have changed.
>
> The easiest thing is to just replace the MD5 in
> $RDBASE/Code/cmake/Modules/FindInchi.cmake with what you're getting (after
> making sure it is in fact the correct zip file of course).
>
> -greg
>
>
> On Tue, May 14, 2024 at 1:04 PM James Wallace
&g
I'm trying to compile RDKit 2023_03_3 into a Docker container, but the
CMake MD5 check fails for the Inchi library. Is there a way of disabling
this check, because my presumption is the library has changed going
forward, but for compatibility reasons, I want to keep this version as
close to stock
I've been using the substructure match with query molecules to do an
R-Group decomposition. This works well, except in the case where the query
molecule contains a 'bridged atom in a ring. Take this example (I've
replaced the irrelevant part with a Y atom for confidentiality)
, 24 Jan 2022 at 13:17, James Wallace wrote:
> So, arer you saying it's because I'm making the hydrogen part explicit?
> I'll try without that and see what I get. Thanks.
>
> On Mon, 24 Jan 2022 at 12:35, Wim Dehaen wrote:
>
>> Hi,
>> I think that is not expected be
gt; reaction smarts i also get the expected product that includes the stereo
> center.
> I think if your problem persists it would be good to paste a whole code
> block that outputs the undesired product.
> best wishes
> wim
>
>
> On Mon, Jan 24, 2022 at 11:31 AM James Wal
I've been trying to use the RunReactants portion of the ChemicalReaction
enumeration with chiral reagents, and a chiral reaction, but I don't seem
to get chiral products out.
For example, using a template reaction:
C[C@@H](Oc1(C(=O)O)c1)c1c1.[NH3:1]>>C[C@
port general CSV, I'd suggest
> using pandas or python's builtin csv module... it seems like overkill, but
> dealing with all the oddness that can show up in CSVs is really not easy.
>
> Best,
> -greg
>
>
> On Mon, Jan 10, 2022 at 11:15 AM James Wallace
> wrote:
>
>
As the subject suggests, I'm trying to find a universal solution for
reading CSVs via the SmilesMolSupplier (as the input setup could be single
column or multiple column, using the pandas tools for interconversion is
overkill)
The general structure I use for analysing the CSV is:
with
>
> -greg
>
>
> On Sun, Dec 5, 2021 at 8:24 PM James Wallace wrote:
>
>> Here's the specific example that I was referring to:
>>
>> I used a reaction with this SMILES, making a ChemicalReaction out of it
>> using the add reactant templates:
>>
>
t you have done and what you'd like to
> achieve.
> Ideally, could you please post:
>
> * the reaction you are using
> * some example reactants
> * the desired product(s)
> * the undesired product(s)
>
> Thanks, cheers
> p.
>
> On Thu, Dec 2, 2021 at 6:03 PM
Hi,
I've been working with the EnumerateLibraryFromReaction function to
generate some quick access molecule libraries, using standard lists of
reagents.
However, when I get the output back, I notice that I get results that chop
up the reactants I use wherever they match the reaction rule, so for
I've been looking into Free-Wilson, attempting to rework the Pat Walters
code (https://github.com/PatWalters/Free-Wilson) for doing this to
something more suited to batch use.
With the RDKit having a full RGroupDecomposition library that can generate
the data directly, this seems like a good
reg
>
>
>
>
>
> On Wed, Mar 13, 2019 at 12:17 PM James Wallace
> wrote:
>
>> I know there are MolSuppliers and ForwardMolSuppliers for handling
>> multiple entries in a stream-like way from SDFiles, but I don’t see a
>> reaction equivalent for RDFiles. M
I know there are MolSuppliers and ForwardMolSuppliers for handling multiple
entries in a stream-like way from SDFiles, but I don’t see a reaction
equivalent for RDFiles. My use case is one in which users have submitted
multiple sketched reactions as RXN, for each to be validated and considered
on
;
> Furthermore, your molecule only has implicit hydrogen atoms, so you
> should not expect any bonds involving H unless you add explicit hydrogen
> atoms.
>
> HTH, cheers
> p.
>
> On 11/29/18 12:01, James Wallace wrote:
> > I'm trying to use the Java wrapper to do a
I'm trying to use the Java wrapper to do a basic molecule
fragmentation, greedily matching against anything that fits the SMARTS
"[*;R]-;!@[*]" (effectively any regular bond that isn't part of a ring
system)
As a test case, I'm using a structure with a few obvious bonds that
can be broken, namely
I've been trying to resolve some issues we seem to be having with
sanitization of molecules in the Java/KNIME runtime, and I have the
sanifix4 python script, but I'm not sure all the functions that it's based
off are available in the C/Java build. Is there an equivalent for those, or
is there some
Is the code working as designed (ultimately I want to feed lists of these
together, but I'm trying one at a time for now)?
On 27 October 2016 at 12:02, James Wallace <jeawall...@gmail.com> wrote:
> Hi,
> I'm trying to replicate the Schneider categorisations with a local set of
> react
Hi,
I'm trying to replicate the Schneider categorisations with a local set of
reactions that I have stored in SMILES. I currently have the categorisation
filters as Reaction SMARTS, and I was hoping to do a standard substructure
comparison between the SMARTS and the SMILES, but can't seem to do
map number of the product's atom (if available).
If this would be useful, let us know, I would be happy to have a
tester prior to release.
Brian Kelley
On Thu, Jan 21, 2016 at 9:41 AM, James Wallace
<chp11...@sheffield.ac.uk <mailto:chp11...@sheffield.ac.uk>> wrote:
Hi,
I'm using the KNIME implementation to write my own nodes, and I'm
running into an issue. For the process I'm trying to do I'm trying to
subtract the MCS between two molecules away from the larger molecule, to
leave a list of fragments. I'm aware of the substructure matching, but
I'm not
, but with an inferior dictionary,
because I'm building it from first principles. As you may be aware, the
project already uses a lot of the KNIME RDKit functionality for the
backend, so an approach that lets me keep more of that interoperability
is a big plus.
Yours,
James Wallace (Sheffield
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