This manual gives you a walk-through on how to use the Topological Analysis Plugin:
The Topology Analysis Plugin calculates different topological descriptors for a molecule. The example below shows the result window of the plugin.
Fig.1 Topological descriptors calculated and displayed for molecules
These options can be set in the Topology Analysis Options window, as shown below with the Atom/Bond Tab opened.
Fig. 2 Topology Analysis Options window
The Decimal places and the Single fragment mode set the number of decimal places for the calculation results and the displaying mode of the molecules, respectively.
Available topological descriptors
The following descriptors can be calculated (each group of descriptors can be found under a separate tab of the options window):
- 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.
- Asymmetric atom count: the number of asymmetric atoms (having four different ligands).
- Atom count: number of atoms in the molecule including hydrogens.
- Bond count: number of bonds in the molecule including bonds of hydrogen atoms.
- 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).
- 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.
- Ring atom count: number of ring atoms.
- Ring bond count: number of ring bonds.
- 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.
- Stereo double bond count: number of double bonds with defined stereochemistry.
Other topological descriptors