Prior to this version, V3000 sdf files could be read, but would be written back out in V2000 format. Now these files will be written back out as V3000 files.
SDFDataTable function, allows viewing compound image and data in a web browser.
read.SDFset can now skip over compounds with syntax errors in sdf files.
The functions 'getIds', 'searchString', and 'searchSim' have been modified to query pubchem directly rather than going through the intermediate web service 'ChemmineTools'.
Plots can be generated using OpenBabel library (requires ChemmineOB package and OpenBabel)
Functions to query data from PubChem directly.
Fingerprint search now provides E-values
New SDF plotting function, draw_sdf
Faster atompair generation
Support for viewing features from SQL database
Added function to generate 3D coordinates
SMARTS Search availible through ChemmineOB
Folding of FPset objects
Support for SQL database updates by compound name
Coordinate re-generation via ChemmineOB improves structure rendering
Integration of OpenBabel functionalities via new ChemmineOB add-on package
Improved SMILES support via new SMIset object class and SMILES import/export functions
Many other compound formats are now supported via ChemmineOB
Accelerated similarity searching of large small molecule data sets via new eiR add-on package
Jarvis-Patrick clustering of large small molecule data sets
SQLite support for small molecule management
Streaming functionality for SDFs enables processing of millions of molecules on a laptop
Fast and memory efficient fingerprint searches with atom pair fingerprints or PubChem fingerprints
Flexible maximum common substructure (MCS) search support provided by new fmcs.R add-on package