Re: [Rdkit-discuss] rdkit & Coordination chemistry on Mg

[Marco Stenta]

Thanks, Jan,
the dative bond works in a number of cases with other metals. (rdkit
2021.9.5)
This one works fine:

rdmol = Chem.MolFromSmiles('[O-]->[Fe+2]<-[O-]', sanitize=True)  #
case 1 coordinate bonds
assert rdmol is not None

this one with Mg divalent does not

rdmol = Chem.MolFromSmiles('[O-]->[Mg+2]<-[O-]', sanitize=True)  #
case 1 coordinate bonds
assert rdmol is not None



can you read in the smiles you sent me? I can't
I am doing anything wrong here?
cheers,
m

rdmol = Chem.MolFromSmiles('C1CO->[Fe+2](O)(<-OC1)(<-O)(<-O)(<-O))=O',
sanitize=True)  # case 1 coordinate bonds
assert rdmol is not None
print(rdmol)


Il giorno mar 22 mar 2022 alle ore 15:13 Jan Halborg Jensen <
jhjen...@chem.ku.dk> ha scritto:

> Hi Marco
>
> You can define dative bonds like
> this: C1CO->[Fe+2](O)(<-OC1)(<-O)(<-O)(<-O)
>
> Best regards, Jan
>
> On 22 Mar 2022, at 15.07, Marco Stenta  wrote:
>
> You don't often get email from marco.ste...@gmail.com. Learn why this is
> important <http://aka.ms/LearnAboutSenderIdentification>
> Dear RDKitters,
> I am struggling with working organometals and coordination complexes.
> with a small team, we are creating a series of recommendations to draw
> correctly organometals (catalyst, complexes, etc), so that we can use them
> in our chemoinformatics pipeline.
>
> I know it is a horrible mess out there, but we are trying to achieve some
> consistency, rather than full correctness.
>
> I guess there is something with the accepted valence for Mg.
>
> Now the purpose of this is to have a smiles representation of these metal
> complexes that are not fragmented (with the dot) so that I keep the notion
> of bond where there is (or I believe) one
>
> for instance, for the edta complex this smiles works fine:
> [Na+].[Na+].[Mg++].[O-]C(=O)CN(CCN(CC([O-])=O)CC([O-])=O)CC([O-])=O
>
> but I would really distinguish the fact that there is a bond between the
> [O-]/N and the [Mg++ ] while there is none with the two [Na+]
>
> 
> I can read it in without sanitization, but it fails for everything I
> nato to do after with the molecules.
>
>
> in theory, dative bonds should not affect the valence of receiving atoms,
> right?
>
> any suggestion for reading in the enclosed v3000 molfile and keeping the
> bonding info?
> or sharing what you are doing with metals
>
> Thanks a lot in advance,
>
> kind regards
>
> Marco
>
> f1 = 'edta_case.mol'
>
> rdmol = Chem.MolFromMolFile(f1, sanitize=True)
> print(rdmol)
> Chem.MolToSmiles(rdmol)
>
>  the rdmol is None in my case
>
>
>
>
>
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[Rdkit-discuss] rdkit & Coordination chemistry on Mg

[Marco Stenta]

Dear RDKitters,
I am struggling with working organometals and coordination complexes.
with a small team, we are creating a series of recommendations to draw
correctly organometals (catalyst, complexes, etc), so that we can use them
in our chemoinformatics pipeline.

I know it is a horrible mess out there, but we are trying to achieve some
consistency, rather than full correctness.

I guess there is something with the accepted valence for Mg.

Now the purpose of this is to have a smiles representation of these metal
complexes that are not fragmented (with the dot) so that I keep the notion
of bond where there is (or I believe) one

for instance, for the edta complex this smiles works fine:
[Na+].[Na+].[Mg++].[O-]C(=O)CN(CCN(CC([O-])=O)CC([O-])=O)CC([O-])=O

but I would really distinguish the fact that there is a bond between the
[O-]/N and the [Mg++ ] while there is none with the two [Na+]

[image: image.png]
I can read it in without sanitization, but it fails for everything I
nato to do after with the molecules.


in theory, dative bonds should not affect the valence of receiving atoms,
right?

any suggestion for reading in the enclosed v3000 molfile and keeping the
bonding info?
or sharing what you are doing with metals

Thanks a lot in advance,

kind regards

Marco

f1 = 'edta_case.mol'

rdmol = Chem.MolFromMolFile(f1, sanitize=True)
print(rdmol)
Chem.MolToSmiles(rdmol)

 the rdmol is None in my case


edta_case.mol
Description: Binary data
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[Rdkit-discuss] rdkit and pip

[Marco Stenta]

Dear Colleagues,
I recently came across this
https://pypi.org/project/rdkit-pypi/

is pip going to be supported officially by the dev community? any plan?
getting out of the conda dependency might be beneficial to get
slightly slimmer docker images.

Thanks

cheers,
m
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Re: [Rdkit-discuss] proper technical term for generating virtual compounds with rdkit and smarts

[Marco Stenta]

Hi Folks,
We are building a tool that generates libraries of compounds based on a
list of reactants and a set of compatible reactants, and allows selection
of the products.
 We define the process as "product-based reactant selection" from an old
paper (at the end of the day we need to make these compounds!)
We call the product "Library Design Tool" considering the Design composed
of generation (enumeration) and selection phases.
Our people got used to the term reaction-based enumeration (but I am not
sure if they still distinguish from R-Group-Enumeration), virtual products
and the like, but in hindsight in silico synthesis ... definitely not bad.

Cheeers,
m

Il giorno ven 25 set 2020 alle ore 15:26 Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> ha scritto:

> We use "reaction-based enumeration" to distinguish it from "R-group
> enumeration". Both are types of virtual library enumeration.
>
> R-group enumeration allows you to attach any R-group anywhere. It is
> simple and fast but you can easily create implausible (or hard to
> synthesize) molecules if you are not careful.
>
> Reaction-based enumeration at least guarantees that you already have
> reactants with the right functional groups in the right places, and if you
> make your reactions sophisticated enough you can even check for other
> disqualifying conditions such as interfering functional groups.
>
> Of course in a context where it is not immediately obvious that you are
> talking about doing it on a computer, I suppose something along the lines
> of "virtual reaction-based enumeration" might make sense.
>
> Best,
> Ivan
>
>
> On Fri, Sep 25, 2020 at 4:26 AM Thomas Strunz 
> wrote:
>
>> Hi Brian,
>>
>> commercial tools usually use the term "reaction-based enumeration" or
>> "reaction-based library design".
>>
>> Best Regards,
>>
>> Thomas
>>
>> --
>> *Von:* Bennion, Brian via Rdkit-discuss <
>> rdkit-discuss@lists.sourceforge.net>
>> *Gesendet:* Freitag, 25. September 2020 07:19
>> *An:* RDKit Discuss 
>> *Betreff:* [Rdkit-discuss] proper technical term for generating virtual
>> compounds with rdkit and smarts
>>
>> hello
>>
>> I have a paper in review and is intended for a large audience that has
>> synthetic chemists, biologist and comp chem.
>> One reviewer had issues with the term in-silico syntheses.
>> I used rdkit and smarts reactions to generate large libraries of
>> compounds for our research project.  Is there a better term to use?  I feel
>> "chemical enumeration" is just as foreign.
>>
>> The abstract is below.
>>
>> The current standard treatment for organophosphate poisoning primarily
>> relies on the use of small molecule-based oximes that can efficiently
>> restore acetylcholinesterase (AChE) activity.  Despite their efficacy in
>> reactivating AChE, the action of drugs like 2-pralidoxime (2-PAM) is
>> primarily limited to the peripheral nervous system (PNS) and, thus,
>> provides no protection to the central nervous system (CNS).  This lack
>> of action in the CNS stems from the ionic nature of the drugs; they
>> cannot cross the blood-brain barrier (BBB) to access to any nerve
>> agent-inhibited AChE therein.  In this report, we present a small
>> molecule oxime, called LLNL-02, that can diffuse across the BBB for
>> reactivation of nerve agent-inhibited AChE in the CNS.  Our 
>> candidate-development
>> approach utilizes a combination of parallel chemical and in - silico
>> syntheses, computational modeling, and a battery of detailed in vitro
>> and in vivo assessments that have identified LLNL-02 as a top CNS-active 
>> candidate
>> against nerve agent poisoning.   Additional experiments to determine acute
>> and chronic  toxicity as required for regulatory approval are ongoing.
>>
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[Rdkit-discuss] oxidation number

[Marco Stenta]

Dear RDKitters,
I am devising some metrics to score chemical routes for my colleagues in
process chemistry.
One such metrics involves the usage of the atomic oxidation number
https://www.periodni.com/oxidation_numbers_calculator.php
I have a python script that does it, using an electro-negativity table,
rather than rules or smarts,
but it is not very elegant or efficient...

Did any of you use it, or are interested in this? What about having this as
an atomic property? Worth asking it as a new feature of rdkict?

Cheers,
Marco







Mail
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[Rdkit-discuss] Sayle tautomer hash in RDKit

[Marco Stenta]

Dear Colleagues,
I recently came across some notes from Noel and Roger about this molecular
hashing.

https://baoilleach.blogspot.com/2018/01/implementing-sayle-tautomer-hash-with.html
https://nextmovesoftware.com/blog/2013/04/25/finding-all-types-of-every-mer/#footnote-1
https://nextmovesoftware.com/blog/2016/06/22/fishing-for-matched-series-in-a-sea-of-structure-representations/

Noel implemented it fr pybel (first link) and I would like to implement it
for RDKit, but somehow I do not get the same results as Noel. here below my
code
What is that I get wrong?

Thanks a lot for your help. I will post the solution as a comment to Noel's
blog post once we have one.

Cheers,
m


from rdkit import Chem
from rdkit.Chem import AllChem

def tautomerhash(smi):
rdmol = Chem.MolFromSmiles(smi)
m = Chem.RemoveHs(rdmol)
formalcharges = 0
hcount = 0

for atom in m.GetAtoms():
formalcharges += atom.GetFormalCharge()
atom.SetFormalCharge(0)
if atom.GetAtomicNum() != 6: # non-carbon
hcount += atom.GetNumImplicitHs()
atom.SetNoImplicit(True)
atom.SetIsAromatic(False)

for bond in m.GetBonds():
bond.SetBondType(Chem.rdchem.BondType.SINGLE)
bond.SetIsAromatic(False)

#rmol.SetAromaticPerceived() # no point triggering perception
s = Chem.MolToSmiles(m,canonical=True)

o = "%s_%d" % (s, hcount-formalcharges)
#print (hcount, formalcharges, hcount-formalcharges, s)
return o


if __name__ == "__main__":
smis = ["*c1c(c(C(=N)O)cc2nc([nH]c12)C(=O)[O-])N(=O)=O",
"*c1c(c(C(=O)N)cc2[nH]c(nc12)C(=O)O)[N+](=O)[O-]"]


#smis = ['N#[O+]', 'O=[N]']
for smi in smis:
print(smi, tautomerhash(smi))
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Re: [Rdkit-discuss] RDKIT 2018.3 and MMPDB problem

[Marco Stenta]

Dear Andrew,
I had some time to set an environment for it and test it: it works fine, as
far as my tests go. I will switch to this version and to the latest RDKIT
now.

Thanks a lot for your help.

some questions:
Is there any plan to:
include MCS as a fragmentation method?
extend to matched series?
include "fuzzy" environment definitions based on pharmacophores (as BI
people did)?

I am currently using the database file to explore the rules mainly via
visual inspection through spotfire by means of a series of joins to
generate suitable tables: would anybody be interested in this (also helping
improving it)?

Cheers,
marco

2018-05-07 14:50 GMT+02:00 Taka Seri :

> Dear Andrew,
>
> I installed following version of mmpdb with new version of rdkit.
> And it worked fine!
> I appreciate your work.
> Kind regards,
>
> Takayuki
>
> On Apr 27, 2018, at 00:20, Andrew Dalke  wrote:
> > Please try out:
> >  http://dalkescientific.com/mmpdb-2.1b1.tar.gz
> >
> > or my fork at:
> >  https://github.com/adalke/mmpdb
> >
> > and let me know of any problems.
>
> Has anyone downloaded and tested this code? I would like to push it to the 
> main
> repository and start the process of doing a new release.
>
> Cheers,
>
>
> 
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[Rdkit-discuss] RDKIT 2018.3 and MMPDB problem

[Marco Stenta]

Dear Colleagues,
I just installed on conda env the new rdkit version
 and wanted to try mmpdb but upon testing I got the error below
reverting back to rdkit=2017.09.3.0 it works fine (I still get some errors
but it goes thrugh)

It is a bug, am I doing anything obviously wrong?

Any help will be higly appreciated.

Cheers,
Marco


#details of my environment
#conda 4.4.10
conda create --name mmpdb_env python=3.6
source activate mmpdb_env

conda install -c rdkit rdkit

git clone https://github.com/rdkit/mmpdb.git
cd mmpdb/
python setup.py install

git clone https://github.com/rogerbinns/apsw.git
cd apsw
python setup.py fetch --all build --enable-all-extensions install test

git clone https://github.com/rogerbinns/apsw.git
cd apsw
#python setup.py fetch --all build --enable-all-extensions install test
#does not fetches from where I am: use this instead  (no amalgamation or
download of sqlite, for headers, etc)
python setup.py  build --enable-all-extensions install test
python test.py

https://github.com/esnme/ultrajson.git
cd ultrajson
python setup.py install




mmpdb fragment test_data.smi -o test_data.fragments
Failure: file 'test_data.smi', line 1, record #1: first line is 'Oc1c1
phenol'
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/multiprocessing/pool.py",
line 119, in worker
result = (True, func(*args, **kwds))
  File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/do_fragment.py",
line 363, in _as_list
return list(method(normalized_mol, fragment_filter,
num_normalized_heavies))
  File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/fragment_algorithm.py",
line 690, in fragment_mol
for x in _fragment_mol(mol, fragment_filter, num_heavies):
  File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/fragment_algorithm.py",
line 722, in _fragment_mol
for fragmentation in fragmentations:
  File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/fragment_algorithm.py",
line 368, in make_single_cut
constant_smiles_with_H = replace_wildcard_with_H(constant_smiles)
  File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/fragment_algorithm.py",
line 302, in replace_wildcard_with_H
assert smiles.count("[*]") == 1, smiles
AssertionError: *O
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/u776341/.conda/envs/mmpdb_env/bin/mmpdb", line 10, in 
commandline.main()
  File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/commandline.py",
line 988, in main
parsed_args.command(parsed_args.subparser, parsed_args)
  File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/commandline.py",
line 173, in fragment_command
do_fragment.fragment_command(parser, args)
  File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/do_fragment.py",
line 531, in fragment_command
writer.write_records(records)
  File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/fragment_io.py",
line 396, in write_records
for rec in fragment_records:
  File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/site-packages/mmpdblib/do_fragment.py",
line 433, in make_fragment_records
fragments = result.get()
  File
"/home/u776341/.conda/envs/mmpdb_env/lib/python3.6/multiprocessing/pool.py",
line 644, in get
raise self._value
AssertionError: *O











#revert rdkit back
conda install -c rdkit rdkit=2017.09.3.0


python test_fragment.py

[10:03:40] SMARTS Parse Error: syntax error for input: 'Q4'
...[10:03:42] SMARTS Parse Error: syntax error for input: 'Q4'
[10:03:42] SMILES Parse Error: syntax error for input:
'Oc1c1O,record'
.[10:03:42] SMILES Parse Error: syntax error for input: 'Oc1c1O,record'
.[10:03:42] SMILES Parse Error: syntax error for input: 'Oc1c1O,record'
.[10:03:42] SMILES Parse Error: syntax error for input: 'Oc1c1O,record'
...[10:03:44] SMILES Parse Error: syntax error for input:
'Oc1c1Orecord'
[10:03:44] SMILES Parse Error: syntax error for input: 'Nc1c1Centry'
..
--
Ran 59 tests in 5.291s
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[Rdkit-discuss] Post Doc in Artificial Intelligence & Active Ingredients Design + Workshop announcement

[Marco Stenta]

Dear All,
we are looking for someone with AI skills to do chemoinformatics work at
Syngenta,
knowledge of RDKit is, of course, part of the required skill-set.

Have a look here:
https://www.linkedin.com/feed/update/urn:li:activity:6392826810215727104

or apply directly here
https://syngentacrop.taleo.net/careersection/switzerland/jobdetail.ftl?job=1801163=GMT%2B02%3A00



Also, we are organizing a workshop on this very same topic at our site near
Basel, together with ROCHE, NOVARTIS, IDORSIA, LONZA and the swiss chemical
society
have a look here and register:
http://ai18.chemistrycongresses.ch/en/


Sorry for using this space for advertisement, but I guess this audience is
really the right one :-)

Cheers,
marco
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

[Marco Stenta]

 +1 to the MolVS project as well.

cheers
marco

2018-01-16 18:19 GMT+01:00 JP :

> Joining the fray, +1 for MolVS
>
> On 16 January 2018 at 16:00, Brian Cole  wrote:
>
>> +1 to the MolVS project as well.
>>
>> Perhaps an easy bite-size project is to incorporate the open source mae
>> parser code into core RDKit: https://github.com/schrodinger/maeparser
>>
>>
>> On Mon, Jan 15, 2018 at 9:08 PM, Francois BERENGER <
>> beren...@bioreg.kyushu-u.ac.jp> wrote:
>>
>>> On 01/16/2018 05:51 AM, Tim Dudgeon wrote:
>>> > Incorporating and "industrialising" Matt's MolVS tautomer and
>>> > standardizer code?
>>> > http://molvs.readthedocs.io/en/latest/index.html
>>>
>>> If we can vote, I would vote for this one.
>>>
>>> > On 15/01/18 07:09, Greg Landrum wrote:
>>> >> Dear all,
>>> >>
>>> >> We've been invited again to participate in the OpenChemistry
>>> >> application for Google Summer of Code.
>>> >>
>>> >> In order to participate we need ideas for projects and mentors to go
>>> >> along with them.
>>> >>
>>> >> The current list of RDKit ideas is being maintained here:
>>> >> http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
>>> >>
>>> >> (Note: at the point that I'm pressing "send", that's still a copy of
>>> >> last year's project ideas).
>>> >>
>>> >> If you're willing to be a mentor (please ask me about the ~5
>>> >> hours/week required here) or have ideas, please reply to this thread.
>>> >>
>>> >> Best,
>>> >> -greg
>>> >>
>>> >>
>>> >> 
>>> --
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>>> >>
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>>> >
>>> >
>>> > 
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>>> >
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>>
>>
>> 
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Re: [Rdkit-discuss] Ring membership

[Marco Stenta]

Hi Greg,
I missed the @ bit for bonds: thanks for the tip: I will definitely use it.
Still not matching donor and acceptors in the same ring is something I need
to achieve.
I'll work on Paul's suggestion and report back if I have any success in it.

Cheers,
m

2016-09-29 17:03 GMT+02:00 Greg Landrum <greg.land...@gmail.com>:

> Paul already mentioned an approach using the molecule's RingInfo
> structure, which you could certainly use to see if the RDKit thinks the two
> molecules are part of the same smallest ring.
> I suspect that you might want something a bit more general (apologies that
> I don't have a copy of that paper handy, so I can't read what the Roche
> folks used).
>
> Fortunately, the more general case actually turns out to be easier.
> I believe that what you want is to just determine whether or not the path
> between the two atoms is composed solely of ring bonds.
> You could express this in SMARTS as:
> {DONOR}@*@*@{ACCEPTOR}
> That's the three-bond separation case.
> Where {DONOR} and {ACCEPTOR} are the SMARTS definitions you would like to
> use for those atoms. The "@" in SMARTS means "Ring bond", so this pattern
> corresponds to a donor separated by three ring bonds from an acceptor.
>
> This will, unfortunately, also match the case where the donor and acceptor
> are adjacent to each other in a 5 membered ring. If it's important than you
> not match that, you'll have to do a bit more work.
>
> Best,
> -greg
>
>
>
> _
> From: Marco Stenta <marco.ste...@gmail.com>
> Sent: Thursday, September 29, 2016 4:13 PM
> Subject: [Rdkit-discuss] Ring membership
> To: <rdkit-discuss@lists.sourceforge.net>
>
>
>
> Dear Colleagues,
> I am working on intramolecular hydrogen bonds, formed between
> donor-acceptors separated by 2,3,4 atoms, as described in the Roche paper:
> Kuhn, B.; Mohr, P.; Stahl, M. J. Med. Chem. 2010, 53, 2601.
>
> I will use SMARTS and RDKIT to identify and classify IMHB.
>
> I see from documentation how to identify atoms that are members of a ring,
> how can I identify if two atoms are member of the same ring?
>
>
> Example:
>
> Donor--X-Y---Acceptor
>
> NCC=O
>
> This will match
> C1CC(NC1)C=O
>
> but I would lie to flag if two or more atoms belong to the same ring, as
> this will impact the capability of IMHB to opne and close.
>
>
> Do you have any suggestion?
>
> cheers,
> Marco
>
>
>
>
>
>
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[Rdkit-discuss] Ring membership

[Marco Stenta]

Dear Colleagues,
I am working on intramolecular hydrogen bonds, formed between
donor-acceptors separated by 2,3,4 atoms, as described in the Roche paper:
Kuhn, B.; Mohr, P.; Stahl, M. J. Med. Chem. 2010, 53, 2601.

I will use SMARTS and RDKIT to identify and classify IMHB.

I see from documentation how to identify atoms that are members of a ring,
how can I identify if two atoms are member of the same ring?


Example:

Donor--X-Y---Acceptor

NCC=O

This will match
C1CC(NC1)C=O

but I would lie to flag if two or more atoms belong to the same ring, as
this will impact the capability of IMHB to opne and close.


Do you have any suggestion?

cheers,
Marco
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