Just a note on this - in CDK 1.5 the Pattern class is preferred as the
universal isomorphism tester is actually doing MCS (much harder).
Pattern ptrn = Pattern.findIdentical(butane);
for (Mol m : mols)
ptrn.matches(m);
In general though this is the slowest way to do it (n^2) vs (n log n) with
Hi John,
If the reader produces and IQueryAtomContainer IQueryAtoms/IQueryBonds then
it's simply a matter of passing it into the Pattern class (of UIT). This
will do a test of the query against real molecules - if you want to check
if one query equals another that's more tricky (I think RDKit has
So is there a reasonable way to do that? can we just generate canonical
form for molecules (like SMILES, then compare the SMILES)? Is it reasonable
for this? Or other methods? Thanks.
Yep Unique SMILES (canon,no stereo), Absolute SMILES (canon,with stereo) or
InChI should do what you need.
J
Thanks. I will see. Thank you very much.
On Tue, Jul 7, 2015 at 5:03 PM, Egon Willighagen egon.willigha...@gmail.com
wrote:
Dear Zheng Shi,
I think what you are looking for is isomorphism checking. If the
chemical graph of two structures is the same, they are called
isomorphic. The
Of course, please remember that if your input is not so clean (various
charge states, unclearly defined stereochemistry, etc), then you may
want to do some normalization before you do isomorphism checking or
SMILES/InChI generation. The InChI generation does some normalization,
but not all. If
Dear Zheng Shi,
I think what you are looking for is isomorphism checking. If the
chemical graph of two structures is the same, they are called
isomorphic. The following Groovy code shows a very basic example:
butane = MoleculeFactory.makeAlkane(4);
isomorphismTester = new
Thanks, John -
On the same vein: what is the appropriate way to handle these comparisons when
the source is an MDL V3000 with placeholder atoms/wildcards (nots, etc)? Is
there a CDK test that can handle this or would I have to implement a custom
comparison library?
John
On Jul 7,
Hi,
The CDK has always been intended as a toolbox (Lego like) rather than an
application. There are a couple of reasons for this but primarily there
isn't always a single or best way to accomplish a particular task. If you
would like such functionality I believe workflow tools (Knime-CDK) offer a
The compare means to tell if two molecules are equal. Suppose I have a
molecule B, which is generated by molecule A during a reaction: A - B, and
I get a molecule C, which is also generated by molecule A during a
reaction: A-C. I want to tell whether B and C are the same. Usually we can
visualize
Hi,
I just wonder whether there are any functions in cdk that could be used to
compare two molecule. Suppose I have two sdf files, I want to check whether
one molecule in the first file is the same as the other molecule in the
second file. Are there any functions in cdk that can achieve this? Or
10 matches
Mail list logo
