Ivan's solution, using the SMARTS extension [r{12-}], is what I would use
for this.
I would suggest using the permanent documentation link though:
http://rdkit.org/docs/RDKit_Book.html#smarts-support-and-extensions
That's the one that I keep up to date.
A note to Dave's point about anthracene:
Hello Paolo,
Many thanks for the support – I think this would be very useful for anyone
trying to catch messages generated in this fashion.
Really nice work.
Thanks,
mike
From: Paolo Tosco
Sent: 09 October 2019 23:34
To: Mike Mazanetz
Cc: 'RDKit Discuss'
Subject: Re:
Hi Mike,
please find here a solution which I have just tested and works well on
both Unix and Windows.
You need to redirect the C++ stderr stream with ctypes around the call
whose output you wish to grab.
This can be done defining a context manager that uses ctypes:
import os
import sys
Hi Mike,
as I promised I'll put together something for you to capture warnings;
I'll try to get it done tonight.
p.
On 10/09/19 18:10, Mike Mazanetz wrote:
Hi,
Many thanks this, it is very helpful to see some code.
Yes, as it stands, I am yet to get warnings which are seen in stdout
Hi,
Many thanks this, it is very helpful to see some code.
Yes, as it stands, I am yet to get warnings which are seen in stdout being sent
to a file, only errors seem to find their way to my files.
Usually Warnings about stereochemistry don’t get captured. Anyone see this,
I’m guessing
Hi David,
Thanks for the tip! I just found it in the documentation; the syntax is
[r{12-20}]. See
http://rdkit.org/docs_temp/RDKit_Book.html#smarts-support-and-extensions
Note that this doesn't suffer from the hard-coded limitation I mentioned,
and you can even specify open ranges such as
Hi Ivan,
There is an RDKit extension to SMARTS that allows something like [r12-20].
I can’t check the exact syntax at the moment. You might want to check that
atoms are not in smaller rings as well, so as not to pull up things like
anthracene which might not be something you’d want to class as a
Hi Macjek and Mike,
If I understand your question correctly, you can specify InChI option
parameters when calculating InChIs. Here is an example:
m = Chem.MolFromSmiles('CCC1=CN=C(NC1=O)NC')
Chem.MolToInchi(m)
'InChI=1S/C7H11N3O/c1-3-5-4-9-7(8-2)10-6(5)11/h4H,3H2,1-2H3,(H2,8,9,10,11)'
Now, try
Dear Thomas,
I'm not aware of any RDKit function that distinguishes macrocycles .
However, based on the definition of 12 or more membered rings, you may use
the following function to get molecules that have rings with 12 or more
atoms from a list of molecules:
def GetMacrocycles(mols):
Mike,
On top of what Greg said what might be particularly useful is an options
parameter where you can pass some non default params to InChI call.
śr., 9 paź 2019, 07:22 użytkownik Greg Landrum
napisał:
> Hi Mike,
>
> The InChI API itself is not exposed. The contents of the module are in the
>
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