30 April 2015
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
SGroups releated bugs were fixed
Indigo now calculates stereocenters for SMARTS like
Custom collection names loading in molfile V3000
Bug with superatoms saving was fixed
Other small bugfixes
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 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')
See examples page to find more usage examples.
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.
Release includes also other stereo and cis/trans improvements: loading/serialization, bidirection mode, haworth projection, etc.