Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

2020-04-01 Thread Ganesh Shahane 
Thank you Dr. Schuffenhauer. This makes sense.

--
Best,
Ganesh


On Wed, Apr 1, 2020 at 5:36 PM Schuffenhauer, Ansgar <
ansgar.schuffenha...@novartis.com> wrote:

> Hi Ganesh
>
> Chemical motives of fragments are not adding simply up. The linkage of two
> fragments creates new motives at the fragment linkage points not present in
> either of the fragments, and the circular substructures of the once
> terminal atoms are disappearing.
> Depending on the type of fragmentation and assembly strategy you use, even
> stereocenters could be created by fragment linkage
>
>
> Best regards
>
>
> Ansgar Schuffenhauer
> Senior Investigator I
> T +41 79 608 9063
> ansgar.schuffenha...@novartis.com
>
> Novartis Pharma AG
> NIBR
>
> -Original Message-
> From: rdkit-discuss-requ...@lists.sourceforge.net <
> rdkit-discuss-requ...@lists.sourceforge.net>
> Sent: Mittwoch, 1. April 2020 15:15
> To: rdkit-discuss@lists.sourceforge.net
> Subject: Rdkit-discuss Digest, Vol 150, Issue 4
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>
>1. Re: Synthetic Accessibility (SA) score (Alan Kerstjens Medina)
>
>
> --
>
> Message: 1
> Date: Wed, 1 Apr 2020 10:58:56 +
> From: Alan Kerstjens Medina 
> To: Ganesh Shahane 
> Cc: "rdkit-discuss@lists.sourceforge.net"
> 
> Subject: Re: [Rdkit-discuss] Synthetic Accessibility (SA) score
> Message-ID:
> <
> am0pr09mb3858a943619170c30254a7efa4...@am0pr09mb3858.eurprd09.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="windows-1252"
>
> Hi Ganesh,
>
> To delve a bit deeper into this, if I recall correctly, SA score is
> calculated based on both:
>
>   1.  The prevalence of your molecule?s chemical motifs in a virtual
> library of synthesizable compounds.
>   2.  A set of logarithmic formulas that take as parameters molecular
> features associated with chemical complexity, like the ring complexity or
> number of stereocenters.
> Consequently, like Axel and Nils have pointed out before me, the sum of
> fragment SA scores shouldn?t be the same as that of a whole molecule. This
> is because you have more chemical motifs in your larger molecule (think of
> how fingerprints are generated) and because you can?t sum logarithms in the
> same way you sum real numbers.
>
> You can find the details in the original publication:
>
> Ertl, P., & Schuffenhauer, A. (2009). Estimation of synthetic
> accessibility score of drug-like molecules based on molecular complexity
> and fragment contributions. Journal of Cheminformatics, 1(1), 1?11.
> https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1186_1758-2D2946-2D1-2D8=DwICAg=ZbgFmJjg4pdtrnL2HUJUDw=5QXEEnQo9VkJH7cIXFb_E4UmFhbbILws-P-WlR4_pzpv_6dQk_-xFQGH00p03i-I=w39sgK-SCsl2RmZF3hc9J7GZnaERmOcPmrT2osTwPrc=SpDRDob2_4abUGK1H8zKdWcOyMo0Ofrqid7Q_0UuQPs=
> From: Nils Weskamp<mailto:nils.wesk...@gmail.com>
> Sent: 01 April 2020 12:48
> To: Ganesh Shahane<mailto:ganesh7shah...@gmail.com>
> Cc: rdkit-discuss@lists.sourceforge.net rdkit-discuss@lists.sourceforge.net>
> Subject: Re: [Rdkit-discuss] Synthetic Accessibility (SA) score
>
> Hi Ganesh,
>
> I would like to challenge your premise. Why do you think that synthetic
> accessibility should add up like that?
>
> Theoretically, I would expect that the combination of A,B and C to ABC
> will require some synthetic effort - so should be SA(A) + SA(B) + SA(C) <
> SA(ABC).
>
> Technically, the combination of the three fragments will change the
> properties and environment of at least some atoms in the molecule, so that
> should have an influence on the result. I suspect it will be difficult to
> define a score with the desired properties without making use of the
> fragmentation scheme you are using.
>
> Best regards,
> Nils
>
>
> On Wed, Apr 1, 2020 at

Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

2020-04-01 Thread Schuffenhauer, Ansgar 
Hi Ganesh

Chemical motives of fragments are not adding simply up. The linkage of two 
fragments creates new motives at the fragment linkage points not present in 
either of the fragments, and the circular substructures of the once terminal 
atoms are disappearing.
Depending on the type of fragmentation and assembly strategy you use, even 
stereocenters could be created by fragment linkage


Best regards


Ansgar Schuffenhauer
Senior Investigator I
T +41 79 608 9063
ansgar.schuffenha...@novartis.com

Novartis Pharma AG
NIBR

-Original Message-
From: rdkit-discuss-requ...@lists.sourceforge.net 
 
Sent: Mittwoch, 1. April 2020 15:15
To: rdkit-discuss@lists.sourceforge.net
Subject: Rdkit-discuss Digest, Vol 150, Issue 4

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Today's Topics:

   1. Re: Synthetic Accessibility (SA) score (Alan Kerstjens Medina)


--

Message: 1
Date: Wed, 1 Apr 2020 10:58:56 +
From: Alan Kerstjens Medina 
To: Ganesh Shahane 
Cc: "rdkit-discuss@lists.sourceforge.net"
    
Subject: Re: [Rdkit-discuss] Synthetic Accessibility (SA) score
Message-ID:



Content-Type: text/plain; charset="windows-1252"

Hi Ganesh,

To delve a bit deeper into this, if I recall correctly, SA score is calculated 
based on both:

  1.  The prevalence of your molecule?s chemical motifs in a virtual library of 
synthesizable compounds.
  2.  A set of logarithmic formulas that take as parameters molecular features 
associated with chemical complexity, like the ring complexity or number of 
stereocenters.
Consequently, like Axel and Nils have pointed out before me, the sum of 
fragment SA scores shouldn?t be the same as that of a whole molecule. This is 
because you have more chemical motifs in your larger molecule (think of how 
fingerprints are generated) and because you can?t sum logarithms in the same 
way you sum real numbers.

You can find the details in the original publication:

Ertl, P., & Schuffenhauer, A. (2009). Estimation of synthetic accessibility 
score of drug-like molecules based on molecular complexity and fragment 
contributions. Journal of Cheminformatics, 1(1), 1?11. 
https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1186_1758-2D2946-2D1-2D8=DwICAg=ZbgFmJjg4pdtrnL2HUJUDw=5QXEEnQo9VkJH7cIXFb_E4UmFhbbILws-P-WlR4_pzpv_6dQk_-xFQGH00p03i-I=w39sgK-SCsl2RmZF3hc9J7GZnaERmOcPmrT2osTwPrc=SpDRDob2_4abUGK1H8zKdWcOyMo0Ofrqid7Q_0UuQPs=
From: Nils Weskamp<mailto:nils.wesk...@gmail.com>
Sent: 01 April 2020 12:48
To: Ganesh Shahane<mailto:ganesh7shah...@gmail.com>
Cc: 
rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

Hi Ganesh,

I would like to challenge your premise. Why do you think that synthetic 
accessibility should add up like that?

Theoretically, I would expect that the combination of A,B and C to ABC will 
require some synthetic effort - so should be SA(A) + SA(B) + SA(C) < SA(ABC).

Technically, the combination of the three fragments will change the properties 
and environment of at least some atoms in the molecule, so that should have an 
influence on the result. I suspect it will be difficult to define a score with 
the desired properties without making use of the fragmentation scheme you are 
using.

Best regards,
Nils


On Wed, Apr 1, 2020 at 12:36 PM Ganesh Shahane 
mailto:ganesh7shah...@gmail.com>> wrote:
Hi Axel,

Thank you for your response.

Yes, I tried to implement the aforementioned script. It works very well on 
whole molecules.

However, I am trying to implement the script on fragments. For example, if I 
have fragments: A, B and C that makes up a whole molecule "ABC", then the sum 
of SA scores of the fragments should be equal to SA score of the whole molecule.

Right now, the summation doesn't add up.

I was wondering if there is a correction that needs to be made to the sum of SA 
scores such that it is equal to the SA score of the whole molecule.

--
Best,
Ganesh


On Mon, Mar 30, 2020 at 4:30 PM Axel Pahl 
mailto:axelp...@gmx.de>> wrote:
Hi Ganesh,

are you aware that the SA Sco

Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

2020-04-01 Thread Alan Kerstjens Medina 
Hi Ganesh,

To delve a bit deeper into this, if I recall correctly, SA score is calculated 
based on both:

  1.  The prevalence of your molecule’s chemical motifs in a virtual library of 
synthesizable compounds.
  2.  A set of logarithmic formulas that take as parameters molecular features 
associated with chemical complexity, like the ring complexity or number of 
stereocenters.
Consequently, like Axel and Nils have pointed out before me, the sum of 
fragment SA scores shouldn’t be the same as that of a whole molecule. This is 
because you have more chemical motifs in your larger molecule (think of how 
fingerprints are generated) and because you can’t sum logarithms in the same 
way you sum real numbers.

You can find the details in the original publication:

Ertl, P., & Schuffenhauer, A. (2009). Estimation of synthetic accessibility 
score of drug-like molecules based on molecular complexity and fragment 
contributions. Journal of Cheminformatics, 1(1), 1–11. 
https://doi.org/10.1186/1758-2946-1-8
From: Nils Weskamp<mailto:nils.wesk...@gmail.com>
Sent: 01 April 2020 12:48
To: Ganesh Shahane<mailto:ganesh7shah...@gmail.com>
Cc: 
rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

Hi Ganesh,

I would like to challenge your premise. Why do you think that synthetic 
accessibility should add up like that?

Theoretically, I would expect that the combination of A,B and C to ABC will 
require some synthetic effort - so should be SA(A) + SA(B) + SA(C) < SA(ABC).

Technically, the combination of the three fragments will change the properties 
and environment of at least some atoms in the molecule, so that should have an 
influence on the result. I suspect it will be difficult to define a score with 
the desired properties without making use of the fragmentation scheme you are 
using.

Best regards,
Nils


On Wed, Apr 1, 2020 at 12:36 PM Ganesh Shahane 
mailto:ganesh7shah...@gmail.com>> wrote:
Hi Axel,

Thank you for your response.

Yes, I tried to implement the aforementioned script. It works very well on 
whole molecules.

However, I am trying to implement the script on fragments. For example, if I 
have fragments: A, B and C that makes up a whole molecule "ABC", then the sum 
of SA scores of the fragments should be equal to SA score of the whole molecule.

Right now, the summation doesn't add up.

I was wondering if there is a correction that needs to be made to the sum of SA 
scores such that it is equal to the SA score of the whole molecule.

--
Best,
Ganesh


On Mon, Mar 30, 2020 at 4:30 PM Axel Pahl 
mailto:axelp...@gmx.de>> wrote:
Hi Ganesh,

are you aware that the SA Score IS implemented in RDKit:

https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score

Kind regards,
Axel


On 30.03.20 16:55, Ganesh Shahane wrote:
Dear RDKitters,

I am trying a to find a way to implement the SA score as a sum of fragments 
contributions from this paper:

Ertl, Peter, and Ansgar Schuffenhauer. 2009. “Estimation of Synthetic 
Accessibility Score of Drug-like Molecules Based on Molecular Complexity and 
Fragment Contributions.” Journal of Cheminformatics 1 (1): 8.

For example, if I have three different fragments: A, B and C and their 
respective SA scores, then the SA score of molecule "A+B+C" should be the sum 
of all three fragment SA scores.

In practice though, the fragment SA scores do not add up.

I was wondering if anyone across the cheminformatics community has successfully 
implemented this or a similar strategy?

--
Best,
Ganesh




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Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

2020-04-01 Thread Ganesh Shahane 
Hi Alan,

Thank you for pointing that out. Somehow I missed the part about the
logarithms while going through the article and your explanation makes much
more sense now.

--
Best,
Ganesh


On Wed, Apr 1, 2020 at 11:59 AM Alan Kerstjens Medina <
alankerstj...@hotmail.com> wrote:

> Hi Ganesh,
>
>
>
> To delve a bit deeper into this, if I recall correctly, SA score is
> calculated based on both:
>
>1. The prevalence of your molecule’s chemical motifs in a virtual
>library of synthesizable compounds.
>2. A set of logarithmic formulas that take as parameters molecular
>features associated with chemical complexity, like the ring complexity or
>number of stereocenters.
>
> Consequently, like Axel and Nils have pointed out before me, the sum of
> fragment SA scores shouldn’t be the same as that of a whole molecule. This
> is because you have more chemical motifs in your larger molecule (think of
> how fingerprints are generated) and because you can’t sum logarithms in the
> same way you sum real numbers.
>
>
>
> You can find the details in the original publication:
>
> Ertl, P., & Schuffenhauer, A. (2009). Estimation of synthetic
> accessibility score of drug-like molecules based on molecular complexity
> and fragment contributions. *Journal of Cheminformatics*, *1*(1), 1–11.
> https://doi.org/10.1186/1758-2946-1-8
>
> *From: *Nils Weskamp 
> *Sent: *01 April 2020 12:48
> *To: *Ganesh Shahane 
> *Cc: *rdkit-discuss@lists.sourceforge.net
> *Subject: *Re: [Rdkit-discuss] Synthetic Accessibility (SA) score
>
>
>
> Hi Ganesh,
>
>
>
> I would like to challenge your premise. Why do you think that synthetic
> accessibility should add up like that?
>
>
>
> Theoretically, I would expect that the combination of A,B and C to ABC
> will require some synthetic effort - so should be SA(A) + SA(B) + SA(C) <
> SA(ABC).
>
>
>
> Technically, the combination of the three fragments will change the
> properties and environment of at least some atoms in the molecule, so that
> should have an influence on the result. I suspect it will be difficult to
> define a score with the desired properties without making use of the
> fragmentation scheme you are using.
>
>
>
> Best regards,
>
> Nils
>
>
>
>
>
> On Wed, Apr 1, 2020 at 12:36 PM Ganesh Shahane 
> wrote:
>
> Hi Axel,
>
>
>
> Thank you for your response.
>
>
>
> Yes, I tried to implement the aforementioned script. It works very well on
> whole molecules.
>
>
>
> However, I am trying to implement the script on fragments. For example, if
> I have fragments: A, B and C that makes up a whole molecule "ABC", then the
> sum of SA scores of the fragments should be equal to SA score of the whole
> molecule.
>
>
>
> Right now, the summation doesn't add up.
>
>
>
> I was wondering if there is a correction that needs to be made to the sum
> of SA scores such that it is equal to the SA score of the whole molecule.
>
>
>
> --
>
> Best,
>
> Ganesh
>
>
>
>
>
> On Mon, Mar 30, 2020 at 4:30 PM Axel Pahl  wrote:
>
> Hi Ganesh,
>
> are you aware that the SA Score IS implemented in RDKit:
>
> https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score
>
> Kind regards,
> Axel
>
>
> On 30.03.20 16:55, Ganesh Shahane wrote:
>
> Dear RDKitters,
>
>
>
> I am trying a to find a way to implement the SA score as a sum of
> fragments contributions from this paper:
>
>
>
> Ertl, Peter, and Ansgar Schuffenhauer. 2009. “Estimation of Synthetic
> Accessibility Score of Drug-like Molecules Based on Molecular Complexity
> and Fragment Contributions.” *Journal of Cheminformatics* 1 (1): 8.
>
>
>
> For example, if I have three different fragments: A, B and C and their
> respective SA scores, then the SA score of molecule "A+B+C" should be the
> sum of all three fragment SA scores.
>
>
>
> In practice though, the fragment SA scores do not add up.
>
>
>
> I was wondering if anyone across the cheminformatics community has
> successfully implemented this or a similar strategy?
>
>
>
> --
>
> Best,
>
> Ganesh
>
>
>
>
> ___
>
> Rdkit-discuss mailing list
>
> Rdkit-discuss@lists.sourceforge.net
>
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
> ___
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> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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>
>
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Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

2020-04-01 Thread Ganesh Shahane 
Hi Nils and Axel,

Thank you very much for your response.

I am trying to develop a de-novo drug design framework that uses fragments
as building blocks to assemble a molecule inside a target protein active
site.

The algorithm that I am using assembles fragments into molecules such that
the resulting molecules satisfy a certain properties.

However, the properties have to be additive, like for example: the
molecular weight or polar surface area, where the sum of the fragments is
equal to that of the whole molecule.

I have incorporated a number of such fragment-based additive properties,
and when trying to incorporate the SA_score, I realised that it didn't work.

--
Best,
Ganesh


On Wed, Apr 1, 2020 at 11:47 AM Nils Weskamp  wrote:

> Hi Ganesh,
>
> I would like to challenge your premise. Why do you think that synthetic
> accessibility should add up like that?
>
> Theoretically, I would expect that the combination of A,B and C to ABC
> will require some synthetic effort - so should be SA(A) + SA(B) + SA(C) <
> SA(ABC).
>
> Technically, the combination of the three fragments will change the
> properties and environment of at least some atoms in the molecule, so that
> should have an influence on the result. I suspect it will be difficult to
> define a score with the desired properties without making use of the
> fragmentation scheme you are using.
>
> Best regards,
> Nils
>
>
> On Wed, Apr 1, 2020 at 12:36 PM Ganesh Shahane 
> wrote:
>
>> Hi Axel,
>>
>> Thank you for your response.
>>
>> Yes, I tried to implement the aforementioned script. It works very well
>> on whole molecules.
>>
>> However, I am trying to implement the script on fragments. For example,
>> if I have fragments: A, B and C that makes up a whole molecule "ABC", then
>> the sum of SA scores of the fragments should be equal to SA score of the
>> whole molecule.
>>
>> Right now, the summation doesn't add up.
>>
>> I was wondering if there is a correction that needs to be made to the sum
>> of SA scores such that it is equal to the SA score of the whole molecule.
>>
>> --
>> Best,
>> Ganesh
>>
>>
>> On Mon, Mar 30, 2020 at 4:30 PM Axel Pahl  wrote:
>>
>>> Hi Ganesh,
>>>
>>> are you aware that the SA Score IS implemented in RDKit:
>>>
>>> https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score
>>>
>>> Kind regards,
>>> Axel
>>>
>>>
>>>
>>> On 30.03.20 16:55, Ganesh Shahane wrote:
>>>
>>> Dear RDKitters,
>>>
>>> I am trying a to find a way to implement the SA score as a sum of
>>> fragments contributions from this paper:
>>>
>>> Ertl, Peter, and Ansgar Schuffenhauer. 2009. “Estimation of Synthetic
>>> Accessibility Score of Drug-like Molecules Based on Molecular Complexity
>>> and Fragment Contributions.” *Journal of Cheminformatics* 1 (1): 8.
>>>
>>> For example, if I have three different fragments: A, B and C and their
>>> respective SA scores, then the SA score of molecule "A+B+C" should be the
>>> sum of all three fragment SA scores.
>>>
>>> In practice though, the fragment SA scores do not add up.
>>>
>>> I was wondering if anyone across the cheminformatics community has
>>> successfully implemented this or a similar strategy?
>>>
>>> --
>>> Best,
>>> Ganesh
>>>
>>>
>>> ___
>>> Rdkit-discuss mailing 
>>> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>> ___
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>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>> ___
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>>
>
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Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

2020-04-01 Thread Nils Weskamp 
Hi Ganesh,

I would like to challenge your premise. Why do you think that synthetic
accessibility should add up like that?

Theoretically, I would expect that the combination of A,B and C to ABC will
require some synthetic effort - so should be SA(A) + SA(B) + SA(C) <
SA(ABC).

Technically, the combination of the three fragments will change the
properties and environment of at least some atoms in the molecule, so that
should have an influence on the result. I suspect it will be difficult to
define a score with the desired properties without making use of the
fragmentation scheme you are using.

Best regards,
Nils


On Wed, Apr 1, 2020 at 12:36 PM Ganesh Shahane 
wrote:

> Hi Axel,
>
> Thank you for your response.
>
> Yes, I tried to implement the aforementioned script. It works very well on
> whole molecules.
>
> However, I am trying to implement the script on fragments. For example, if
> I have fragments: A, B and C that makes up a whole molecule "ABC", then the
> sum of SA scores of the fragments should be equal to SA score of the whole
> molecule.
>
> Right now, the summation doesn't add up.
>
> I was wondering if there is a correction that needs to be made to the sum
> of SA scores such that it is equal to the SA score of the whole molecule.
>
> --
> Best,
> Ganesh
>
>
> On Mon, Mar 30, 2020 at 4:30 PM Axel Pahl  wrote:
>
>> Hi Ganesh,
>>
>> are you aware that the SA Score IS implemented in RDKit:
>>
>> https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score
>>
>> Kind regards,
>> Axel
>>
>>
>>
>> On 30.03.20 16:55, Ganesh Shahane wrote:
>>
>> Dear RDKitters,
>>
>> I am trying a to find a way to implement the SA score as a sum of
>> fragments contributions from this paper:
>>
>> Ertl, Peter, and Ansgar Schuffenhauer. 2009. “Estimation of Synthetic
>> Accessibility Score of Drug-like Molecules Based on Molecular Complexity
>> and Fragment Contributions.” *Journal of Cheminformatics* 1 (1): 8.
>>
>> For example, if I have three different fragments: A, B and C and their
>> respective SA scores, then the SA score of molecule "A+B+C" should be the
>> sum of all three fragment SA scores.
>>
>> In practice though, the fragment SA scores do not add up.
>>
>> I was wondering if anyone across the cheminformatics community has
>> successfully implemented this or a similar strategy?
>>
>> --
>> Best,
>> Ganesh
>>
>>
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Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

2020-04-01 Thread Axel Pahl 

Hi Ganesh,

I guess the synthesis of a fragment can be quite different from the
synthesis of a whole molecule containing that fragment, so I don't know
if it is a valid assumtion that the SA scores of the fragments have to
add up to the SA score of the whiole molecule.

Kind regards,
Axel

On 01.04.20 12:34, Ganesh Shahane wrote:

Hi Axel,

Thank you for your response.

Yes, I tried to implement the aforementioned script. It works very
well on whole molecules.

However, I am trying to implement the script on fragments.
For example, if I have fragments: A, B and C that makes up a whole
molecule "ABC", then the sum of SA scores of the fragments should be
equal to SA score of the whole molecule.

Right now, the summation doesn't add up.

I was wondering if there is a correction that needs to be made to the
sum of SA scores such that it is equal to the SA score of the whole
molecule.

--
Best,
Ganesh


On Mon, Mar 30, 2020 at 4:30 PM Axel Pahl mailto:axelp...@gmx.de>> wrote:

Hi Ganesh,

are you aware that the SA Score IS implemented in RDKit:

https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score

Kind regards,
Axel



On 30.03.20 16:55, Ganesh Shahane wrote:

Dear RDKitters,

I am trying a to find a way to implement the SA score as a sum of
fragments contributions from this paper:

Ertl, Peter, and Ansgar Schuffenhauer. 2009. “Estimation of
Synthetic Accessibility Score of Drug-like Molecules Based on
Molecular Complexity and Fragment Contributions.” /Journal of
Cheminformatics/ 1 (1): 8.

For example, if I have three different fragments: A, B and C and
their respective SA scores, then the SA score of molecule "A+B+C"
should be the sum of all three fragment SA scores.

In practice though, the fragment SA scores do not add up.

I was wondering if anyone across the cheminformatics community
has successfully implemented this or a similar strategy?

--
Best,
Ganesh


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Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

2020-04-01 Thread Ganesh Shahane 
Hi Axel,

Thank you for your response.

Yes, I tried to implement the aforementioned script. It works very well on
whole molecules.

However, I am trying to implement the script on fragments. For example, if
I have fragments: A, B and C that makes up a whole molecule "ABC", then the
sum of SA scores of the fragments should be equal to SA score of the whole
molecule.

Right now, the summation doesn't add up.

I was wondering if there is a correction that needs to be made to the sum
of SA scores such that it is equal to the SA score of the whole molecule.

--
Best,
Ganesh


On Mon, Mar 30, 2020 at 4:30 PM Axel Pahl  wrote:

> Hi Ganesh,
>
> are you aware that the SA Score IS implemented in RDKit:
>
> https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score
>
> Kind regards,
> Axel
>
>
>
> On 30.03.20 16:55, Ganesh Shahane wrote:
>
> Dear RDKitters,
>
> I am trying a to find a way to implement the SA score as a sum of
> fragments contributions from this paper:
>
> Ertl, Peter, and Ansgar Schuffenhauer. 2009. “Estimation of Synthetic
> Accessibility Score of Drug-like Molecules Based on Molecular Complexity
> and Fragment Contributions.” *Journal of Cheminformatics* 1 (1): 8.
>
> For example, if I have three different fragments: A, B and C and their
> respective SA scores, then the SA score of molecule "A+B+C" should be the
> sum of all three fragment SA scores.
>
> In practice though, the fragment SA scores do not add up.
>
> I was wondering if anyone across the cheminformatics community has
> successfully implemented this or a similar strategy?
>
> --
> Best,
> Ganesh
>
>
> ___
> Rdkit-discuss mailing 
> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

2020-03-30 Thread Axel Pahl 

Hi Ganesh,

are you aware that the SA Score IS implemented in RDKit:

https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score

Kind regards,
Axel



On 30.03.20 16:55, Ganesh Shahane wrote:

Dear RDKitters,

I am trying a to find a way to implement the SA score as a sum of
fragments contributions from this paper:

Ertl, Peter, and Ansgar Schuffenhauer. 2009. “Estimation of Synthetic
Accessibility Score of Drug-like Molecules Based on Molecular
Complexity and Fragment Contributions.” /Journal of Cheminformatics/ 1
(1): 8.

For example, if I have three different fragments: A, B and C and their
respective SA scores, then the SA score of molecule "A+B+C" should be
the sum of all three fragment SA scores.

In practice though, the fragment SA scores do not add up.

I was wondering if anyone across the cheminformatics community has
successfully implemented this or a similar strategy?

--
Best,
Ganesh


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[Rdkit-discuss] Synthetic Accessibility (SA) score

2020-03-30 Thread Ganesh Shahane 
Dear RDKitters,

I am trying a to find a way to implement the SA score as a sum of fragments
contributions from this paper:

Ertl, Peter, and Ansgar Schuffenhauer. 2009. “Estimation of Synthetic
Accessibility Score of Drug-like Molecules Based on Molecular Complexity
and Fragment Contributions.” *Journal of Cheminformatics* 1 (1): 8.

For example, if I have three different fragments: A, B and C and their
respective SA scores, then the SA score of molecule "A+B+C" should be the
sum of all three fragment SA scores.

In practice though, the fragment SA scores do not add up.

I was wondering if anyone across the cheminformatics community has
successfully implemented this or a similar strategy?

--
Best,
Ganesh
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