there any libraries to convert mol structures into a
bitstring representation.
Fingerprinter class is solution for this question.
But here i you are missing something
if the query is a substructure of any molecule in the
database.
Substructure searching is the only way out for this.
I am thinking for trying to match a query mol against a database
Matching Mol file as a query, is not really good approach i think.
If we use the Mol file as a query for substructure searching,
then that would be world's most CPU extensive method.
(if we are talking about MDL mol not Sybyl MOL2)
The substructure CDK matching algorithm as expected is very CPU
intensive.
Without any comparison we can't say that CDK matching algorithm is CPU
extensive.
Because i am using CDK substructure search in my software
http://sushilronghe.tripod.com/visualization/molpharm.html
and results are coming as fast as UNITY,and CCSD.
(Actual comparison is not done yet).
Therefore a fast bistring comparision to rule out most
structures (e.g. has it got an aromatic ring represented in the
bitstring) before the more deep substructure matching would be very
beneficial.
This is absolutely fantastic idea.
But what would be the benefit of that kind of search.
If some one really want to use the information of the atoms given in MOL
file we can use the atomtype class.
Also if we are using the fingerprinting CDK need to Process the molecule.
and same for substructure search. SO i don't think there will be any great
difference
i think!
********************************
sushil ronghe
Center of Pharmacoinformatics
India
*********************************
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