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
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 it’s the same for failed InChI’s too?
Thanks,
mike
*From:*Scalfani, Vincent <vfscalf...@ua.edu>
*Sent:* 09 October 2019 14:40
*To:* Maciek Wójcikowski <mac...@wojcikowski.pl>; Greg Landrum
<greg.land...@gmail.com>
*Cc:* RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
*Subject:* Re: [Rdkit-discuss] Inchi which flavour??
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 with one of the non-standard options such as FixedH:
Chem.MolToInchi(m,'/FixedH')
'InChI=1/C7H11N3O/c1-3-5-4-9-7(8-2)10-6(5)11/h4H,3H2,1-2H3,(H2,8,9,10,11)/f/h8,10H'
To answer the question of what happens when the InChI calculation
fails, I get an empty string.
m =
Chem.MolFromSmiles('[C@H]1([C@H](C1C2[C@@H]([C@@H]2C(=O)O)C(=O)O)C(=O)O)C(=O)O')
Chem.MolToInchi(m)
' '
There is also an InChI option that can warn on empty structures, and
calculate an empty InChI, which I am assuming is supposed to be
‘InChI=1S//’, however, when trying this option I get the same result
as above.
Chem.MolToInchi(m,'/WarnOnEmptyStructure')
' '
I hope that helps.
Vin
*From:*Maciek Wójcikowski <mac...@wojcikowski.pl
<mailto:mac...@wojcikowski.pl>>
*Sent:* Wednesday, October 9, 2019 3:41 AM
*To:* Greg Landrum <greg.land...@gmail.com
<mailto:greg.land...@gmail.com>>
*Cc:* RDKit Discuss <rdkit-discuss@lists.sourceforge.net
<mailto:rdkit-discuss@lists.sourceforge.net>>
*Subject:* Re: [Rdkit-discuss] Inchi which flavour??
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 <greg.land...@gmail.com
<mailto:greg.land...@gmail.com>> napisał:
Hi Mike,
The InChI API itself is not exposed. The contents of the
module are in the documentation along with some explanations of
how to call it:
http://rdkit.org/docs/source/rdkit.Chem.rdinchi.html
If something is missing there, please let us know.
-greg
On Tue, Oct 8, 2019 at 5:20 PM <mi...@novadatasolutions.co.uk
<mailto:mi...@novadatasolutions.co.uk>> wrote:
Dear RdKit users,
I was reading the inchi module docs and I couldn't find
methods to call the InChI API. Are these exposed in RDKit?
It says the default is the standard Inchi. What happens when
this conversion fails?
Thanks,
Mike
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