Calculator Plugins

Geometry

Topology Analysis Plugin

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).
• Chiral center count: the number of tetrahedral stereogenic centers. This function identifies two chiral centers in 1,4-dimethylcyclohexane, which does not contain asymmetric atoms.
• 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.

Geometry Plugin

The Geometry plugin provides characteristic values related to the geometrical structure of a molecule. It can calculate interatomic distances, bond angles, dihedral angles, steric hindrance and Dreiding energy. The calculation can predict and use the lowest energy conformer of the input structure.

Calculations

• Dreiding energy: energy related to the stability of the actual 3D structure (conformation) of the molecule.
• Steric hindrance: steric hindrance of an atom calculated from the covalent radii values and geometrical distances.
• Distance: distance between two atoms.
• Bond angle: the angle that is formed between two adjacent bonds on the same atom.
• Dihedral angle: dihedral angle of four atoms.

Polar Surface Area Plugin (2D)

Polar surface area (PSA) is formed by polar atoms of a molecule. It is a descriptor that shows good correlation with passive molecular transport through membranes, and so allows estimation of transport properties of drugs. Estimation of topoligical polar surface area (TPSA) is based on the method given in Ref.4.. The method provides results which are practically identical with the 3D PSA, while calculation time of TPSA is approximately 100-times faster. This method is more suitable for fast bioavailability screening of large virtual libraries. The TPSA value can be calculated both for the neutral form and the major microspecies.

Molecular Surface Area Plugin (3D)

There are two types of available molecular surface area calculations: Van der Waals and solvent accessible. Calculation method is based on the publication of Ferrara et al. (Ref.6.).