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Patch/reactonsmarts #204

Merged
merged 16 commits into from Jun 5, 2016
Merged

Patch/reactonsmarts #204

merged 16 commits into from Jun 5, 2016

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johnmay
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@johnmay johnmay commented Jun 3, 2016

Fun patch, CDK can now run Reaction SMARTS, they are treated no different from normal SMARTS and can be run against reactions.

johnmay added 16 commits June 3, 2016 15:06
@johnmay
Correct parsing and building of reaction SMARTS queries. Relatively s…
f924784 
…imple adaption to existing parser.
@johnmay
Rename query atom to reflect it's purpose.
f9a12b4
@johnmay
Allow stereo elements to be set on query atom containers.
de5fbcc
@johnmay
Conversion to/from inline reaction (molecules) that will allow us to …
729f5db 
…easily implement matching.
@johnmay
Update component grouping predicate to consider reaction components a…
94b92dc 
…s connected (even if they are ionic).
@johnmay
Fix imports.
4cae2a9
@johnmay
ReactionRole enum was moved from the SMARTS atom to the cdk-interface…
e8baa77 
…s module.
@johnmay
Wire up Pattern implementation to accept reactions, a few basic tests…
19c8f91 
… are included for sanity checking.
@johnmay
Watch out for null component ids.
821d427
@johnmay
Parse atom map into the AST.
cb1dc0e
@johnmay
Use StringBuilder not StringBuffer for non-threaded appends.
f275cea
@johnmay
Copy across AAM idx to the resulting SMARTS Query Atoms.
11c5235
@johnmay
Correct map propagation when no right expression.
f2b70f9
@johnmay
A structure pattern filter for atom-atom maps.
f3fa698
@johnmay
Tidy up how filters are applied in the SmartsPattern and include the …
9eef3b3 
…new Atom-Atom Mapping filter.
@johnmay
Allow optional map token in SMARTS parser.
4d2e5d3
@egonw
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egonw commented Jun 5, 2016

Look good and fun!

@egonw egonw merged commit 40eea14 into master Jun 5, 2016
@johnmay johnmay deleted the patch/reactonsmarts branch June 5, 2016 17:18
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mrwns commented Jun 9, 2016

awesome! I will have a look!

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@johnmay @egonw @mrwns