Re: [Rdkit-discuss] Incorrect Aromaticity?

[Hao]

@Dan The issue I meant was in the first line, where it writes the 5
membered ring as aromatic. Thanks for the response Ivan. I thought each
atom in an aromatic ring must contribute but I guess not. Very cool!

On Wed, Oct 30, 2019 at 3:08 PM Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> wrote:

> It is aromatic according to the RDKit aromaticity model described here:
> https://www.rdkit.org/docs/RDKit_Book.html#aromaticity
>
> The O and N each contribute 2 electrons. Each of the carbons shared with
> the 6-member ring contribute one electron. The carbonyl is sp2 and
> contributes zero electrons. The total is 6, which satisfies the 4n+2 rule.
>
> Ivan
>
> On Wed, Oct 30, 2019 at 3:00 PM Hao  wrote:
>
>> Hello,
>>
>> It seems like RDKit is making my molecule aromatic when I don't think it
>> should it. Here's the original smiles: c1ccc2c(c1)OC(N2)=O. A snippet of
>> the workflow:
>> [image: image.png]
>> As you can see it makes the 5 membered ring aromatic. My chemistry isn't
>> strong, so if someone can elucidate what I'm seeing, that would be
>> very helpful.
>>
>> Thanks!
>> Hao
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Re: [Rdkit-discuss] Incorrect Aromaticity?

[Ivan Tubert-Brohman]

It is aromatic according to the RDKit aromaticity model described here:
https://www.rdkit.org/docs/RDKit_Book.html#aromaticity

The O and N each contribute 2 electrons. Each of the carbons shared with
the 6-member ring contribute one electron. The carbonyl is sp2 and
contributes zero electrons. The total is 6, which satisfies the 4n+2 rule.

Ivan

On Wed, Oct 30, 2019 at 3:00 PM Hao  wrote:

> Hello,
>
> It seems like RDKit is making my molecule aromatic when I don't think it
> should it. Here's the original smiles: c1ccc2c(c1)OC(N2)=O. A snippet of
> the workflow:
> [image: image.png]
> As you can see it makes the 5 membered ring aromatic. My chemistry isn't
> strong, so if someone can elucidate what I'm seeing, that would be
> very helpful.
>
> Thanks!
> Hao
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Re: [Rdkit-discuss] Incorrect Aromaticity?

[Dan Nealschneider]

You've specified that the ring is aromatic in your smiles input. Did you
mean "C1CCC2C(C1)OC(N2)=O"?

*dan nealschneider* | senior developer
[image: Schrodinger Logo] 


On Wed, Oct 30, 2019 at 12:00 PM Hao  wrote:

> Hello,
>
> It seems like RDKit is making my molecule aromatic when I don't think it
> should it. Here's the original smiles: c1ccc2c(c1)OC(N2)=O. A snippet of
> the workflow:
> [image: image.png]
> As you can see it makes the 5 membered ring aromatic. My chemistry isn't
> strong, so if someone can elucidate what I'm seeing, that would be
> very helpful.
>
> Thanks!
> Hao
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[Rdkit-discuss] Incorrect Aromaticity?

[Hao]

Hello,

It seems like RDKit is making my molecule aromatic when I don't think it
should it. Here's the original smiles: c1ccc2c(c1)OC(N2)=O. A snippet of
the workflow:
[image: image.png]
As you can see it makes the 5 membered ring aromatic. My chemistry isn't
strong, so if someone can elucidate what I'm seeing, that would be
very helpful.

Thanks!
Hao
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Re: [Rdkit-discuss] Stereochemistry in rdkit

[Greg Landrum]

On Wed, Oct 30, 2019 at 10:28 AM Lukas Pravda  wrote:

>
> Thank you for the answer. I used to use the stereochemistry assignment the
> way you describe, but someone complained that in one of the molecules they
> knew the stereochemistry was incorrect.
>

Do you mean the R/S labels were incorrect or that somehow the structure (or
perhaps the drawing of the structure) was wrong?
The first is not completely unexpected given that the algorithm used to
assign CIP labels is approximate. This is fixable by doing an
implementation following the guidelines in the paper I link to below, but
that is a decidedly non-trivial amount of work.
A problem with the structure (or the way it's drawn), on the other hand,
would be a bug that is probably more easily fixable.

A question I should probably ask: why do you actually need R/S labels?


> It was suggested that we use the stereochemistry we have in db, so I
> changed that to setting atom tags (which randomly fixed those couple of
> issues, but apparently broke everything else down.
>
> I was wondering how does rdkit work out R/S from inchi string?
>

The InChI code translates InChI string into a datastructure that the RDKit
interprets to create an RDKit molecule. This datastructure includes parity
information analogous to what the RDKit uses internally (though based on
atom order if I remember correctly). Once we have an RDKit molecule
AssignStereochemistry() is called to set the approximate R/S labels.

-greg



>
>
> Lukas
>
>
>
> *From: *Greg Landrum 
> *Date: *Wednesday, 30 October 2019 at 04:28
> *To: *Lukas Pravda 
> *Cc: *RDKIT mailing list 
> *Subject: *Re: [Rdkit-discuss] Stereochemistry in rdkit
>
>
>
> Hi Lukas,
>
>
>
> The stereochemistry tags that the RDKit uses in determining bond wedging
> (or for SMILES, generating 3D coordinates, etc.) are the ChiralTags on the
> atoms: CHI_TETRAHEDRAL_CW and CHI_TETRAHEDRAL_CCW. The current RDKit stereo
> representation is relative to the ordering of the bonds around an atom, not
> the ordering of neighboring atoms. So CHI_TETRAHEDRAL_CW means that when
> you look down the first bond towards the central atom you rotate clockwise
> to move from the second bond to the third.
>
>
>
> The CIP (R/S) atomic properties are set by AssignStereochemistry() using
> the ChiralTags. Note that the R/S assignments are only approximate, the
> actual CIP rules are quite complex (great paper on this here:
> https://pubs.acs.org/doi/abs/10.1021/acs.jcim.8b00324) and we've not made
> a serious attempt to get this right.
>
>
>
> It isn't currently possible to assign CIP R/S labels to atoms and use
> those to set the ChiralTags. It would be possible to put together a bit of
> Python that can do this, but it would only be as accurate as the RDKit's
> assignment of CIP priorities. I can put together a demo of how to do this,
> but I think/hope it's not actually what you need...
>
>
>
> If you have 3D coordinates, the absolute best way to set the ChiralTags
> (and thus have the chiral representation correct) is to use
> AssignStereochemistryFrom3D(). This will set the ChiralTags on the atoms as
> well as assigning the CIP codes (to the extent that those are correct).
> Here's a gist showing how this works:
>
> https://gist.github.com/greglandrum/aa802edd1bc49ac0452beff52d55
>
>
>
> I hope this helps,
>
> -greg
>
>
>
>
>
>
>
> On Tue, Oct 29, 2019 at 12:13 PM Lukas Pravda  wrote:
>
> Hi guys,
>
>
>
> I got completely puzzled by stereochemistry and the way to set it in
> rdkit. Among others we use rdkit to get 2D depictions. What I do in my code
> is that I construct molecule from scratch and  set chiral tags to
> CHI_TETRAHEDRAL_CW for R, CHI_TETRAHEDRAL_CCW for S (this is the metadata
> we have for each atom, where applicable), otherwise CHI_UNSPECIFIED. Then I
> run sanitization on the molecule and generate images. That seems to be
> working incorrectly even for simple cases:  e.g.:
> https://pdbe.org/chem/004
>
>
>
> When constructing the molecule I set the stereocenter for the CA atom to
> CHI_TETRAHEDRAL_CCW (S), but when I then try to perceive the R/S by
> FindMolChiralCenters(force=false) it says ‘R’, so as the image. This is
> wrong. I can also directly set _CIPCODE for each atom where applicable to
> S/R directly (along with the chiral tags). Then the chiral atom is
> perceived as S by FindMolChiralCenters(force=false), but then again the
> image still says R.
>
>
>
> When I set neither the chiral tag nor the _CIPCODe and run
>  AssignAtomChiralTagsFromStructure() and AssignStereochemistry()  on the
> mol the atom under question gets atom tag CHI_TETRAHEDRAL_CW (I assume
> incorrectly), the _CIPCODE is correct (S) and the image is correct
> (why) as well (attached). So my question is, how do I set
> stereochemistry on individual atoms, so that it is perceived by rdkit and
> is not overwritten in any subsequent step.
>
>
>
> I hope the above mentioned description makes at least some sense. If not,
> I’ll try to distill a code 

Re: [Rdkit-discuss] fingerprint a molecule with pseudoatoms denoted by 'Du'

[SCHEEN Jenke]

Thanks Paolo, this works brilliantly. Let's hope astatine inhibitors won't gain 
in popularity 


Best,

Jenke



From: Paolo Tosco 
Sent: 30 October 2019 13:25
To: SCHEEN Jenke ; RDKit Discuss 

Subject: Re: [Rdkit-discuss] fingerprint a molecule with pseudoatoms denoted by 
'Du'


Hi Jenke,


I have put together a small gist showing a slightly hacky way to round-trip a 
molecule containing dummy atoms through a PDB block (assuming that your 
molecules do not contain astatine). If your dummy atoms are called "DU" rather 
than " *", you may just change the replace() expression with something that 
fits your needs.


HTH, cheers

p.

On 10/30/19 12:06, SCHEEN Jenke wrote:
Hi RDKitters,

I'm trying to use rdkit to generate molecular fingerprints (such as AP or ECFP) 
on molecules that have non-interactive pseudoatoms ('dummy atoms', denoted by 
Du). I attached a sample PDB file containing the dummy atoms on positions 
21-24. Reading this file (Chem.rdmolfiles.MolFromPDBFile("test.pdb", 
sanitize=False) throws a post-condition violation because the element 'Du' 
isn't recognised, which makes sense. I've been searching online and haven't 
been able to find any workarounds, do you have any suggestions?

Some notes:

  *   I'm hoping that once rdkit is able to read in the pdb file the mol object 
can be parsed without the FP constructor (e.g. AllChem.GetMorganFingerprint) 
complaining.
  *   The use of the term dummy atoms here should not be confused with the 
dummy atoms depiction in fragmentising molecules in rdkit (where * is the 
smiles notation).
  *   For this project all I aim to do is generate structural fingerprints for 
these types of ligands. This means I won't have to worry about defining 
chemical properties to Du.
  *   The context for this issue is that we're aiming to featurise the ligands 
for an ML protocol where the dummy atoms are one of the major descriptors of 
the problem.

  *   I thought manually inserting a 119th element in atomic_data.cpp might 
resolve the issue but I've been unable to locate the file in my conda 
installation.
  *   The ODDT python API seems to parse the Du element without any issues but 
is limited in its FP generator diversity.


Best,

Jenke


The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336.




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Re: [Rdkit-discuss] fingerprint a molecule with pseudoatoms denoted by 'Du'

[Paolo Tosco]

Hi Jenke,


I have put together a small gist showing a slightly hacky way to 
round-trip a molecule containing dummy atoms through a PDB block 
(assuming that your molecules do not contain astatine). If your dummy 
atoms are called "DU" rather than " *", you may just change the 
replace() expression with something that fits your needs.



HTH, cheers

p.


On 10/30/19 12:06, SCHEEN Jenke wrote:

Hi RDKitters,

I'm trying to use rdkit to generate molecular fingerprints (such as AP 
or ECFP) on molecules that have non-interactive pseudoatoms ('dummy 
atoms', denoted by Du). I attached a sample PDB file containing the 
dummy atoms on positions 21-24. Reading this file 
(Chem.rdmolfiles.MolFromPDBFile("test.pdb", sanitize=False) throws a 
post-condition violation because the element 'Du' isn't recognised, 
which makes sense. I've been searching online and haven't been able to 
find any workarounds, do you have any suggestions?


Some notes:

  * I'm hoping that once rdkit is able to read in the pdb file the mol
object can be parsed without the FP constructor (e.g.
AllChem.GetMorganFingerprint) complaining.
  * The use of the term dummy atoms here should not be confused with
the dummy atoms depiction in fragmentising molecules in rdkit
(where * is the smiles notation).
  * For this project all I aim to do is generate structural
fingerprints for these types of ligands. This means I won't have
to worry about defining chemical properties to Du.
  * The context for this issue is that we're aiming to featurise the
ligands for an ML protocol where the dummy atoms are one of the
major descriptors of the problem.

  * I thought manually inserting a 119th element in atomic_data.cpp
might resolve the issue but I've been unable to locate the file in
my conda installation.
  * The ODDT python API seems to parse the Du element without any
issues but is limited in its FP generator diversity.


Best,

Jenke

The University of Edinburgh is a charitable body, registered in 
Scotland, with registration number SC005336.





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[Rdkit-discuss] fingerprint a molecule with pseudoatoms denoted by 'Du'

[SCHEEN Jenke]

Hi RDKitters,

I'm trying to use rdkit to generate molecular fingerprints (such as AP or ECFP) 
on molecules that have non-interactive pseudoatoms ('dummy atoms', denoted by 
Du). I attached a sample PDB file containing the dummy atoms on positions 
21-24. Reading this file (Chem.rdmolfiles.MolFromPDBFile("test.pdb", 
sanitize=False) throws a post-condition violation because the element 'Du' 
isn't recognised, which makes sense. I've been searching online and haven't 
been able to find any workarounds, do you have any suggestions?

Some notes:

  *   I'm hoping that once rdkit is able to read in the pdb file the mol object 
can be parsed without the FP constructor (e.g. AllChem.GetMorganFingerprint) 
complaining.
  *   The use of the term dummy atoms here should not be confused with the 
dummy atoms depiction in fragmentising molecules in rdkit (where * is the 
smiles notation).
  *   For this project all I aim to do is generate structural fingerprints for 
these types of ligands. This means I won't have to worry about defining 
chemical properties to Du.
  *   The context for this issue is that we're aiming to featurise the ligands 
for an ML protocol where the dummy atoms are one of the major descriptors of 
the problem.

  *   I thought manually inserting a 119th element in atomic_data.cpp might 
resolve the issue but I've been unable to locate the file in my conda 
installation.
  *   The ODDT python API seems to parse the Du element without any issues but 
is limited in its FP generator diversity.


Best,

Jenke


The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336.


test.pdb
Description: test.pdb
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Re: [Rdkit-discuss] how to set the stereochemistry of a molecule

[Alfredo Quevedo]

thank you Greg for the hint,

Kind regards

Alfredo

⁣Enviado desde BlueMail ​

En 30 de octubre de 2019 07:03, en 07:03, Greg Landrum  
escribió:
>On Wed, Oct 30, 2019 at 10:16 AM Alfredo Quevedo
>
>wrote:
>
>> thank you very much Hongbin for the detailed answer and for pointing
>the
>> information.
>> So, it is possible to manually change the tag  from CW to CCW?
>>
>
>Yes, Atoms have a SetChiralTag() method that you can use for this.
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Re: [Rdkit-discuss] how to set the stereochemistry of a molecule

[Greg Landrum]

On Wed, Oct 30, 2019 at 10:16 AM Alfredo Quevedo 
wrote:

> thank you very much Hongbin for the detailed answer and for pointing the
> information.
> So, it is possible to manually change the tag  from CW to CCW?
>

Yes, Atoms have a SetChiralTag() method that you can use for this.
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Re: [Rdkit-discuss] Stereochemistry in rdkit

[Lukas Pravda]

Hi Greg,

 

Thank you for the answer. I used to use the stereochemistry assignment the way 
you describe, but someone complained that in one of the molecules they knew the 
stereochemistry was incorrect. It was suggested that we use the stereochemistry 
we have in db, so I changed that to setting atom tags (which randomly fixed 
those couple of issues, but apparently broke everything else down.

 

I was wondering how does rdkit work out R/S from inchi string?

 

Lukas

 

From: Greg Landrum 
Date: Wednesday, 30 October 2019 at 04:28
To: Lukas Pravda 
Cc: RDKIT mailing list 
Subject: Re: [Rdkit-discuss] Stereochemistry in rdkit

 

Hi Lukas,

 

The stereochemistry tags that the RDKit uses in determining bond wedging (or 
for SMILES, generating 3D coordinates, etc.) are the ChiralTags on the atoms: 
CHI_TETRAHEDRAL_CW and CHI_TETRAHEDRAL_CCW. The current RDKit stereo 
representation is relative to the ordering of the bonds around an atom, not the 
ordering of neighboring atoms. So CHI_TETRAHEDRAL_CW means that when you look 
down the first bond towards the central atom you rotate clockwise to move from 
the second bond to the third.

 

The CIP (R/S) atomic properties are set by AssignStereochemistry() using the 
ChiralTags. Note that the R/S assignments are only approximate, the actual CIP 
rules are quite complex (great paper on this here: 
https://pubs.acs.org/doi/abs/10.1021/acs.jcim.8b00324) and we've not made a 
serious attempt to get this right.

 

It isn't currently possible to assign CIP R/S labels to atoms and use those to 
set the ChiralTags. It would be possible to put together a bit of Python that 
can do this, but it would only be as accurate as the RDKit's assignment of CIP 
priorities. I can put together a demo of how to do this, but I think/hope it's 
not actually what you need...

 

If you have 3D coordinates, the absolute best way to set the ChiralTags (and 
thus have the chiral representation correct) is to use 
AssignStereochemistryFrom3D(). This will set the ChiralTags on the atoms as 
well as assigning the CIP codes (to the extent that those are correct). Here's 
a gist showing how this works:

https://gist.github.com/greglandrum/aa802edd1bc49ac0452beff52d55

 

I hope this helps,

-greg

 

 

 

On Tue, Oct 29, 2019 at 12:13 PM Lukas Pravda  wrote:

Hi guys,

 

I got completely puzzled by stereochemistry and the way to set it in rdkit. 
Among others we use rdkit to get 2D depictions. What I do in my code is that I 
construct molecule from scratch and  set chiral tags to CHI_TETRAHEDRAL_CW for 
R, CHI_TETRAHEDRAL_CCW for S (this is the metadata we have for each atom, where 
applicable), otherwise CHI_UNSPECIFIED. Then I run sanitization on the molecule 
and generate images. That seems to be working incorrectly even for simple 
cases:  e.g.: https://pdbe.org/chem/004

 

When constructing the molecule I set the stereocenter for the CA atom to 
CHI_TETRAHEDRAL_CCW (S), but when I then try to perceive the R/S by 
FindMolChiralCenters(force=false) it says ‘R’, so as the image. This is wrong. 
I can also directly set _CIPCODE for each atom where applicable to S/R directly 
(along with the chiral tags). Then the chiral atom is perceived as S by 
FindMolChiralCenters(force=false), but then again the image still says R.  

 

When I set neither the chiral tag nor the _CIPCODe and run  
AssignAtomChiralTagsFromStructure() and AssignStereochemistry()  on the mol the 
atom under question gets atom tag CHI_TETRAHEDRAL_CW (I assume incorrectly), 
the _CIPCODE is correct (S) and the image is correct (why) as well 
(attached). So my question is, how do I set stereochemistry on individual 
atoms, so that it is perceived by rdkit and is not overwritten in any 
subsequent step.

 

I hope the above mentioned description makes at least some sense. If not, I’ll 
try to distill a code sample for constructing this molecule from raw data.

 

I also reproduced the same steps on the  http://pdbe.org/chem/THR, which also 
gives wrong results when I set chiral tags manually (bond wedging should not be 
on methyl group I assume. Interestingly here the setting chiral atoms from the 
structure by rdkit gives incorrect results as well (attached).

 

For rdkit set tags I get

 

CA - CHI_TETRAHEDRAL_CCW (S) – (correct)

CB - CHI_TETRAHEDRAL_CCW (R) – (incorrect should be TETRAHEDRAL_CW - R)

 

I’d be grateful for any piece of advice. Because I have no idea what I have 
been doing wrong the whole time.

 

My settings:

Rdkit: 2019.09.1/2019.03.2

Conda: 4.7.12

Python 3.7.4

os mac 10.15

 

Best,

Lukas

 

 

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Re: [Rdkit-discuss] how to set the stereochemistry of a molecule

[Alfredo Quevedo]

thank you very much Hongbin for the detailed answer and for pointing the 
information.
So, it is possible to manually change the tag  from CW to CCW?
kind regards

Alfredo

⁣Enviado desde BlueMail ​

En 30 de octubre de 2019 01:32, en 01:32, Greg Landrum  
escribió:
>Hongbin has the answer here completely correct (thanks Hongbin!).
>
>And the reason it's CCW instead of ACW is that I say "counterclockwise"
>and
>not "anticlockwise" :-)
>
>-greg
>
>On Wed, Oct 30, 2019 at 3:07 AM Hongbin Yang 
>wrote:
>
>> Hello Alfredo,
>>
>> The tag "CHI_TETRAHEDRAL_CW" means clockwise and CCW means
>anti-clockwise
>> (I have no idea why it is coded CCW rather than ACW, but whatever ;)
>).
>> These chiral tags are related but not corresponding to the absolute
>> chirality (R/S) defined in organic chemistry.
>>
>> Look at the SMILES you provided and you will find that both of the
>chiral
>> carbons are [C@@H].
>> According to the theory of Smiles in DayLight (
>> https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html 3.3.3)
>> > The symbol "@" indicates that the following neighbors are listed
>> anticlockwise (it is a "visual mnemonic" in that the symbol looks
>like an
>> anticlockwise spiral around a central circle). "@@" indicates that
>the
>> neighbors are listed clockwise (you guessed it, anti-anti-clockwise).
>> Then you may have realized that the tags "CHI_TETRAHEDRAL_CW" are
>> corresponding to your SMILES but not the real chirality.
>>
>> I suggest you read the chapter 3.3.3 to understand the meaning of
>"chiral
>> tag", then you will understand why they are not the absolute
>chirality.
>>
>> Absolute chirality depends on the chiral tag as well as the 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，Alfredo Quevedo
>>  wrote：
>>
>> Good morning,
>>>
>>> I am trying to manually set/change the stereochemistry of a chiral
>>> center of a molecule, and I cant understand how to set the
>>> CHI_TETRAHEDRAL_CW/CHI_TETRAHEDRAL_CCW tag on a certain atom. So far
>my
>>> script does the following:
>>>
>>> -
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>>
>>>
>molecule='C[C@@H](C(=O)COc1c(F)c(F)cc(F)c1F)n1cc([C@@H](NCc2ccc3c(c2)OCO3)c2ncc[nH]2)nn1'
>>>
>>> molecule_smiles=Chem.MolFromSmiles(molecule)
>>> chiralty=Chem.FindMolChiralCenters(molecule_smiles)
>>> centers=len(chiralty)
>>>
>>> for i in range(centers):
>>>  current_center=chiralty[i][1]
>>>  print(current_center)
>>>  center_to_change=chiralty[i][0]
>>>  print(center_to_change)
>>>
>>>
>>> for a in molecule_smiles.GetAtoms():
>>>  print(a.GetChiralTag())
>>>
>>> 
>>>
>>> executing the above mentioned script I can see that the molecule has
>2
>>> chiral centers, the first one on index 1, which is S, and the second
>>> one, with index 19, which is R. Both chiral tags are set to:
>>> CHI_TETRAHEDRAL_CW. now, I want to manually change the configuration
>of
>>> index 19 to S, so I want to change its tag to CHI_TETRAHEDRAL_CCW.
>>>
>>> Which would be the command to set this tag and how is the index
>indicated?
>>>
>>> thanks in advance for the help,
>>>
>>> kind regards
>>>
>>> Alfredo
>>>
>>>
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Re: [Rdkit-discuss] 2019.09.1 RDKit Release

[Francois Berenger]

On 25/10/2019 16:20, Greg Landrum wrote:

Dear all,

I'm pleased to announce that the next version of the RDKit - 2019.09 -
is released. The release notes are below.

The release files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2019_09_1

Binaries have been uploaded to anaconda.org [1]
(https://anaconda.org/rdkit).
The available conda binaries for this release are:
Linux 64bit: python 3.6, 3.7
Mac OS 64bit: python 3.6, 3.7
Windows 64bit: python 3.6, 3.7

Conda builds of the PostgreSQL cartridge are also available:
Linux 64bit: postgresql 9.6, 10, 11
Mac OS 64bit: postgresql 9.6, 10, 11

I believe that conda-forge will also switch to the new version in the
near future.

The online version of the documentation at rdkit.org [2]
(http://rdkit.org/docs/index.html) has been updated.

Some things that will be finished over the next couple of days:
- The conda build scripts will be updated to reflect the new version
- The homebrew script


Dear all,

The brew recipe has been updated.

If it doesn't work for you, please submit an issue here:

https://github.com/rdkit/homebrew-rdkit/issues

Regards,
Francois.


Thanks to everyone who submitted code, bug reports, and suggestions
for this release!

Please let me know if you find any problems with the release or have
suggestions for the next one, which is scheduled for March/April 2020.

Best Regards,
-greg

# Release_2019.09.1
(Changes relative to Release_2019.03.1)

## Important
- The atomic van der Waals radii used by the RDKit were
corrected/updated in #2154.
  This leads to different results when generating conformations,
molecular volumes,
  and molecular shapes.

## Backwards incompatible changes
- See the note about atomic van der Waals radii above.
- As part of the enhancements to the MolDraw2D class, we changed the
type of
  DrawColour from a tuple to be an actual struct. We also added a 4th
element to
  capture alpha values. This should have no affect on Python code (the
alpha
  value is optional when providing color tuples), but will require
changes to C++
  and Java/C# code that is using DrawColour.
- When reading Mol blocks, atoms with the symbol "R" are now converted
into
  queries that match any atom when doing a substructure search
(analogous to "*"
  in SMARTS). The previous behavior was to only match other dummy
atoms
- When loading SDF files using PandasTools.LoadSDF(), we now default
to
  producing isomeric smiles in pandas tables.  To reproduce the
original
  behavior, use isomericSmiles=False in the call to the function.
- The SMARTS generated by the RDKit no longer contains redundant
wildcard
  queries. This means the SMARTS strings generated by this release
will generally
  be different from that in previous releases, although the results
produced by
  the queries should not change.
- The RGroupDecomposition code now removes Hs from output R groups by
default.
  To restore the old behavior create an RGroupDecompositionParameters
object and
  set removeHydrogensPostMatch to false.
- The default values for some of the new fingerprint generators have
been changed so
  that they more closely resemble the original fingerprinting code. In
  particular most fingerprinters no longer do count simulation by
default and
  the RDKit fingerprint now sets two bits per feature by default.
- The SMARTS generated for MCS results using the ringMatchesRingOnly
or
  completeRingsOnly options now includes ring-membership queries.

## Highlights:
- The substructure matching code is now about 30% faster. This also
improves the
  speed of reaction matching and the FMCS code. (#2500)
- A minimal JavaScript wrapper has been added as part of the core
release. (#2444)
- It's now possible to get information about why molecule sanitization
failed. (#2587)
- A flexible new molecular hashing scheme has been added. (#2636)

## Acknowledgements:
Patricia Bento, Francois Berenger, Jason Biggs, David Cosgrove, Andrew
Dalke,
Thomas Duigou, Eloy Felix, Guillaume Godin, Lester Hedges, Anne
Hersey,
Christoph Hillisch, Christopher Ing, Jan Holst Jensen, Gareth Jones,
Eisuke
Kawashima, Brian Kelley, Alan Kerstjens, Karl Leswing, Pat Lorton,
John
Mayfield, Mike Mazanetz, Dan Nealschneider, Noel O'Boyle, Stephen
Roughley,
Roger Sayle, Ricardo Rodriguez Schmidt, Paula Schmiel, Peter St. John,
Marvin
Steijaert, Matt Swain, Amol Thakkar Paolo Tosco, Yi-Shu Tu, Ricardo
Vianello,
Marc Wittke, '7FeiW', 'c56pony', 'sirbiscuit'

## Bug Fixes:
  - MCS returning partial rings with completeRingsOnly=True
 (github issue #945 from greglandrum)
  - Alternating canonical SMILES for fused ring with N
 (github issue #1028 from greglandrum)
  - Atom index out of range error
 (github issue #1868 from A-Thakkar)
  - Incorrect cis/trans stereo symbol for conjugated ring
 (github issue #2023 from baoilleach)
  - Hardcoded max length of SMARTs string cut of input query for
FragCatlog
 (github issue #2163 from 7FeiW)
  - VSA_EState {1, ..., 10} calculated by rdkit