Checkmol

Jul 20, 2023

Analyze molecules for the presence of functional groups

Checkmol is a command-line utility program which reads molecular structure files in different formats and analyzes the input molecule for the presence of various functional groups and structural elements. At present, approx. 200 different functional groups are recognized. This output can be easily placed into a database table, permitting the creation of chemical databases with a functional group search option. Checkmol also outputs a set of statistical values derived from a given molecule, which can also be used for quick retrieval from a database. These values include the number of atoms, bonds, and rings, the number of differently hybridized carbon, oxgen, and nitrogen atoms, the number of C=O double bonds, the number of rings of different sizes, the number of rings containing nitrogen, oxygen, sulfur, the number of aromatic rings, the number of heterocyclic rings, etc. The combination of all of these values for a given molecule represents some kind of “fingerprint” which is useful for rapid pre-selection in a database structure/substructure search prior to a full atom-by-atom match.

Matchmol complements the capabilities of checkmol. It compares two or more molecular structures and determines whether one of them is a substructure of the other one. This is done by a full atom-by-atom comparison of the input structures. Thus, matchmol can be used as a back-end program for structure/substructure search operations in chemical databases.

The port installs both checkmol and matchmol.



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