re: [Rdkit-discuss] Kekulizing thiazoles

](=[O:6])[C:7][Cl:8]>>[N:4][c:2]1[s:3][c:5][c:7][n:1]1' rxn = AllChem.ReactionFromSmarts(rxn_smarts) product = rxn.RunReactants((thiourea, haloketone))[0][0] Chem.SanitizeMol(product) Chem.MolToSmiles(product) Out[33]: 'Cc1nc(N(C)C)sc1-c1c1' On Tue, Jan 17, 2017 at 9:29 AM, Curt F

Re: [Rdkit-discuss] a SMILES that rdkit cannot read

> I ran it in jupyter via browser. Both docker/ubuntu and windows were > tested and found that jupyter won't give error. Ipython or python in > terminal(cmd) would show this error. > > That problem is related to how Jupyter interacts with python kernels. It's not an RDKit issue. If you check the

Re: [Rdkit-discuss] (no subject)

Hi Markus, I suspect the problem is that your SMARTS query is not as specific as you might think. For example, RDKit does not understand how many rings there are in your SMARTS query. Each [a] could be an atom arbitrarily connected to many other rings that wouldn't be a part of the substructure

Re: [Rdkit-discuss] (no subject)

Last week, Greg gave us a nice example of substructure matching using a SMARTS query (see below). I learned a lot from this thread, not the least of which was to use the IPythonConsole module and to enable SVG for beautiful drawings. This style is indeed much better than the old drawings. I was

Re: [Rdkit-discuss] new rdkit-tutorial repository

I think this is an amazing idea. Thanks for starting it Greg! I'm looking forward to porting some of my own self-tutorial Jupyter notebooks into this repo. Curt On Sat, Oct 8, 2016 at 10:33 PM, Greg Landrum wrote: > Dear all, > > Based on a bunch of feedback I've

Re: [Rdkit-discuss] conda / Windows update to 2016.09 release gives error

command, it identified the proper boost to install along with the 2016.03 rdkit. I now have a functioning rdkit again, but would still be interested in hearing from anyone that experiences a similar problem. On Thu, Dec 8, 2016 at 9:27 AM, Curt Fischer <curt.r.fisc...@gmail.com> wrote: >

[Rdkit-discuss] UpdatePropertyCache() after RunReactants

Hi all, I recently wanted to use RDKit to model the famous copper-catalyzed cycloaddition of alkynes and azides. I eventually got things working, kind of, but had two questions. First, I was surprised to find that the products of RunReactants don't have update property caches. Is this

Re: [Rdkit-discuss] UpdatePropertyCache() after RunReactants

kit.org/docs/GettingStartedInPython.html# > chemical-reactions : "the molecules that are produced by the chemical > reaction processing code are not sanitized". > > Best, > Michal > > On 12 January 2017 at 17:22, Curt Fischer <curt.r.fisc...@gmail.com> > wrote: >

Re: [Rdkit-discuss] SD file read error

I also got this to run with no problem in a Jupyter notebook. BUT...I did see the error messages Milinda mentioned in the terminal that was running the jupyter notebook server. If I do *from rdkit.Chem.Draw import IPythonConsole *before running the code, I see all the errors/warnings in Jupyter.

Re: [Rdkit-discuss] File Conversion?

This is not really possible. Fasta files contain only sequence information, not 3D structural information. Curt On Sun, Dec 4, 2016 at 7:00 AM, Carl MacGentey wrote: > Dear RDKit Discussion Group- > > > > Is it possible to convert fasta files (DNA nucleotide sequences)

Re: [Rdkit-discuss] Fwd: conda / Windows update to 2016.09 release gives error

.path.join(*condaDir) > > I think it should work. > > Sorry for the inconvenience here; we will fix it before running the next > conda builds. > > -greg > > > On Wed, Jan 4, 2017 at 1:44 AM, Curt Fischer <curt.r.fisc...@gmail.com> > wrote: > >> >>

[Rdkit-discuss] Fwd: conda / Windows update to 2016.09 release gives error

.path.join(condaDir) > > This causes the AttributeError because it incorrectly passes a list to > os.path.join, with no asterisk for unpacking the list into *args. The first > line is also incorrect. > > I built the package myself from the recipe, and didn't see this issue. > > Matt >

Re: [Rdkit-discuss] numpy array to bit vector

If you are looking for something quick and dirty, you could stay in numpy to calculate Tanimoto. *from rdkit import Chem* *from rdkit.Chem import AllChem* *import numpy as np* *from __future__ import division* *mol1 = Chem.MolFromSmiles('CCO')* *mol2 = Chem.MolFromSmiles('CCC')* *fp1 =

Re: [Rdkit-discuss] numpy array to bit vector

Hi Greg, On Thu, Mar 16, 2017 at 9:05 PM, Greg Landrum wrote: > I'm a bit confused by all this. The RDKit has Tanimoto (and a bunch of > other similarity measures) built in: > > Good point (as always). I'd been assuming that for some reason that OP had fingerprints that

[Rdkit-discuss] forcing better depictions for macrocycles

Hi RDKit community, RDKit's default 2D-depictions of macrocycles are very "round". I found some slides from John Mayfield that come from a 2016 UK RDKit user group meeting that says the same thing.

Re: [Rdkit-discuss] Check If Atom Is in Two Small Rings

Brian's solution is obviously better (shorter, uses less functions) than mine. (Although mine assumes that you want atoms that are part of _exactly_ two rings, not atoms that are part of _at least_ two rings as Brian's does. Probably Brian's solution is what you want but worth noting.) CF On

Re: [Rdkit-discuss] forcing better depictions for macrocycles

D* objects instead of Point2D objects, so I'm not sure how I can get *Point2D* objects. Help appreciated! Curt On Wed, Apr 5, 2017 at 12:38 AM, Greg Landrum <greg.land...@gmail.com> wrote: > Hi Curt, > > > On Tue, Apr 4, 2017 at 12:03 PM, Curt Fischer <curt.r.fisc...@gmai

Re: [Rdkit-discuss] Information contained in SMARTS and SMILES

Hi Thilo, Interesting question. rdkit-discuss members should know you also posted a very similar question to https://chemistry.stackexchange.com/questions/72880/is-converting-smarts-to-smiles-a-lossless-operation . If an interesting answer materializes here, it would be useful to post it there,

[Rdkit-discuss] difficulties with AllChem.EmbedMultipleConfs() on a macrocycle

Hi all, I really like combination of rdkit and py3dmol and have been able to replicate e.g. Greg's notebook here: http://nbviewer.jupyter.org/github/greglandrum/rdkit_blog/blob/master/notebooks/Trying%20py3Dmol.ipynb But I can't seem to get AllChem.EmbedMultipleConfs() to generate any valid

Re: [Rdkit-discuss] difficulties with AllChem.EmbedMultipleConfs() on a macrocycle

As this occurs with both DG and ETKDG, it may be due to the tests to ensure > that the chiral centers are correct. I will have a closer look (hopefully > with Greg’s help). > > Best, > Sereina > > > > > > On 02 Mar 2017, at 19:34, Curt Fischer <curt.r.fisc...@gmail

Re: [Rdkit-discuss] Announce: RDKit for Excel.

This is great! Thanks Jan. I haven't tried it yet, but based on the GitHub README it looks like this is only for Excel on a Windows box. Is that right, or can Mac versions of Excel also work? And since it's come up on the mailing list recently, is there a plan to expand to/move to Python 3 at

Re: [Rdkit-discuss] difficulties with AllChem.EmbedMultipleConfs() on a macrocycle

lChem.EmbedMolecule(mh,ps) >> Out[17]: -1 >> >> >> >> I'm not sure that there's a straightforward solution to this problem >> without code changes, but I'll do a bit of looking to see if I can figure >> something out. >> >> -greg >> >> &g

Re: [Rdkit-discuss] nitro-compounds from smarts

Rafal, > this three Mols (m1, m2, m33) below should all represent nitrobenzene, > right? > >>> m33=Chem.MolFromSmarts('c1c1[N+](=O)[O-]') > >>> m1=Chem.MolFromSmiles('c1c1[N+](=O)[O-]') > >>> m2=Chem.MolFromSmiles('c1c1N(=O)(=O)') > I guess m33 represents nitrobenzene in a sense,

Re: [Rdkit-discuss] bad inchi or parsing problem?

I'm not 100% sure about this particular case, but I suspect this is a limitation of InChI. For example, the InChI representation of zwitterionic phenylalanine (negative COO-, positive NH3+) and "neutral" phenylalanine (neutral COOH, neutral NH2) is exactly the same. This is by design. See

Re: [Rdkit-discuss] suggestions for comprehensive searchable database of natural products

I'd also be interested in Juptyer notebooks for this. Thanks Tyler! Curt On Tue, Nov 28, 2017 at 8:26 AM, Tyler Backman wrote: > Hi Jim, > > MiBIG is a useful database of natural product gene clusters and > structures, which you can download in JSON format here, and use

Re: [Rdkit-discuss] two rdkit versions, always one is used

I find it also helps to install nb_conda in all the conda environments that I use Jupyter in. What happens when you do jupyter kernelspec list ? Curt On Wed, Oct 25, 2017 at 8:29 AM, Greg Landrum wrote: > Hopefully you are using conda environments and not virtual envs,

[Rdkit-discuss] multiple SMARTS that match only if in the same fragment

Hi rdkit fiends! The [Daylight SMARTS example page]( https://daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html) gives several examples for "multiple group" smarts, including these strings: ([Cl!$(Cl~c)].[c!$(c~Cl)]) ([Cl]).([c]) ([Cl].[c])

Re: [Rdkit-discuss] multiple SMARTS that match only if in the same fragment

nt level grouping requiring matches in different components, >>i.e. (C).(C) >> >> OK, the way it's worded it sounds like (C.C) might be supported (since > that would be requiring matches in the same component), but as you've seen, > it isn't supported either... > > Ivan