On Mon, Dec 2, 2013 at 1:03 PM, Michal Krompiec
wrote:
>
> > ReplaceSubstructs() is designed for the very simple case of replacing a
> > piece of the molecule that is connected via one bond. It has the
> significant
> > limitation that it (currently) assumes that the bond will be formed to
> the
>
Dear Greg,
Thanks for the answer.
> ReplaceSubstructs() is designed for the very simple case of replacing a
> piece of the molecule that is connected via one bond. It has the significant
> limitation that it (currently) assumes that the bond will be formed to the
> first atom in the replacement.
I
On Mon, Dec 2, 2013 at 11:53 AM, Michal Krompiec
wrote:
> But does CombineMols create any new bonds?
>
It does not, but you can add bonds by converting to an EditableMol and
working there.
Something like this:
In [2]: m = Chem.MolFromSmiles('c1c1N')
In [3]: m2 = Chem.MolFromSmiles('CC(=O)'
Dear Greg,
But does CombineMols create any new bonds?
What is the simplest/fastest way of joining two molecules (fragments)
together? (i.e. is there anything simpler than using
ReplaceSubstructs)
Best wishes,
Michal
On 1 December 2013 04:40, Greg Landrum wrote:
> This is the approach I would us
Thanks for the replies.
I was looking for the combine molecules function. I use the reaction based
joining for ordered connections I want to make. I was looking for something a
bit more basic though.
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Resea
This is the approach I would use. It allows you to skip the SMILES
generation and parsing steps.
On Fri, Nov 29, 2013 at 5:31 PM, Markus Hartenfeller <
markus.hartenfel...@molecularhealth.com> wrote:
> Hi Nick,
>
> I'm not 100% sure, but this might do what you are looking for:
>
> Chem.CombineM
Suppose we have 2 fragments, A and B, with free valences marked as
some dummy atoms. For example, A=CH3* and B=HO*. We want a general
method to combine A and B, in this example the result should be CH3OH.
There are at least 3 ways to do it.
1. Use the trick from SMILIB: replace dummies with %11, a
Hi Nick,
I'm not 100% sure, but this might do what you are looking for:
Chem.CombineMols(molFrags[i], molFrags[i+1])
Best,
Markus
On 11/29/2013 05:03 PM, Nicholas Firth wrote:
> Hi RDKitters,
>
> This may be a silly question, but I'm wondering if there's any functionality
> in RDKit to add tw
Hi RDKitters,
This may be a silly question, but I'm wondering if there's any functionality in
RDKit to add two molecules together? I've been writing to SMILES and joining
with a '.' and then reading back in. This feels very cludgy.
Basically I have two fragments of molecules and I want to add t
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