In these thread I will be making an announcements about new nodes and changes in the existing nodes.
We have started adding reaction nodes. These is only one functional node for reactions now, but we will add more soon.
Changes in the version 1.0.0.0001075 from the nightly build:
1. New translators nodes for converting RxnCell into Indigo cell and vice versa (query reactions are also supported).
2. New Reaction Automapper node for automatic atom-to-atom mapping for reaction.
3. There are additional options for Atom Replacer node: replace only highlighted atoms, replace only specific atom type. Thanks to Simon (richards99) for the suggestion: http://tech.knime.org/forum/indigo/atom-replacer-feature-request
There are small bug currently in this node, but it will be fixed in the next nightly build.
4. There is an additions option for Substructure Matcher: Align by query. Thanks to James (James Davidson) for the suggestion: http://tech.knime.org/forum/indigo/substructure-matcher-align-matched-structures
5. Indigo Renderer is now set as non-default renderer for MolCell, SDFCell, CMLCell, SmilesCell, SmartsCell. Renderer can be selected by clicking right button on the column header in a table with molecules.
6. Translator nodes now automatically find column to translate. It is not necessary to configure them unless there are some ambiguity. Also translator nodes now accept string values for input.
7. Indigo Renderer now can render query molecules better. But currently produced image appears to be wider then is can be. Thanks Steve (s.roughley) for mentioning this: http://tech.knime.org/forum/indigo/substructure-match-counter-and-query-molecule-to-indigo-nodes-suggested-imporvements
1. "red-black tree: at(): key not found" exception when a lot of Indigo objects are used. Thanks to Simon (richards99) for providing this bug report: http://tech.knime.org/forum/indigo/atom-replacer-node-bug
2. Minor bug was fixed in the dialog for Molecule Substructure Matcher.
Plans for the nearest future:
1. Add more nodes for reactions: reaction substructure search, combinatorial chemistry, reaction-based transformation of molecules.
2. Add file readers and savers for reactions. There is a lack of reaction readers in the Knime core.
3. Implement suggestions that wre gived here.
With best regards,
GGA Software LLC