Indigo 1.2.1

30 April 2015

Summary

New features and improvements:

  • Bingo NoSQL new plugin for Indigo was released.( Please see details)
  • standardize() function was implemented ( details)
  • SGroup better support. Loading, saving, searching, editing different types of SGroups
  • canonicalSmiles() for Reactions ( see examples)
  • Molfile V3000 type9 and type10 bonds support was implemented
  • ChemDraw CDX reader was implemented ( details)
  • Improvements for Reaction Product Enumeration. New option for skipping layout while enumeration was added. (see options .)
  • Stereo and cis-trans configuration better support ( details)
  • Bidirectional stereocenters mode (used by ChemDraw) support was implemented. stereochemistry-bidirectional-mode option was added.
  • Stereocenters detection for the haworth projection was implemented. New option stereochemistry-detect-haworth-projection was added

Bugfixes:

  • SGroups releated bugs were fixed
  • Indigo now calculates stereocenters for SMARTS like [*@H](~*)~* ( details)
  • Bug with countComponents() was fixed
  • Custom collection names loading in molfile V3000
  • Bug with superatoms saving was fixed
  • Other small bugfixes

Details

Bingo NoSQL plugin

Bingo NoSQL is a Indigo plugin and non-relational database management system for storing chemical information and searching through it. With this plugin you can create databases which will be located on the hard drive of your local machine or some remote server. Bingo NoSQL uses only own and OS functionality for creating and accessing the databases, so there is no need in installing any additional third-party software. For storing chemical structures and other extra information memory-mapped files technology was used. This technology shows better performance than using direct read and write operations, so I/O delays have no significant effect on the Bingo NoSQL speed. See the Bingo NoSQL page

Standardize

standardize method can be used to the “standardizing” of the molecule or query (stereo, charges, geometry, valences, atoms and bonds properties) in accordance with requirements. The list of applied modifications is defined by options activated in Indigo (full list of available standardize options is described in the corresponding Options section).

indigo.setOption("standardize-stereo", True);

mol1 = indigo.loadMolecule('CCN1C(SC(C)N1)')
mol2 = mol1.clone()

mol2.standardize()

array = indigo.createArray()

mol1.setProperty("grid-comment", "before")
mol2.setProperty("grid-comment", "after")

array.arrayAdd(mol1)
array.arrayAdd(mol2)

indigo.setOption("render-grid-title-property", "grid-comment")
indigo.setOption("render-grid-margins", "20, 10")
indigo.setOption("render-grid-title-offset", "10")

indigoRenderer.renderGridToFile(array, None, 2, 'result.png')
../../../_images/indigorenderer_527964ef842912c52f81607c9069f8eb49b9ea7f.svg

See examples page to find more usage examples.

CDX Format

Chemdraw CDX format support was implemented. New method iterateCDXFile was added into Indigo API. See details

Stereo better support

Improvements and fixes were applied for the stereo algorithm. Now Indigo restores stereo configurations according to the given information. Here is an example where stereo configuration is defined incorrectly. But for SMARTS pattern it is required to find all molecules with any stereo-center, thus no errors should be raised while SMARTS loading.

../../../_images/indigorenderer_74eb5f6fb86cb61ee72d740216b1cbc54ddbcb41.svg

Release includes also other stereo and cis/trans improvements: loading/serialization, bidirection mode, haworth projection, etc.