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How can I run SMSD using Java Thread….is SMSD thread safe?

The short answer is “YES” you can.

Here is a snippet to demonstrate that SMSD is thread safe.

https://github.com/asad/ThreadSMSD

The latest version of the SMSD is not also thread safe but it also comes with optimised matchers (bond and atom).

For, example you could demand it to respect the ring matching (restrict) while finding MCS.

Thus an MCS between a query SMILES “ONC1=CC=CC=C1” and target SMILES “O1C=CC=CN1C1=CC=CC=C1”.

a) without ring matcher is “ONC1=CC=CC=C1”

b) with ring matcher is “C1=CC=CC=C1”

This might be useful for few SMSD users.

Find MCS without ring matching restrictions

MCS with ring matcher OFF flag.

Respect rings while finding MCS

Respect rings while finding MCS (non ring to ring matches are skipped). MCS with ring matcher ON flag.