Nightly builds: New nodes and node changes announcements

Community Extensions
1

Hello,

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
Fixed bug:
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,
Mikhail
GGA Software LLC
2

Hello!

Yesterday we have uploaded the new version of Indigo nodes. Since today you can try version 1.1.0.0001123 as usual from http://tech.knime.org/update/community-contributions/nightly 

This release contains improvements for Atom Replacer and Substructure Match Counter nodes. Also Indigo renderer is now better handles all internal exceptions for invalid molecules.

Changes in the version 1.1.0.0001123:

1. Atom Replacer node now supports the list of atoms to replace. This list contains all predefined element categories in the periodic table from the Wikipedia: Metals, Alkali metals, Alkaline earth metals, Metals, Nonmetals, Metalloids, and etc. Also user can specify custom list of atoms to replace including pseudoatoms, and also you can replace any atom with R-site (R1, R2, R3, ...) and vice versa.

2. Substructure Match Counter node can now accept multiple number of queries. For each query column with counter is added. If highlighting is turned on, then all matches for the all queries are highlighted.

3. Indigo renderer now shows why molecules is not rendered, missing cells.

With best regards,
Mikhail Rybalkin
GGA Software LLC

3

Hello KNIME users,

Changes in the version 1.1.0.0001124 of Indigo nodes:

  1. Atom Replacer node:
    •     has predefined list with R-groups
    •     can replace attachment points
  2. Substructure Matcher node:
    •     accepts multiple number of queries
    •     option for appending column with queries row ID (to use in Joiner node with queries table). If mutiple queires matches the target, then IDs are written in a comma-separated form.
    •     option for appending column with the number of queries matched
    •     option to match all queries, or a specified number of queries

I have introduced small bug in Substructure Match: after the node was created you need to specify option to match all queries, or "at least x queires" manually. In the next nightly build  tomorrow it will be fixed (1.1.0.0001127). All node that were created with the previous version should work correctly.

With best regards,
Mikhail Rybalkin
GGA Software LLC

4

Hello!

The next version of Indigo Nodes (1.1.0.201201191806) is available for installation from the nightly builds: http://tech.knime.org/update/community-contributions/nightly

As it was promised we are adding a reactions support to our nodes. In the previous version there was only Reaction Automapper node. In this version all the general purpose manipulators, the Substructure Matcher node, and the Fingerpring node support reactions.

Main changes:

1. We have changed internal node settings saving in a proper way. This has very big drawback: all the settings should be specified again in the configuration windows, unless you are using default values. We are trying to make our code simplier, but adding a conversion from a previous format to a new one is too complicated. Let us know, if it is too hard to specify node settings again, but it was out fault that we didn't do this from the beginning.

2. Reactions support in the following nodes: Substructure Matcher, Aromatize, Dearomatizer, Atom Replacer, Feature Remover, Hydrogen Adder, Hydrogen Remover, Indigo Fingerprint, Valence Checker.

3. Indigo Nodes can now be used on Red Hat Enterprise Linux! Previous version required a Cairo 1.8 library being installed, and on the Red Hat Enterprise Linux 6.1 (and lower) this causes the KNIME application crush. Now Indigo nodes are working on almost all version of Windows, Linux and Mac OS X.

4. User interface improvements: new node icons, node groups, dialogs, better autoconfiguration, missing cells handling and etc.

Other changes:

1. Atom-to-atom mapping improvements. Thanks to Simon for the suggestion and for the bug report: http://tech.knime.org/forum/indigo/reaction-automapper and http://tech.knime.org/forum/indigo/reaction-automapper-errors

2. Chirality flag is saved to the molfiles. Thanks to Simon for the suggestion: http://tech.knime.org/forum/indigo/chirality-flags

3. Indigo now works with molecules with more than 8 R-groups. Thanks to James Davidson for the bug report: http://tech.knime.org/forum/indigo/changes-to-scaffold-finder-node

4. A lot of other small improvements: canonical SMILES are now calculated for a structures with invalid valences too (in most cases), some issues with explicit hydrogens has been fixed, and more.

Planned nodes:
1. Reaction Splitter and Combiner nodes: http://tech.knime.org/forum/indigo/reaction-to-individual-molecules
2. Bond Replacer node to replace all the bonds with single ones in order to get a skeleton of a molecule: http://tech.knime.org/forum/indigo/scaffolds-frameworks

Noticed issues: Substructure Matcher node highlighting is broken. Hope that this will be fixed today.

We are participating in the 5th KNIME Users Group Meeting, and looking forward to seeing you there. Thank you for helping us to make this project better. We plan to release a stable version by Feb 1 before KNIME UGM, and your comments, bug reports and suggestions are very helpful!

Best regards,
Mikhail Rybalkin
GGA Software

5

Hello again,

Changes in the Indigo KNIME Nodes 1.1.0.201201261932 (nightly build):

1. New nodes for combining and splitting molecules and reactions: Component Combiner, Reaction Builder, and Reaction Splitter
Thanks to Simon and Steve for the discussion: http://tech.knime.org/forum/indigo/reaction-to-individual-molecules

2. We have added the Molecule Transformation node for changing a molecule accoring to a reaction-based set of rules. This node applies the transformation patterns for each part of the molecule. Look at the examples here: http://ggasoftware.com/opensource/indigo/concepts/transformation

3. Settings are now compatible with the stable version. All new nodes should load previous settings without errors.

4. Issue with substructure highlighting has been also fixed.

Best regards,
Mikhail Rybalkin
GGA Software LLC

6

Hello!

The next version of Indigo Nodes is ready for testing. You can update it from the nightly builds repository: http://tech.knime.org/update/community-contributions/nightly

We assume that this version can be moved to the stable releases, after we get user feedbacks that everything is compatible with the stable version.

Changes in the version 1.1.0.201201291733:

1. Combinatorial Reaction Enumeration node has been added. You can look at the examples: http://ggasoftware.com/opensource/indigo/concepts/combichem
Not all the features have been integrated into the KNIME node yet, such as intramolecular interactions, and multistep reactions.

2. First version of the InChI strings support. Now the Molecule to Indigo node accepts InChI strings as an input, and the Indigo to Molecule node can generate both InChI and InChIKey.

3. Bond Replacer node has been added. It can be used to get the molecule skeleton, by replacing all the bonds (or highlighted ones) with a specified bond type.

Best regards,
Mikhail Rybalkin
GGA Software Services LLC

7

Hello!

We have prepared the next version of Indigo Nodes, and they are available from the nightly builds repository: http://tech.knime.org/update/community-contributions/nightly

We took a small break in our conversation after the KNIME USM in order to summarize conversation results. This is why we didn't respond you in the threads.

In the version Simon has already found a regression that the Reaction Automapper does not do anything. We have already fixed this issue today, and tomorrow you can install the next nightly build.

Changes in the version 1.1.0.201202162303:

1. New memory model was applied for IndigoDataCells. The new model is stable to huge data sets. Thanks to Hinnerick and Steve: http://tech.knime.org/forum/indigo/memory-errors-and-instability-after-nightly-update

2. Internal format for the Indigo cells was changed, and you have to reexecute all your workflows if you are saving your workflows with the data (if you Indigo Nodes have green mark).

3. Cosmetic in node names, more convenient nodes order. Thanks to Simon: http://tech.knime.org/forum/indigo/minor-change-to-the-order-of-the-indigo-directories

4. Some incompatibility between the settings the stable nodes and nightly build nodes was fixed.

5. Molecules Transformation description was fixed. Thanks to Simon: http://tech.knime.org/forum/indigo/molecule-transform-node-description-bug

6. Bug with incorrect molecules for Scaffold node was fixed. Thanks to Hinnerick: https://groups.google.com/group/indigo-bugs/browse_thread/thread/16faf897c090bc04

7. Possible exceptions and runtime errors for molecules with incorrect valence were replaced by warnings. Thanks to Hinnerick

8. Bond replacer node now supports Reactions

9. 2d coordinates node was added. Thanks to Simon: http://tech.knime.org/forum/indigo/molecule-cleanup-node

Best regards,
Mikhail Rybalkin
GGA Software Services LLC

8

Hello!

Changes in the latest nightly build of Indigo Nodes 1.1.2:

1. Fixed InChI computation caused KNIME application temintation. Thanks to Hinnerk: https://groups.google.com/d/msg/indigo-bugs/Fvr4l8CQvAQ/r_HYDxumALAJ

2. Options for Tverksy metric for Similarity Node was restored. Thanks to Simon: http://tech.knime.org/forum/indigo/fingerprint-similarity-improvement-request

3. Fixed memory issues with substructure matcher. Thanks to fab: http://tech.knime.org/forum/indigo/error-in-loop

Best regards,
Mikhail
GGA Software Services

9

Hello!


Changes in the nightly build of Indigo Nodes 1.1.7:

1. Atom numbering is the same as in the original molecule: http://tech.knime.org/forum/indigo/indigo-bug-in-handling-sdfs

2. Core Indigo library was updated. Different issues has been fixed there.

Best regards,
Mikhail
GGA Software Services
 

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Changes in the nightly build of Indigo Nodes 1.1.8:

1. New Isomer Enumerator node: http://tech.knime.org/forum/indigo/isomer-enumerator-node-request

2. IndigoFingerprint node has an option to output values in the dense format: http://tech.knime.org/forum/indigo/molecule-fingerprint-to-string-converter

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Changes in the nightly build of Indigo Nodes 1.1.12:

  1. New Highlighter node to highlight atoms and bonds according to a list of indices. Also this node can clear existing highlighting. Thanks to Simon and Guido: http://tech.knime.org/forum/indigo/selected-atoms-get-lost
  2. New properties in the molecule Properties Node: "highlighted atoms" and "highlighted bonds".
  3. Substructure Match Counter Node can use values from a query table column as names for the counter columns. Thanks to Dr_Van_Nostrand and InsilicoConsulting: http://tech.knime.org/forum/indigo/substructure-match-counter

There were no announcements about previous versions because they didn't have new functionality:

  • In the version 1.1.9 we fixed issues with Feature Remover node: http://tech.knime.org/forum/indigo/problem-with-feature-remover
  • The version 1.1.10 has a fixed a regression with Atom Replacer node when replacing R-groups.
  • In the version 1.1.11 we updated core Indigo library up to the version 1.1.8. Now Indigo serialized format is compatible with all stable version.

I'm going to update stable build of Indigo KNIME nodes with this version in 1-2 weeks. Your feedback is very important to ensure that there are not issues left. You can help us with sending any issues you found with our nodes.

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Changes in the nightly build of Indigo Nodes 1.1.13:

  1. Indigo to Molecule node can produce InChI aux information, and this AuxInfo can be converted into a molecule using Molecule to Indigo node. Thanks to Nico for suggestion: http://tech.knime.org/forum/indigo/inchi-conversion-into-2d-structure#comment-28514
  2. Combinatorial Reaction Enumeration node has an additional option with the products limit: https://groups.google.com/d/msg/indigo-general/TAqjxONDdco/ZDZmkHWCauMJ
  3. We upaded our core libary to to the version Indigo 1.1.10

Your feedback keeps us working on Indigo nodes for Knime!

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