[Rdkit-discuss] AllChem.ReplaceSubstructs question

[Markus Metz]

Hello:
I am puzzled by the output from ReplaceSubstructs as it can produce two
fragments.
So I went and tried the examples in the manual and I observed this:
The example in the intro manual with the recursive smarts pattern works as
expected.
repl = Chem.MolFromSmiles('OC')
patt = Chem.MolFromSmarts('[$(NC(=O))]')
m = Chem.MolFromSmiles('CC(=O)N')
rms = AllChem.ReplaceSubstructs(m,patt,repl)
One expected product is formed.

The example form the ReplaceSubstructs manual produces two solutions.
I have used the following commands:
from rdkit import Chem
from rdkit.Chem import AllChem

#ReplaceSubstructs(‘CCOC’,’OC’,’NC’) -> (‘CCNC’,)
repl = Chem.MolFromSmiles('NC')
patt = Chem.MolFromSmarts('OC')
m = Chem.MolFromSmiles('CCOC')
rms = AllChem.ReplaceSubstructs(m,patt,repl)

for rm in rms:
   print(CHem.MolToSmiles(rm))

output is: C.CNC and CCNC

Why is the first result produced?
I checked the mailing list and could find this older threat
https://sourceforge.net/p/rdkit/mailman/message/28777648/.
But the answer to the related question is missing.

rdkit version is 2020.03.1dev1

Best wishes,
Markus
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Re: [Rdkit-discuss] Anaconda and RDkit

[Alan Kerstjens Medina]

Hello Francesco,

To quote your email: “But now, I'm not in Python. So I type py”

Is this a typo? I’m not aware of the Python interpreter launching when you type 
“py”. If it does you may have defined an alias and you may be launching a 
different Python executable. If you’re using the Anaconda3 Python executable it 
should say so on your terminal when you launch the interpreter, something along 
the lines of:

Python 3.7.6 (default, Jan  8 2020, 20:23:39) [MSC v.1916 64 bit (AMD64)] :: 
Anaconda, Inc. on win32

Since you mention copying over files to the C:\ drive it seems you have also 
tried to either use the precompiled RDKit binaries or build it from source. 
This may have caused some issues with your environment variables. You should 
check that your PATH variable includes the path to the Anaconda3 folder, and 
that the RDBASE variable points to the Anaconda3 RDKit environment folder. I 
also second Jenny’s advice: if you don’t intend on using the C++ API there’s no 
reason to have those RDKit files in C:\ as it may cause some conflicts when 
searching for libraries. It would be best to remove them.

Best regards,
Alan

From: David Cosgrove
Sent: 05 March 2020 18:52
To: Francesco Coppola
Cc: 
rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Anaconda and RDkit

Of no help to Francesco whatsoever, but to save anyone else the bother...
I’ve just taken the “from __future__...” bit out of the getting started docs in 
the PR I have open at the moment. It doesn’t seem worth its own PR but it needs 
to be acknowledged that we are now in the future .

Dave


On Thu, 5 Mar 2020 at 16:25, Francesco Coppola 
mailto:coppolafrancesco1...@gmail.com>> wrote:
Hi,

I'm Francesco Coppola a recent graduate student in Medicinal Chemistry in 
Italy. Now I'm in Manchester and I'm doing a traineeship in computational 
chemistry. During my thesis work, I deal with Docking programs (and they always 
had an interface), now instead I'm trying to work with Python, Terminal and 
interpreter.

I have searched on a thousand sites and blogs but I just can't install RDKit on 
a Windows pc.
In particular, I have a problem when I would activate the environment.

I have the latest version of RDKit (the folder is on my desktop and just 
copied/pasted in c: ).

First I followed this command:

conda create -c rdkit -n my-rdkit-env rdkit

Done this installation, I type:

conda activate my-rdkit-env

Now in Ananaconda Prompt, I see:

(my-rdkit-env) c:\Users\HP>

(and in fact, I can find this file "my-rdkit-env in the folder env of Anaconda3)

But now, I'm not in Python. So I type
py

and Python 3.8.2 starts

>>>

Now I follow this guide: 
https://www.rdkit.org/docs/GettingStartedInPython.html, and I Type the first 
two command line:

>>> from __future__ import print_function

>>> from rdkit import Chem
But it don't works.

Traceback (most recent call last):
   File ", line 1, in 
ModuleNotFoundError: No module named 'rdkit'
>>>

I need a guide that tells me what to do step by step.

Sorry if I disturbed you, I hope you can help me..I'm completely inexperienced 
but I am trying to learn.

Sorry for the trouble.

Best regards
Francesco
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http://cozchemix.co.uk

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Re: [Rdkit-discuss] Are any of the UGM talks recorded?

[Jennifer Wei via Rdkit-discuss]

OK Thanks, I'll just have to try and come next time then.

On Thu, Mar 5, 2020 at 3:50 AM Greg Landrum  wrote:

> Hi Jennifer,
>
> We don't have recordings of any of the UGM presentations. Sorry.
>
> -greg
>
>
> On Wed, Mar 4, 2020 at 6:57 PM Jennifer Wei via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
>> Hi All,
>>
>> I was wondering if any of the UGM talks are recorded. I'm particularly
>> interested in this talk
>> 
>> by Robert Sayle from the 2019 UGM.
>>
>> Thanks!
>> Jennifer
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>>
>
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Re: [Rdkit-discuss] Anaconda and RDkit

[David Cosgrove]

Of no help to Francesco whatsoever, but to save anyone else the bother...
I’ve just taken the “from __future__...” bit out of the getting started
docs in the PR I have open at the moment. It doesn’t seem worth its own PR
but it needs to be acknowledged that we are now in the future .

Dave


On Thu, 5 Mar 2020 at 16:25, Francesco Coppola <
coppolafrancesco1...@gmail.com> wrote:

> Hi,
>
> I'm Francesco Coppola a recent graduate student in Medicinal Chemistry in
> Italy. Now I'm in Manchester and I'm doing a traineeship in computational
> chemistry. During my thesis work, I deal with Docking programs (and they
> always had an interface), now instead I'm trying to work with Python,
> Terminal and interpreter.
>
> I have searched on a thousand sites and blogs but I just can't install
> RDKit on a Windows pc.
> In particular, I have a problem when I would activate the environment.
>
> I have the latest version of RDKit (the folder is on my desktop and *just*
> copied/pasted in c: ).
>
> First I followed this command:
>
> conda create -c rdkit -n my-rdkit-env rdkit
>
> Done this installation, I type:
>
> conda activate my-rdkit-env
>
> Now in Ananaconda Prompt, I see:
>
> (my-rdkit-env) c:\Users\HP>
>
> (and in fact, I can find this file "my-rdkit-env in the folder env of
> Anaconda3)
>
> But now, I'm not in Python. So I type
> py
>
> and Python 3.8.2 starts
>
> >>>
>
> Now I follow this guide:
> https://www.rdkit.org/docs/GettingStartedInPython.html, and I Type the
> first two command line:
>
> >>> from __future__ import print_function>>> from rdkit import Chem
>
> But it don't works.
>
> Traceback (most recent call last):
>File ", line 1, in 
> ModuleNotFoundError: No module named 'rdkit'
> >>>
>
> I need a guide that tells me what to do step by step.
>
> Sorry if I disturbed you, I hope you can help me..I'm completely
> inexperienced but I am trying to learn.
>
> Sorry for the trouble.
>
> Best regards
> Francesco
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
-- 
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
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Re: [Rdkit-discuss] Anaconda and RDkit

[Jenny h]

Hi Francesco,

being new in the field everything can be confusing especially with conda ;)

Just to make it clear: do you have a folder named RDKit in C://?  If so
just deleted the folder and it should be working. (A student of mine did
the Same)

To clarify: anaconda installs RDKit from an online source so there ist No
need to Download anything manually after you did the conda Install.

If that does not help I have a detailed how- to which I can send to you
tomorrow.

Best,
Jennifer

Francesco Coppola  schrieb am Do., 5. März
2020, 17:25:

> Hi,
>
> I'm Francesco Coppola a recent graduate student in Medicinal Chemistry in
> Italy. Now I'm in Manchester and I'm doing a traineeship in computational
> chemistry. During my thesis work, I deal with Docking programs (and they
> always had an interface), now instead I'm trying to work with Python,
> Terminal and interpreter.
>
> I have searched on a thousand sites and blogs but I just can't install
> RDKit on a Windows pc.
> In particular, I have a problem when I would activate the environment.
>
> I have the latest version of RDKit (the folder is on my desktop and *just*
> copied/pasted in c: ).
>
> First I followed this command:
>
> conda create -c rdkit -n my-rdkit-env rdkit
>
> Done this installation, I type:
>
> conda activate my-rdkit-env
>
> Now in Ananaconda Prompt, I see:
>
> (my-rdkit-env) c:\Users\HP>
>
> (and in fact, I can find this file "my-rdkit-env in the folder env of
> Anaconda3)
>
> But now, I'm not in Python. So I type
> py
>
> and Python 3.8.2 starts
>
> >>>
>
> Now I follow this guide:
> https://www.rdkit.org/docs/GettingStartedInPython.html, and I Type the
> first two command line:
>
> >>> from __future__ import print_function>>> from rdkit import Chem
>
> But it don't works.
>
> Traceback (most recent call last):
>File ", line 1, in 
> ModuleNotFoundError: No module named 'rdkit'
> >>>
>
> I need a guide that tells me what to do step by step.
>
> Sorry if I disturbed you, I hope you can help me..I'm completely
> inexperienced but I am trying to learn.
>
> Sorry for the trouble.
>
> Best regards
> Francesco
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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[Rdkit-discuss] Anaconda and RDkit

[Francesco Coppola]

Hi,

I'm Francesco Coppola a recent graduate student in Medicinal Chemistry in
Italy. Now I'm in Manchester and I'm doing a traineeship in computational
chemistry. During my thesis work, I deal with Docking programs (and they
always had an interface), now instead I'm trying to work with Python,
Terminal and interpreter.

I have searched on a thousand sites and blogs but I just can't install
RDKit on a Windows pc.
In particular, I have a problem when I would activate the environment.

I have the latest version of RDKit (the folder is on my desktop and *just*
copied/pasted in c: ).

First I followed this command:

conda create -c rdkit -n my-rdkit-env rdkit

Done this installation, I type:

conda activate my-rdkit-env

Now in Ananaconda Prompt, I see:

(my-rdkit-env) c:\Users\HP>

(and in fact, I can find this file "my-rdkit-env in the folder env of
Anaconda3)

But now, I'm not in Python. So I type
py

and Python 3.8.2 starts

>>>

Now I follow this guide:
https://www.rdkit.org/docs/GettingStartedInPython.html, and I Type the
first two command line:

>>> from __future__ import print_function>>> from rdkit import Chem

But it don't works.

Traceback (most recent call last):
   File ", line 1, in 
ModuleNotFoundError: No module named 'rdkit'
>>>

I need a guide that tells me what to do step by step.

Sorry if I disturbed you, I hope you can help me..I'm completely
inexperienced but I am trying to learn.

Sorry for the trouble.

Best regards
Francesco
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Re: [Rdkit-discuss] Are any of the UGM talks recorded?

[Greg Landrum]

Hi Jennifer,

We don't have recordings of any of the UGM presentations. Sorry.

-greg


On Wed, Mar 4, 2020 at 6:57 PM Jennifer Wei via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:

> Hi All,
>
> I was wondering if any of the UGM talks are recorded. I'm particularly
> interested in this talk
> 
> by Robert Sayle from the 2019 UGM.
>
> Thanks!
> Jennifer
> ___
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>
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