Rdkit

Jul 20, 2023

Collection of cheminformatics and machine-learning software

Open source toolkit for cheminformatics.

Features

  • Input/Output SMILES/SMARTS, SDF, TDT, SLN 1, Corina mol2 1, PDB, sequence notation, FASTA peptides only, HELM peptides only
  • Substructure searching
  • Canonical SMILES
  • Chirality support i.e. R/S or E/Z labeling
  • Chemical transformations e.g. remove matching substructures
  • Chemical reactions
  • Molecular serialization e.g. mol <-> text
  • 2D depiction, including constrained depiction
  • Fingerprinting Daylight-like, atom pairs, topological torsions, Morgan algorithm, “MACCS keys”, extended reduced graphs, etc.
  • Similarity/diversity picking
  • Gasteiger-Marsili charges
  • Bemis and Murcko scaffold determination
  • Salt stripping
  • Functional-group filters


Checkout these related ports:
  • Zx - MQT ZX A library for working with ZX-diagrams
  • Zotero - Reference management for bibliographic data and research materials
  • Yoda - Particle physics package with classes for data analysis, histogramming
  • Xtb - Semiempirical Extended Tight-Binding Program Package
  • Xmakemol - Molecule Viewer Program Based on Motif Widget
  • Xdrawchem - Two-dimensional molecule drawing program
  • Xcrysden - Crystalline and molecular structure visualisation program
  • Xcfun - Exchange-correlation functionals with arbitrary-order derivatives
  • Wxmacmolplt - Graphical user interface principally for the GAMESS program
  • Wwplot - Plotting tool for experimental physics classes
  • Wannier90 - Maximally-localized Wannier functions (MLWFs) and Wannier90
  • Votca - CSG and XTP libraries for atomistic simulations
  • Voro++ - Three-dimensional computations of the Voronoi tessellation
  • Vmd - Molecular visualization program
  • Vipster - Crystalline and molecular structure visualisation program