Re: [Rdkit-discuss] explicit H atoms

[Greg Landrum]

On Tue, Mar 9, 2021 at 6:15 PM Jason Biggs  wrote:

>
> On Tue, Mar 9, 2021 at 10:49 AM Maciek Wójcikowski 
> wrote:
>
>> Hi Jean-Marc,
>>
>> I know you can draw them, but both SMILES and RDKit internally use two
>> bonds (up/down) directions to assign the bond stereo, which means that
>> there are not
>>
>
> Fortunately the RDKit also allows you to set bond stereo without using the
> bond directions, by setting the bond stereo flag to stereocis or
> stereotrans and then setting the stereoAtoms to say which atoms are cis or
> trans.  Using bond directions for double bond stereo has always seemed
> rather archaic and confusing to me.
>

Though I agree with you completely, unfortunately the IUPAC recommendation
(which the RDKit does not follow, but needs to support) is that you should
indicate unknown bond stereochemistry using a wavy bond (which the RDKit
encodes as bond direction). Here are two excerpt images from the
recommendations (
https://www.degruyter.com/document/doi/10.1351/pac200678101897/html)
[image: image.png][image: image.png]

-greg
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[Rdkit-discuss] Can't load mol2 file.

[Eduardo Mayo]

Hi RDKiters,
Hope you are well. I'm having trouble loading these molecules. Do you know
any walk around??
Bests,
Eduardo

In: rdkit.__version__
Out: '2020.09.5'

In: Chem.MolFromMOL2File('file.mol2')
Out: None

In:Chem.MolFromPDBBlock(pdb_block)
Out:  (Molecule successfully loaded but missing connections)

*file.mol2*
>


@MOLECULE
> pdb3b3b.ent_out_ok
>  26 27 0 0 0
> SMALL
> GASTEIGER
> @ATOM
>   1 N  56.3038  -19.9123   38.1221 N.3 1  LIG   -0.3224
>   2 CA 55.7546  -19.8386   36.7785 C.3 1  LIG0.0489
>   3 C  56.6780  -19.0176   35.8775 C.2 1  LIG0.0588
>   4 O  56.8003  -17.8103   36.1384 O.co2   1  LIG   -0.5482
>   5 CB 54.3375  -19.2367   36.7831 C.3 1  LIG   -0.0052
>   6 CG 53.2279  -20.0619   37.3598 C.ar1  LIG   -0.0205
>   7 CD152.5022  -20.9701   36.6718 C.ar1  LIG0.0060
>   8 CD252.6251  -19.9979   38.6870 C.ar1  LIG0.0029
>   9 CE251.4779  -20.8441   38.7046 C.ar1  LIG0.0467
>  10 CE352.8995  -19.2788   39.8677 C.ar1  LIG   -0.0523
>  11 NE151.4807  -21.4416   37.4637 N.ar1  LIG   -0.3604
>  12 CZ250.6116  -20.9179   39.8080 C.ar1  LIG   -0.0378
>  13 CZ352.0516  -19.3528   40.9911 C.ar1  LIG   -0.0611
>  14 CH250.8981  -20.1559   40.9548 C.ar1  LIG   -0.0598
>  15 OXT57.2414  -19.5929   34.9256 O.co2   1  LIG   -0.5482
>  16 HA 55.6995  -20.8519   36.3812 H   1  LIG0.0523
>  17 HB154.3326  -18.2711   37.2871 H   1  LIG0.0332
>  18 HB254.0496  -19.0290   35.7533 H   1  LIG0.0332
>  19 HD152.6579  -21.2317   35.6382 H   1  LIG0.0810
>  20 HE150.7760  -22.0861   37.1266 H   1  LIG0.1653
>  21 HE353.7741  -18.6562   39.8800 H   1  LIG0.0624
>  22 HZ249.7440  -21.5583   39.7776 H   1  LIG0.0638
>  23 HZ352.2783  -18.7898   41.8812 H   1  LIG0.0618
>  24 HH250.2483  -20.2108   41.8156 H   1  LIG0.0618
>  25 H1 55.7027  -20.4381   38.7435 H   1  LIG0.1188
>  26 H2 57.1830  -20.4155   38.1180 H   1  LIG0.1188
> @BOND
>  1 1 21
>  2 1251
>  3 1261
>  4 2 31
>  5 2 51
>  6 2161
>  7 3 4   ar
>  8 315   ar
>  9 5 61
> 10 5171
> 11 5181
> 12 6 7   ar
> 13 6 8   ar
> 14 711   ar
> 15 7191
> 16 8 9   ar
> 17 810   ar
> 18 912   ar
> 191013   ar
> 2010211
> 21 911   ar
> 2211201
> 231214   ar
> 2412221
> 251314   ar
> 2613231
> 2714241


*pdb_block*
> REMARK  4 active torsions:
> REMARK  status: ('A' for Active; 'I' for Inactive)
> REMARK1  Abetween atoms: N_1  and  CA_2
> REMARK2  Abetween atoms: CA_2  and  C_3
> REMARK3  Abetween atoms: CA_2  and  CB_5
> REMARK4  Abetween atoms: CB_5  and  CG_6
> ATOM  1  CG  LIG d   1  53.228 -20.062  37.360  0.00  0.00
> ATOM  2  CD1 LIG d   1  52.502 -20.970  36.672  0.00  0.00
> ATOM  3  CD2 LIG d   1  52.625 -19.998  38.687  0.00  0.00
> ATOM  4  CE2 LIG d   1  51.478 -20.844  38.705  0.00  0.00
> ATOM  5  CE3 LIG d   1  52.900 -19.279  39.868  0.00  0.00
> ATOM  6  NE1 LIG d   1  51.481 -21.442  37.464  0.00  0.00
> ATOM  7  CZ2 LIG d   1  50.612 -20.918  39.808  0.00  0.00
> ATOM  8  CZ3 LIG d   1  52.052 -19.353  40.991  0.00  0.00
> ATOM  9  CH2 LIG d   1  50.898 -20.156  40.955  0.00  0.00
> ATOM 10  HE1 LIG d   1  50.776 -22.086  37.127  0.00  0.00
> ATOM 11  CB  LIG d   1  54.337 -19.237  36.783  0.00  0.00
> ATOM 12  CA  LIG d   1  55.755 -19.839  36.779  0.00  0.00
> ATOM 13  N   LIG d   1  56.304 -19.912  38.122  0.00  0.00
> ATOM 14  H1  LIG d   1  55.703 -20.438  38.743  0.00  0.00
> ATOM 15  H2  LIG d   1  57.183 -20.416  38.118  0.00  0.00
> ATOM 16  C   LIG d   1  56.678 -19.018  35.877  0.00  0.00
> ATOM 17  O   LIG d   1  56.800 -17.810  36.138  0.00  0.00
> ATOM 18  OXT LIG d   1  57.241 -19.593  34.926  0.00  0.00
>
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Re: [Rdkit-discuss] explicit H atoms

[Ling Chan]

This is the continuation of the previous reply, to elaborate on "the
stripped structure can always be represented using wedged bonds".

One potential problem is that a bond is required to be wedged from both
ends. But this should not happen. For an atom to be chiral, it needs to be
attached to at least 3 other atoms. If it is attached to 3 atoms, its
chirality can be specified by using a wedge on any one of the three bonds.
Hence there should always be enough possibilities to avoid the potential
problem.

I could be wrong. I can't proof it. But this is what it feels like to me,
especially if no atom is bonded to more than 4 other atoms.


Ling Chan  於 2021年3月9日週二 上午11:32寫道：

> Hello Jean-Marc,
>
> This is a very interesting question.
>
> Given any molecule, consider its structure stripped of all H's. There is
> no reason why this stripped structure cannot be represented using wedged
> bonds etc. (Will continue on the next reply.) Hence potential problems can
> only arise when the added Hs themselves introduce new chirality /
> stereochemistry, or that the position of the added H itself is not uniquely
> defined by the stripped structure.
>
> One example I can think of is the secondary amine, if you only consider
> one state  (say if the temperature is so low that it is locked in that
> geometry). But if there is a rule saying that "the implicit hydrogen is
> understood to lie in the plane of the paper", then everything will still be
> fine. Just that the drawings may look a bit strange, as attached.
>
> But for stereo bonds, perhaps there is no escape. You will need to draw
> the explicit hydrogen. See attached.
>
> But then how about the orientation of hydroxyl groups in general? They are
> usually neglected in chemical representations, aren't they??
>
> Ling
>
>
>
>
> Jean-Marc Nuzillard  於 2021年3月9日週二 上午1:04寫道：
>
>> Sure, testosterone may be drawn as
>>
>>
>>
>> Jean-Marc
>>
>>
>> Le 08/03/2021 à 18:26, Rocco Moretti a écrit :
>>
>> On Mon, Mar 8, 2021 at 11:17 AM Paul Emsley 
>> wrote:
>>
>>> On 08/03/2021 13:55, Jean-Marc Nuzillard wrote:
>>> >
>>> > Is it always possible to represent an organic molecule in 2D with all
>>> necessary
>>> > configuration hints (bond wedges pointing to the front or to the back)
>>> > without introducing any explicit hydrogen atom?
>>>
>>> No. Testosterone.
>>>
>>
>> Is that "not possible" or simply "against convention"? One could
>> certainly imagine someone attempting to put the dashed and wedged
>> designations on the ring bonds, and leaving the hydrogens implicit.
>> (Flagrantly ignoring how much it would mess with steroid chemists' brains.)
>>
>>
>> ___
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>> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>>
>> --
>> Jean-Marc Nuzillard
>> Directeur de Recherches au CNRS
>>
>> Institut de Chimie Moléculaire de Reims
>> CNRS UMR 7312
>> Moulin de la Housse
>> CPCBAI, Bâtiment 18
>> BP 1039
>> 51687 REIMS Cedex 2
>> France
>>
>> Tel : 03 26 91 82 10
>> Fax : 03 26 91 31 
>> 66http://www.univ-reims.fr/icmrhttp://eos.univ-reims.fr/LSD/CSNteam.html
>> http://www.univ-reims.fr/LSD/http://www.univ-reims.fr/LSD/JmnSoft/
>>
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>
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Re: [Rdkit-discuss] explicit H atoms

[Ling Chan]

Hello Jean-Marc,

This is a very interesting question.

Given any molecule, consider its structure stripped of all H's. There is no
reason why this stripped structure cannot be represented using wedged bonds
etc. (Will continue on the next reply.) Hence potential problems can only
arise when the added Hs themselves introduce new chirality /
stereochemistry, or that the position of the added H itself is not uniquely
defined by the stripped structure.

One example I can think of is the secondary amine, if you only consider one
state  (say if the temperature is so low that it is locked in that
geometry). But if there is a rule saying that "the implicit hydrogen is
understood to lie in the plane of the paper", then everything will still be
fine. Just that the drawings may look a bit strange, as attached.

But for stereo bonds, perhaps there is no escape. You will need to draw the
explicit hydrogen. See attached.

But then how about the orientation of hydroxyl groups in general? They are
usually neglected in chemical representations, aren't they??

Ling




Jean-Marc Nuzillard  於 2021年3月9日週二 上午1:04寫道：

> Sure, testosterone may be drawn as
>
>
>
> Jean-Marc
>
>
> Le 08/03/2021 à 18:26, Rocco Moretti a écrit :
>
> On Mon, Mar 8, 2021 at 11:17 AM Paul Emsley 
> wrote:
>
>> On 08/03/2021 13:55, Jean-Marc Nuzillard wrote:
>> >
>> > Is it always possible to represent an organic molecule in 2D with all
>> necessary
>> > configuration hints (bond wedges pointing to the front or to the back)
>> > without introducing any explicit hydrogen atom?
>>
>> No. Testosterone.
>>
>
> Is that "not possible" or simply "against convention"? One could certainly
> imagine someone attempting to put the dashed and wedged designations on the
> ring bonds, and leaving the hydrogens implicit. (Flagrantly ignoring how
> much it would mess with steroid chemists' brains.)
>
>
> ___
> Rdkit-discuss mailing 
> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
> --
> Jean-Marc Nuzillard
> Directeur de Recherches au CNRS
>
> Institut de Chimie Moléculaire de Reims
> CNRS UMR 7312
> Moulin de la Housse
> CPCBAI, Bâtiment 18
> BP 1039
> 51687 REIMS Cedex 2
> France
>
> Tel : 03 26 91 82 10
> Fax : 03 26 91 31 
> 66http://www.univ-reims.fr/icmrhttp://eos.univ-reims.fr/LSD/CSNteam.html
> http://www.univ-reims.fr/LSD/http://www.univ-reims.fr/LSD/JmnSoft/
>
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Re: [Rdkit-discuss] explicit H atoms

[Jason Biggs]

Jason Biggs



On Tue, Mar 9, 2021 at 10:49 AM Maciek Wójcikowski 
wrote:

> Hi Jean-Marc,
>
> I know you can draw them, but both SMILES and RDKit internally use two
> bonds (up/down) directions to assign the bond stereo, which means that
> there are not
>

Fortunately the RDKit also allows you to set bond stereo without using the
bond directions, by setting the bond stereo flag to stereocis or
stereotrans and then setting the stereoAtoms to say which atoms are cis or
trans.  Using bond directions for double bond stereo has always seemed
rather archaic and confusing to me.

Jason



> enough bonds to define both double bonds configuration and have the middle
> one undefined at the same time.
> 
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
>
> wt., 9 mar 2021 o 13:14 Jean-Marc Nuzillard 
> napisał(a):
>
>> Hi Maciek,
>>
>> I would find your example rather readable even without explicit H atoms.
>>
>>
>>
>> I drew it like that because I do not have the wavy wedge at hand.
>>
>> Thanks for your proposal,
>> Best,
>>
>> Jean-Marc
>>
>>
>>
>> Le 09/03/2021 à 11:26, Maciek Wójcikowski a écrit :
>>
>> Hi,
>>
>> I'd say that for a tetrahedral stereo that is possible to remove all of
>> Hs. But for double bonds it might not be as easy, or impossible for some
>> edge cases - conjugated double bonds in particular. Here is one:
>>
>> [image: image.png]
>> [H]\C(=C/C)C=C\C([H])=C\C
>>
>>
>> 
>> Pozdrawiam,  |  Best regards,
>> Maciek Wójcikowski
>> mac...@wojcikowski.pl
>>
>>
>> wt., 9 mar 2021 o 10:47 Paul Emsley 
>> napisał(a):
>>
>>> On 09/03/2021 09:01, Jean-Marc Nuzillard wrote:
>>> > Sure, testosterone may be drawn as
>>> > [snip]
>>>
>>> OK :-)
>>>
>>> That's a top quality rendering by the way. How did you make it?
>>>
>>> Paul.
>>>
>>>
>>> ___
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>>>
>>
>>
>> ___
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>>
>>
>>
>> --
>> Jean-Marc Nuzillard
>> Directeur de Recherches au CNRS
>>
>> Institut de Chimie Moléculaire de Reims
>> CNRS UMR 7312
>> Moulin de la Housse
>> CPCBAI, Bâtiment 18
>> BP 1039
>> 51687 REIMS Cedex 2
>> France
>>
>> Tel : 03 26 91 82 10
>> Fax : 03 26 91 31 
>> 66http://www.univ-reims.fr/icmrhttp://eos.univ-reims.fr/LSD/CSNteam.html
>> http://www.univ-reims.fr/LSD/http://www.univ-reims.fr/LSD/JmnSoft/
>>
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Re: [Rdkit-discuss] explicit H atoms

[Maciek Wójcikowski]

Hi Jean-Marc,

I know you can draw them, but both SMILES and RDKit internally use two
bonds (up/down) directions to assign the bond stereo, which means that
there are not enough bonds to define both double bonds configuration and
have the middle one undefined at the same time.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


wt., 9 mar 2021 o 13:14 Jean-Marc Nuzillard 
napisał(a):

> Hi Maciek,
>
> I would find your example rather readable even without explicit H atoms.
>
>
>
> I drew it like that because I do not have the wavy wedge at hand.
>
> Thanks for your proposal,
> Best,
>
> Jean-Marc
>
>
>
> Le 09/03/2021 à 11:26, Maciek Wójcikowski a écrit :
>
> Hi,
>
> I'd say that for a tetrahedral stereo that is possible to remove all of
> Hs. But for double bonds it might not be as easy, or impossible for some
> edge cases - conjugated double bonds in particular. Here is one:
>
> [image: image.png]
> [H]\C(=C/C)C=C\C([H])=C\C
>
>
> 
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
>
> wt., 9 mar 2021 o 10:47 Paul Emsley 
> napisał(a):
>
>> On 09/03/2021 09:01, Jean-Marc Nuzillard wrote:
>> > Sure, testosterone may be drawn as
>> > [snip]
>>
>> OK :-)
>>
>> That's a top quality rendering by the way. How did you make it?
>>
>> Paul.
>>
>>
>> ___
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>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
>
> ___
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>
>
>
> --
> Jean-Marc Nuzillard
> Directeur de Recherches au CNRS
>
> Institut de Chimie Moléculaire de Reims
> CNRS UMR 7312
> Moulin de la Housse
> CPCBAI, Bâtiment 18
> BP 1039
> 51687 REIMS Cedex 2
> France
>
> Tel : 03 26 91 82 10
> Fax : 03 26 91 31 
> 66http://www.univ-reims.fr/icmrhttp://eos.univ-reims.fr/LSD/CSNteam.html
> http://www.univ-reims.fr/LSD/http://www.univ-reims.fr/LSD/JmnSoft/
>
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Re: [Rdkit-discuss] explicit H atoms

[Jean-Marc Nuzillard]

Hi Maciek,

I would find your example rather readable even without explicit H atoms.



I drew it like that because I do not have the wavy wedge at hand.

Thanks for your proposal,
Best,

Jean-Marc



Le 09/03/2021 à 11:26, Maciek Wójcikowski a écrit :

Hi,

I'd say that for a tetrahedral stereo that is possible to remove all 
of Hs. But for double bonds it might not be as easy, or impossible for 
some edge cases - conjugated double bonds in particular. Here is one:

image.png
[H]\C(=C/C)C=C\C([H])=C\C



Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl 


wt., 9 mar 2021 o 10:47 Paul Emsley > napisał(a):


On 09/03/2021 09:01, Jean-Marc Nuzillard wrote:
> Sure, testosterone may be drawn as
> [snip]

OK :-)

That's a top quality rendering by the way. How did you make it?

Paul.


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--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html

http://www.univ-reims.fr/LSD/
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Re: [Rdkit-discuss] explicit H atoms

[Jean-Marc Nuzillard]

The structure I posted was drawn with ChemDraw (now sold by PerkinElmer).

Best,

Jean-Marc

Le 09/03/2021 à 10:44, Paul Emsley a écrit :

On 09/03/2021 09:01, Jean-Marc Nuzillard wrote:

Sure, testosterone may be drawn as
[snip]


OK :-)

That's a top quality rendering by the way. How did you make it?

Paul.


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--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/



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Re: [Rdkit-discuss] explicit H atoms

[Maciek Wójcikowski]

Hi,

I'd say that for a tetrahedral stereo that is possible to remove all of Hs.
But for double bonds it might not be as easy, or impossible for some edge
cases - conjugated double bonds in particular. Here is one:

[image: image.png]
[H]\C(=C/C)C=C\C([H])=C\C



Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


wt., 9 mar 2021 o 10:47 Paul Emsley  napisał(a):

> On 09/03/2021 09:01, Jean-Marc Nuzillard wrote:
> > Sure, testosterone may be drawn as
> > [snip]
>
> OK :-)
>
> That's a top quality rendering by the way. How did you make it?
>
> Paul.
>
>
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Re: [Rdkit-discuss] explicit H atoms

[Paul Emsley]

On 09/03/2021 09:01, Jean-Marc Nuzillard wrote:

Sure, testosterone may be drawn as
[snip]


OK :-)

That's a top quality rendering by the way. How did you make it?

Paul.


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Re: [Rdkit-discuss] explicit H atoms

[Jean-Marc Nuzillard]

Sure, testosterone may be drawn as



Jean-Marc


Le 08/03/2021 à 18:26, Rocco Moretti a écrit :
On Mon, Mar 8, 2021 at 11:17 AM Paul Emsley > wrote:


On 08/03/2021 13:55, Jean-Marc Nuzillard wrote:
>
> Is it always possible to represent an organic molecule in 2D
with all necessary
> configuration hints (bond wedges pointing to the front or to the
back)
> without introducing any explicit hydrogen atom?

No. Testosterone.


Is that "not possible" or simply "against convention"? One could 
certainly imagine someone attempting to put the dashed and wedged 
designations on the ring bonds, and leaving the hydrogens implicit. 
(Flagrantly ignoring how much it would mess with steroid chemists' 
brains.)



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--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/

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