Hi,
I am looking for a method to find the maximum common subgraph of two
IAtomContainer. For each solution, I would like to get the mappings of
matched atoms for both input structures.
The UniversalIsomorphismTester looked like an obvious choice. There is a
method to find the maximum common subgr
There is a fair bit of information associated with the original PR:
https://github.com/cdk/cdk/pull/916
It's my understanding that hydrogens are not automatically adjusted, that
is, modifying the charge on an atom requires adjusting the hydrogen count.
In this comment are references to more infor
Thank you John, as always your answer is much appreciated.
I came across this issue some years ago, so I am aware that this is
anything but simple. I'll certainly be very happy to test any
implementation and provide feedback :)
Uli Fechner
Senior Software Developer
Pending AI
Hi,
I would like to individually layout and then render several structures that
are similar to each other (e.g., share a scaffold).
Is there a way to ensure that these structures are not rotated, that is,
that they are aligned in terms of their shared structural elements?
And to take this one st
Hi,
Welcome to the CDK community.
Atom types can be determined with
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
If you do this before detecting aromaticity, the exception should go away.
Best wishes
Uli
On Thu, Oct 12, 2023 at 3:02 AM Velusamy Velu wrote:
> Hi
>
Hi,
I would like to do some serious javadoc documentation for the
soon-to-come RInChI functionality in CDK.
I could either put this at the class level of one of the main entry
points or - and this would be my preference - in a package-info.java
at the package level.
As the javadoc generation is
Thanks, I like the data structure, it makes a lot of sense given requirements :)
I hope that I can continue working on this for a day or two, so that I
can finish up including some tests
Uli Fechner
Senior Software Developer
Pending AI
u...@pending.ai
https://pending.ai/
The National
er to just take whatever
you can provide.
Uli Fechner
Senior Software Developer
Pending AI
u...@pending.ai
https://pending.ai/
The National Innovation Centre, Suite 112, 4 Cornwallis St., NSW 2015, Australia
On Fri, Oct 21, 2022 at 12:16 AM John Mayfield
wrote:
>
> Sure... it&
t.
>
> On Thu, 20 Oct 2022 at 07:44, Uli Fechner wrote:
>
>> Hi,
>>
>> I had a good look at the code but would appreciate it if you confirm what
>> my assessment is:
>>
>> 1) CDK has support for reading RXN V2000 and RXN V3000 and support for
>> w
Okay, thank you.
We do use RXNMapper and in our experience the numbers they state in their
publication are a bit optimistic...
On Thu, Oct 20, 2022 at 7:25 PM John Mayfield
wrote:
> It does not, personally today I would use the IBM AI based one.
>
> On Thu, 20 Oct 2022 at 07:05, Ul
Hi,
I had a good look at the code but would appreciate it if you confirm what
my assessment is:
1) CDK has support for reading RXN V2000 and RXN V3000 and support for
writing RXN V2000.
2) There is no support for RDF at the moment, neither for reading nor for
writing.
Is that correct? Are there
Hi,
I vaguely remember that there is/was code in the CDK for atom-to-atom
mapping of reactions (wasn't that RDTool?). However, I cannot find that now.
RDTool by Asad uses CDK. But its maintenance seems to be lacking a bit
(last pre-release based on CDK 2.5 is back from Mar 2021).
Does CDK provid
;>> // always the case
>>>> remap.put(atom, output.getAtom(atom.getAtomicNumber() - 1));
>>>> }
>>>> for (IBond bond : source.bonds()) {
>>>> IAtom beg = remap.get(bond.getBegin());
>>>> IAtom
Hi,
I get a NoSuchAtomException when executing the following code (that I
inherited):
public static IAtomContainer extractSubstructure(IAtomContainer
source, List atoms) {
IAtomContainer output =
SilentChemObjectBuilder.getInstance().newAtomContainer();
int k = 0;
for (IAtom atom : at
Hi,
I require the functionality to merge all IAtomContainers in an
AtomContainerSet into a single IAtomContainer then having several
disconnected components / graphs and couldn't find a suitable method in
AtomContainerManipulator and AtomContainerSetManipulator.
IAtomContainer mergedAtomContainer
13/02/27/explicit-and-implicit-hydrogens-taking-liberties-with-valence/
> OPSIN has a good valence checker:
>
> https://github.com/dan2097/opsin/blob/c827542501516a70fb91dce09bc1b275b80d/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/ValencyChecker.java
>
> John
>
> On Mon, 22 Aug 2022
Hi,
I came across an issue today that seemed straightforward at the beginning,
but after a while ceased to appear that easily accessible. Well, I probably
shouldn't be surprised - I guess that is just cheminformatics at its best :)
The following smiles popped up in my workflow:
[Na+].O=C1[N]C=CC=
I summarized the information we exchanged here and opened an issue in the
ambit2 repo.
https://sourceforge.net/p/ambit/feature-requests/103/
On Wed, Aug 17, 2022 at 12:46 PM Uli Fechner wrote:
> Thank you so much for your very helpful message!
>
> I will contact the authors of t
to make sure
> all molecule creation is done via the factories and not "new
> AtomContainer()", that will be less important in future but might be an
> issue here.
>
> Further reading:
> - https://github.com/cdk/cdk/wiki/AtomContainer2
> - SMARTS API release notes:
&
it version
> shouldn't be a problem to try them out.
>
> John
>
> On Tue, 16 Aug 2022 at 03:36, Uli Fechner wrote:
>
>> Thank you John for the helpful information.
>>
>> The declarations seem like an elegant solution. In
>> my understanding, this on
Hi,
I want to apply a SMIRKS pattern to a molecule and get the products as a
result. My understanding is that CDK does not support this at the moment.
Is that correct?
The ambit-smirks package by IdeaConsult seems to offer the functionality I
am looking for. However, it declares a dependency on c
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