Topology Analysis

webinar · 10 years ago

Topology Analysis


The topology analysis plugin provides characteristic values related to the topological structure of a molecule.

Simple

  • Atom count: number of atoms in the molecule including hydrogens.
  • Bond count: number of bonds in the molecule including hydrogens.
  • Cyclomatic number: the smallest number of bonds which must be removed such that no circuit remains. Also known as circuit rank.

Ring

  • Ring count: number of rings in the molecule. This calculation is based on SSSR (Smallest Set of Smallest Rings).
  • Ring atom count: number of ring atoms.
  • Ring bond count: number of ring bonds.
  • Chain atom count: number of chain atoms (non-ring atoms excluding hydrogens).
  • Chain bond count: number of chain bonds (non-ring bonds excluding bonds of hydrogen atoms).
  • Aliphatic ring count: number of those rings in the molecule, which have non-aromatic bonds (SSSR based).
  • Aromatic ring count: number of aromatic rings in the molecule. This number is calculated from the smallest set of smallest aromatic rings (SSSAR), which might contain rings which are not part of the standard SSSR ring set. As a consequence, the sum of the aliphatic ring count and the aromatic ring count can sometimes be greater the the ring count value. The difference is the sign of a macroaromatic ring system.
  • Aliphatic atom count: number of atoms in the molecule having no aromatic bond (excluding hydrogens).
  • Aliphatic bond count: number of non-aromatic bonds in the molecule (excluding bonds of hydrogen atoms).
  • Aromatic atom count: number of atoms in the molecule having aromatic bonds.
  • Aromatic bond count: number of aromatic bonds in the molecule.
  • Carbo ring count: number of those rings in the molecule, which contain carbon atoms only.
  • Hetero ring count: number of those rings in the molecule, which contain hetero atoms.
  • Heteroaromatic ring count: number of aromatic heterocycles in the molecule.
  • Carbooaromatic ring count: number of heterocycles in the molecule containing carbon atoms only (SSSAR based).
  • Fused ring count: number of fused rings in the molecule (having common bonds).
  • Fused aliphatic ring count: number of aliphatic rings having common bonds with other rings.
  • Fused aromatic ring count: number of aromatic rings having common bonds with other rings.
  • Largest ring size: size of the largest ring in the molecule.
  • Smallest ring size: size of the smallest ring in the molecule.

Path based

  • Platt index: sum of the edge degrees of a molecular graph.
  • Randic index: harmonic sum of the geometric means of the node degrees for each edge.

Distance based

  • Balaban index: the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.
  • Distance degree: the sum of the corresponding row values in the distance matrix for each atom.
  • Eccentricity: the greatest value in the corresponding row of the distance matrix for each atom.
  • Harary index: half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the molecule.
  • Hyper Wiener index: a variant of the Wiener index.
  • Szeged index: The Szeged index extends the Wiener index for cyclic graphs by counting the number of atoms on both sides of each bond (those atoms only which are nearer to the given side of the bond than to the other), and sum these counts.
  • Wiener index: the average topological atom distance (half of the sumof all atom distances) in the molecule.
  • Wiener polarity: the number of 3 bond length distances in the molecule.

Other

  • Asymmetric atom count: the number of asymmetric atoms (having four different ligands).
  • Rotatable bond count: number of rotatable bonds in the molecule. Unsaturated bonds, and single bonds connected to hydrogens or terminal atoms, single bonds of amides, sulphonamides and those connecting two hindered aromatic rings (having at least three ortho substituents) are considered non-rotatable.
  • Steric effect index: topological steric effect index (TSEI) of an atom calculated from the covalent radii values and topological distances. The stericEffectIndex is related to the steric hindrance of the given atom.