Simplex representation of molecular structure (SiRMS):

Simplex - tetratomic fragments of fixed composition, structure, chirality and symmetry

Simplex descriptor - number of identical simplexes in a molecule

Example of 2D simplexes generation for formic acid

Simplex example

Simplex labeling example

Advantages:

  • vertexes in simplexes can be labeled by different atomic properties like lipophilcity, partial charge, donor/acceptor of H-bond, etc;
  • simplexes describe individual compounds, multi-fragment compounds and mixtures of chemical compounds;
  • simplex descriptors are interpretable by design.

We have two implementations of simplex descriptors (they are incompartible with each other)

HiT-QSAR SiRMS.py
License Available on request (write a letter to Prof. Kuz’min) GPL-3 (Github page)
OS Windows Windows, Linux
1D simplexes Yes No
2D simplexes Yes Yes
3D simplexes Yes No
Mixtures Yes Yes
Quasi-mixtures Yes Yes
Chemical reactions No Yes
Graphical interface Yes No
Atom labeling by Element, sybyl type, lipophilicity, partial charge, refraction, donor/acceptor of H-bond, electronegativity, van der Vaals attraction/repulsion, etc Element + user-defined
Multi-core support No Experimental
Speed of calculation Slower Faster
© Pavel Polishchuk 2010-2017