[Rdkit-discuss] [Administrivia] changes to list digest settings

[Greg Landrum]

Dear all,

This message is only relevant to people who get the mailing list in digest
format.

Someone who is subscribed to get the mailing list as a digest reported
yesterday that they were getting multiple digests per day, each with a
small number of messages. Since that's not the intent, I just modified the
list settings so that it will send out a single digest per day.

-greg
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Re: [Rdkit-discuss] Looking for additional GSoC co-mentors

[Geoffrey Hutchison]

Wearing my "admin for Open Chemistry" hat for the moment.. As a community, 
we've been very lucky to get a lot of good open source chemistry development 
done over the last few years.

Moreover, many of these students are now exposed to RDKit, cheminformatics, and 
good coding. (In other words, they're good recruits for both academic and 
industrial positions. ;-)

Google is never open about their criteria for allocating the number of slots to 
organizations. Still, groups with more mentors are more likely to get more 
slots.

I'll be more blunt than Greg - without more mentors we will be forced to make 
very hard choices. We'll probably still need to do that, but finding a few more 
co-mentors will certainly help RDKit.

-Geoff


> On Apr 1, 2020, at 2:16 AM, Greg Landrum  wrote:
> 
> Dear all,
> 
> Yesterday was the last day for potential students to submit applications for 
> Google Summer of Code and we got proposals for the following five projects:
> 1) RDKit integration with MongoDB. Python based
> 2) Implement a generalized file reader and a multi-threaded file reader. C++ 
> based
> 3) Integrating trained neural networks (specifically ANI-like force fields) 
> into the RDKit. C++ based
> 4) RDKit-OpenMM integration. C++ based
> 5) Improved RDKit integration with Jupyter, Dask, Pandas, Plotly, and Bokeh. 
> Python based
> 
> There's more about the first four projects here: 
> https://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas 
>  and I'm 
> happy to answer questions about them.
> 
> We have a mentor and co-mentor for each of these projects, but I'm looking 
> for a few more people to act as co-mentors. It doesn't make sense to do a 
> project without at least two mentors - one primary mentor and one co-mentor- 
> and Google is strongly encouraging organizations to have three mentors - one 
> primary and two co-mentors - available for each project. Being a co-mentor is 
> going to require an hour or two a week on average over the course of the 
> program.
> 
> There's more information on the program, including the dates, here:
> https://summerofcode.withgoogle.com/how-it-works/ 
> 
> 
> GSoC is really a great program and being a mentor/co-mentor is a good way to 
> help move both the open-source community and the RDKit forward.
> 
> If you're interested or have questions, feel free to send me email,
> -greg
> 
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Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

[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
>
> Send Rdkit-discuss mailing list submissions to
> rdkit-discuss@lists.sourceforge.net
>
> To subscribe or unsubscribe via the World Wide Web, visit
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_rdkit-2Ddiscuss=DwICAg=ZbgFmJjg4pdtrnL2HUJUDw=5QXEEnQo9VkJH7cIXFb_E4UmFhbbILws-P-WlR4_pzpv_6dQk_-xFQGH00p03i-I=w39sgK-SCsl2RmZF3hc9J7GZnaERmOcPmrT2osTwPrc=5S3iPLyW1E2knLYrWo9DKJeSOI7RQUIjBnhjpTO2EOs=
> or, via email, send a message with subject or body 'help' to
> rdkit-discuss-requ...@lists.sourceforge.net
>
> You can reach the person managing the list at
> rdkit-discuss-ow...@lists.sourceforge.net
>
> When replying, please edit your Subject line so it is more specific than
> "Re: Contents of Rdkit-discuss digest..."
>
>
> 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:
> <
> 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
> Sent: 01 April 2020 12:48
> To: Ganesh Shahane
> 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 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 

Re: [Rdkit-discuss] Installing related issues

[Greg Landrum]

IF you want to use some other python install you could try pointing your
PYTHONPATH at the directory in your conda environment where the RDKit is
installed and make sure that LD_LIBRARY_PATH is pointing to the appropriate
lib directory in that conda environment. IF that doesn't work, we likely
won’t be able to help though.

It would be a ton easier if you installed whatever other stuff you need in
the conda environment or set your PYTHONPATH to point to wherever that
stuff is

-greg


On Wed, 1 Apr 2020 at 18:41, Navid Shervani-Tabar  wrote:

> Any suggestions on how to get it to work? I tried to get rid of the need
> for an environment in RDKit installation using conda-forge on remote
> machine but I need access beyond a user. For packages with pip
> installation available, *pip install --user* does the job.
>
> Navid
>
> On Wed, Apr 1, 2020 at 12:31 PM Greg Landrum 
> wrote:
>
>> That isn’t the python that comes from your conda environment
>>
>> On Wed, 1 Apr 2020 at 16:58, Navid Shervani-Tabar 
>> wrote:
>>
>>> Here are the outputs:
>>>
>>> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]which
>>> python3
>>>
>>> /afs/crc.nd.edu/x86_64_linux/p/pytorch/1.0.0/build-new/bin/python3
>>>
>>> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]python3
>>> -c "from rdkit import Chem;print(Chem.__file__)"
>>>
>>> Traceback (most recent call last):
>>>
>>>   File "", line 1, in 
>>>
>>> ModuleNotFoundError: No module named 'rdkit'
>>>
>>> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]
>>>
>>> Navid
>>>
>>> On Wed, Apr 1, 2020 at 10:40 AM Greg Landrum 
>>> wrote:
>>>
 Are you sure that you get the python from your environment when you do
 "python3 main.py"?

 Please try these two commands:

 which python3
 python3 -c "from rdkit import Chem;print(Chem.__file__)"



 On Tue, Mar 31, 2020 at 11:17 PM Navid Shervani-Tabar <
 nshe...@gmail.com> wrote:

> Hello RDKiters,
>
> I have been using rdkit on my laptop for a while. I was trying to
> install it on my remote repository using conda-forge. It looks like I was
> able to install it but I still get the following error
>
> (Navid_env) [*@crcfe01 ~/Private/Research/code ] conda install -c
> conda-forge rdkit
>
> Collecting package metadata (current_repodata.json): done
>
> Solving environment: done
>
>
>
> ==> WARNING: A newer version of conda exists. <==
>
>   current version: 4.8.2
>
>   latest version: 4.8.3
>
>
> Please update conda by running
>
>
> $ conda update -n base -c defaults conda
>
>
>
>
> # All requested packages already installed.
>
>
> (Navid_env) [*@crcfe01 ~/Private/Research/code ] python3 main.py
>
> Traceback (most recent call last):
>
>   File "main.py", line 6, in 
>
> from VAEtrain import VAEgraph
>
>   File "/afs/
> crc.nd.edu/user/n/*/Private/Research/Scattering-VAE/VAEtrain.py",
> line 22, in 
>
> from utils import tools
>
>   File "/afs/
> crc.nd.edu/user/n/*/Private/Research/Scattering-VAE/utils.py",
> line 6, in 
>
> from rdkit import Chem
>
> ModuleNotFoundError: No module named 'rdkit'
>
> Any idea what might be wrong? (and yes, I have logged in and out
> before running).
>
> Thanks,
> Navid
> ___
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>

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Re: [Rdkit-discuss] Installing related issues

[Navid Shervani-Tabar]

Any suggestions on how to get it to work? I tried to get rid of the need
for an environment in RDKit installation using conda-forge on remote
machine but I need access beyond a user. For packages with pip
installation available, *pip install --user* does the job.

Navid

On Wed, Apr 1, 2020 at 12:31 PM Greg Landrum  wrote:

> That isn’t the python that comes from your conda environment
>
> On Wed, 1 Apr 2020 at 16:58, Navid Shervani-Tabar 
> wrote:
>
>> Here are the outputs:
>>
>> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]which
>> python3
>>
>> /afs/crc.nd.edu/x86_64_linux/p/pytorch/1.0.0/build-new/bin/python3
>>
>> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]python3
>> -c "from rdkit import Chem;print(Chem.__file__)"
>>
>> Traceback (most recent call last):
>>
>>   File "", line 1, in 
>>
>> ModuleNotFoundError: No module named 'rdkit'
>>
>> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]
>>
>> Navid
>>
>> On Wed, Apr 1, 2020 at 10:40 AM Greg Landrum 
>> wrote:
>>
>>> Are you sure that you get the python from your environment when you do
>>> "python3 main.py"?
>>>
>>> Please try these two commands:
>>>
>>> which python3
>>> python3 -c "from rdkit import Chem;print(Chem.__file__)"
>>>
>>>
>>>
>>> On Tue, Mar 31, 2020 at 11:17 PM Navid Shervani-Tabar 
>>> wrote:
>>>
 Hello RDKiters,

 I have been using rdkit on my laptop for a while. I was trying to
 install it on my remote repository using conda-forge. It looks like I was
 able to install it but I still get the following error

 (Navid_env) [*@crcfe01 ~/Private/Research/code ] conda install -c
 conda-forge rdkit

 Collecting package metadata (current_repodata.json): done

 Solving environment: done



 ==> WARNING: A newer version of conda exists. <==

   current version: 4.8.2

   latest version: 4.8.3


 Please update conda by running


 $ conda update -n base -c defaults conda




 # All requested packages already installed.


 (Navid_env) [*@crcfe01 ~/Private/Research/code ] python3 main.py

 Traceback (most recent call last):

   File "main.py", line 6, in 

 from VAEtrain import VAEgraph

   File "/afs/
 crc.nd.edu/user/n/*/Private/Research/Scattering-VAE/VAEtrain.py",
 line 22, in 

 from utils import tools

   File "/afs/
 crc.nd.edu/user/n/*/Private/Research/Scattering-VAE/utils.py",
 line 6, in 

 from rdkit import Chem

 ModuleNotFoundError: No module named 'rdkit'

 Any idea what might be wrong? (and yes, I have logged in and out before
 running).

 Thanks,
 Navid
 ___
 Rdkit-discuss mailing list
 Rdkit-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

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

[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

Send Rdkit-discuss mailing list submissions to
rdkit-discuss@lists.sourceforge.net

To subscribe or unsubscribe via the World Wide Web, visit

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Contents of Rdkit-discuss digest..."


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
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 
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:

Re: [Rdkit-discuss] Installing related issues

[Greg Landrum]

That isn’t the python that comes from your conda environment

On Wed, 1 Apr 2020 at 16:58, Navid Shervani-Tabar  wrote:

> Here are the outputs:
>
> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]which
> python3
>
> /afs/crc.nd.edu/x86_64_linux/p/pytorch/1.0.0/build-new/bin/python3
>
> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]python3
> -c "from rdkit import Chem;print(Chem.__file__)"
>
> Traceback (most recent call last):
>
>   File "", line 1, in 
>
> ModuleNotFoundError: No module named 'rdkit'
>
> (Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]
>
> Navid
>
> On Wed, Apr 1, 2020 at 10:40 AM Greg Landrum 
> wrote:
>
>> Are you sure that you get the python from your environment when you do
>> "python3 main.py"?
>>
>> Please try these two commands:
>>
>> which python3
>> python3 -c "from rdkit import Chem;print(Chem.__file__)"
>>
>>
>>
>> On Tue, Mar 31, 2020 at 11:17 PM Navid Shervani-Tabar 
>> wrote:
>>
>>> Hello RDKiters,
>>>
>>> I have been using rdkit on my laptop for a while. I was trying to
>>> install it on my remote repository using conda-forge. It looks like I was
>>> able to install it but I still get the following error
>>>
>>> (Navid_env) [*@crcfe01 ~/Private/Research/code ] conda install -c
>>> conda-forge rdkit
>>>
>>> Collecting package metadata (current_repodata.json): done
>>>
>>> Solving environment: done
>>>
>>>
>>>
>>> ==> WARNING: A newer version of conda exists. <==
>>>
>>>   current version: 4.8.2
>>>
>>>   latest version: 4.8.3
>>>
>>>
>>> Please update conda by running
>>>
>>>
>>> $ conda update -n base -c defaults conda
>>>
>>>
>>>
>>>
>>> # All requested packages already installed.
>>>
>>>
>>> (Navid_env) [*@crcfe01 ~/Private/Research/code ] python3 main.py
>>>
>>> Traceback (most recent call last):
>>>
>>>   File "main.py", line 6, in 
>>>
>>> from VAEtrain import VAEgraph
>>>
>>>   File "/afs/
>>> crc.nd.edu/user/n/*/Private/Research/Scattering-VAE/VAEtrain.py",
>>> line 22, in 
>>>
>>> from utils import tools
>>>
>>>   File "/afs/
>>> crc.nd.edu/user/n/*/Private/Research/Scattering-VAE/utils.py", line
>>> 6, in 
>>>
>>> from rdkit import Chem
>>>
>>> ModuleNotFoundError: No module named 'rdkit'
>>>
>>> Any idea what might be wrong? (and yes, I have logged in and out before
>>> running).
>>>
>>> Thanks,
>>> Navid
>>> ___
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>
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Re: [Rdkit-discuss] Installing related issues

[Navid Shervani-Tabar]

Here are the outputs:

(Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]which
python3

/afs/crc.nd.edu/x86_64_linux/p/pytorch/1.0.0/build-new/bin/python3

(Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]python3
-c "from rdkit import Chem;print(Chem.__file__)"

Traceback (most recent call last):

  File "", line 1, in 

ModuleNotFoundError: No module named 'rdkit'

(Navid_env) [nshervan@qa-v100-004 ~/Private/Research/Scattering-VAE ]

Navid

On Wed, Apr 1, 2020 at 10:40 AM Greg Landrum  wrote:

> Are you sure that you get the python from your environment when you do
> "python3 main.py"?
>
> Please try these two commands:
>
> which python3
> python3 -c "from rdkit import Chem;print(Chem.__file__)"
>
>
>
> On Tue, Mar 31, 2020 at 11:17 PM Navid Shervani-Tabar 
> wrote:
>
>> Hello RDKiters,
>>
>> I have been using rdkit on my laptop for a while. I was trying to install
>> it on my remote repository using conda-forge. It looks like I was able to
>> install it but I still get the following error
>>
>> (Navid_env) [*@crcfe01 ~/Private/Research/code ] conda install -c
>> conda-forge rdkit
>>
>> Collecting package metadata (current_repodata.json): done
>>
>> Solving environment: done
>>
>>
>>
>> ==> WARNING: A newer version of conda exists. <==
>>
>>   current version: 4.8.2
>>
>>   latest version: 4.8.3
>>
>>
>> Please update conda by running
>>
>>
>> $ conda update -n base -c defaults conda
>>
>>
>>
>>
>> # All requested packages already installed.
>>
>>
>> (Navid_env) [*@crcfe01 ~/Private/Research/code ] python3 main.py
>>
>> Traceback (most recent call last):
>>
>>   File "main.py", line 6, in 
>>
>> from VAEtrain import VAEgraph
>>
>>   File "/afs/
>> crc.nd.edu/user/n/*/Private/Research/Scattering-VAE/VAEtrain.py",
>> line 22, in 
>>
>> from utils import tools
>>
>>   File "/afs/
>> crc.nd.edu/user/n/*/Private/Research/Scattering-VAE/utils.py", line
>> 6, in 
>>
>> from rdkit import Chem
>>
>> ModuleNotFoundError: No module named 'rdkit'
>>
>> Any idea what might be wrong? (and yes, I have logged in and out before
>> running).
>>
>> Thanks,
>> Navid
>> ___
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Re: [Rdkit-discuss] Installing related issues

[Greg Landrum]

Are you sure that you get the python from your environment when you do
"python3 main.py"?

Please try these two commands:

which python3
python3 -c "from rdkit import Chem;print(Chem.__file__)"



On Tue, Mar 31, 2020 at 11:17 PM Navid Shervani-Tabar 
wrote:

> Hello RDKiters,
>
> I have been using rdkit on my laptop for a while. I was trying to install
> it on my remote repository using conda-forge. It looks like I was able to
> install it but I still get the following error
>
> (Navid_env) [*@crcfe01 ~/Private/Research/code ] conda install -c
> conda-forge rdkit
>
> Collecting package metadata (current_repodata.json): done
>
> Solving environment: done
>
>
>
> ==> WARNING: A newer version of conda exists. <==
>
>   current version: 4.8.2
>
>   latest version: 4.8.3
>
>
> Please update conda by running
>
>
> $ conda update -n base -c defaults conda
>
>
>
>
> # All requested packages already installed.
>
>
> (Navid_env) [*@crcfe01 ~/Private/Research/code ] python3 main.py
>
> Traceback (most recent call last):
>
>   File "main.py", line 6, in 
>
> from VAEtrain import VAEgraph
>
>   File "/afs/
> crc.nd.edu/user/n/*/Private/Research/Scattering-VAE/VAEtrain.py",
> line 22, in 
>
> from utils import tools
>
>   File "/afs/
> crc.nd.edu/user/n/*/Private/Research/Scattering-VAE/utils.py", line
> 6, in 
>
> from rdkit import Chem
>
> ModuleNotFoundError: No module named 'rdkit'
>
> Any idea what might be wrong? (and yes, I have logged in and out before
> running).
>
> Thanks,
> Navid
> ___
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>
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Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

[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
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 
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

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

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

[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
>>
>>
>> ___
>> Rdkit-discuss mailing 
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>>
>> ___
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>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

[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

[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
>
>
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Re: [Rdkit-discuss] problem building from source - ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

[Tim Dudgeon]

Thanks Paolo, that fixed it.

On 30/03/2020 15:05, Paolo Tosco wrote:

Hi Tim,

try rm -rf External/CoordGen/coordgen* External/CoordGen/maeparser*

you might have some outdated coordgen libs. Deleting those and 
re-running cmake will download them afresh.


Cheers,
p.

On 30/03/2020 14:51, Tim Dudgeon wrote:

I'm finding an error building from source (on master branch).

Any ideas?

cmake -DPYTHON_EXECUTABLE=/usr/bin/python3 
-DRDK_BUILD_INCHI_SUPPORT=ON  -DRDK_BUILD_AVALON_SUPPORT=ON 
-DRDK_BUILD_PYTHON_WRAPPERS=ON  -DRDK_BUILD_SWIG_WRAPPERS=ON ..

make -j 8


[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileParser.cpp.o
[ 66%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/TplFileWriter.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBParser.cpp.o
[ 67%] Building CXX object 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBWriter.cpp.o
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Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/PDBSupplier.cpp.o
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Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/XYZFileWriter.cpp.o
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Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o
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Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/ProximityBonds.cpp.o
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Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SequenceParsers.cpp.o
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Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/SVGParser.cpp.o
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp: 
In function ‘void 
RDKit::{anonymous}::set_mol_properties(RDKit::RWMol&, const 
schrodinger::mae::Block&)’:
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:214:37: 
error: ‘CT_CHIRALITY_PROP_PREFIX’ is not a member of ‘schrodinger::mae’
  214 | } else if 
(prop.first.find(mae::CT_CHIRALITY_PROP_PREFIX) == 0 ||

  | ^~~~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:215:37: 
error: ‘CT_PSEUDOCHIRALITY_PROP_PREFIX’ is not a member of 
‘schrodinger::mae’

  215 | prop.first.find(mae::CT_PSEUDOCHIRALITY_PROP_PREFIX) == 0) {
  | ^~
/home/timbo/github/rdkit/rdkit/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:217:37: 
error: ‘CT_EZ_PROP_PREFIX’ is not a member of ‘schrodinger::mae’

  217 | } else if (prop.first.find(mae::CT_EZ_PROP_PREFIX) == 0) {
  | ^
make[2]: *** 
[Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/build.make:310: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/MaeMolSupplier.cpp.o] 
Error 1

make[2]: *** Waiting for unfinished jobs
make[1]: *** [CMakeFiles/Makefile2:7238: 
Code/GraphMol/FileParsers/CMakeFiles/FileParsers_static.dir/all] 
Error 2

make: *** [Makefile:163: all] Error 2




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[Rdkit-discuss] Looking for additional GSoC co-mentors

[Greg Landrum]

Dear all,

Yesterday was the last day for potential students to submit applications
for Google Summer of Code and we got proposals for the following five
projects:
1) RDKit integration with MongoDB. Python based
2) Implement a generalized file reader and a multi-threaded file reader.
C++ based
3) Integrating trained neural networks (specifically ANI-like force fields)
into the RDKit. C++ based
4) RDKit-OpenMM integration. C++ based
5) Improved RDKit integration with Jupyter, Dask, Pandas, Plotly, and
Bokeh. Python based

There's more about the first four projects here:
https://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas and I'm
happy to answer questions about them.

We have a mentor and co-mentor for each of these projects, but I'm looking
for a few more people to act as co-mentors. It doesn't make sense to do a
project without at least two mentors - one primary mentor and one
co-mentor- and Google is strongly encouraging organizations to have three
mentors - one primary and two co-mentors - available for each project.
Being a co-mentor is going to require an hour or two a week on average over
the course of the program.

There's more information on the program, including the dates, here:
https://summerofcode.withgoogle.com/how-it-works/

GSoC is really a great program and being a mentor/co-mentor is a good way
to help move both the open-source community and the RDKit forward.

If you're interested or have questions, feel free to send me email,
-greg
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