Multilevel Neighborhoods of Atoms
From Open Babel
| Filename Extensions | mna |
|---|---|
| Chemical MIME Type | |
| Specification URL | |
| Import | No |
| Export | Yes |
| Open Babel Version | >2.2.3 |
Contents |
Options
Write options: -x[flag][parameter] (e.g. -xL1) L# Levels (default = 2)
Additional Comments
General Notes
Multilevel Neighborhoods of Atoms (MNA) descriptors are 2D molecular fragments suitable for use in QSAR modelling. The format outputs a complete descriptor fingerprint per molecule. Thus, a 27-atom (including hydrogen) molecule would result in 27 descriptors, one per line.
Specification
Molecular fragment
MNA descriptors are generated recursively. Starting at the origin, each atom is appended to the descriptor immediately followed by a parenthesized list of its neighbours. This process iterates until the specified distance from the origin, also known as the depth of the descriptor.
Element simplification
Elements are simplified into 32 groups. Each group has a representative symbol used to stand for any element in that group.
| Type | Elements |
|---|---|
| H | H |
| C | C |
| N | N |
| O | O |
| F | F |
| Si | Si |
| P | P |
| S | S |
| Cl | Cl |
| Ca | Ca |
| As | As |
| Se | Se |
| Br | Br |
| Li | Li, Na |
| B | B, Re |
| Mg | Mg, Mn |
| Sn | Sn, Pb |
| Te | Te, Po |
| I | I, At |
| Os | Os, Ir |
| Sc | Sc, Ti, Zr |
| Fe | Fe, Hf, Ta |
| Co | Co, Sb, W |
| Sr | Sr, Ba, Ra |
| Pd | Pd, Pt, Au |
| Be | Be, Zn, Cd, Hg |
| K | K, Rb, Cs, Fr |
| V | V, Cr, Nb, Mo, Tc |
| Ni | Ni, Cu, Ge, Ru, Rh, Ag, Bi |
| In | In, La, Ce, Pr, Nd, Pm, Sm, Eu |
| Al | Al, Ga, Y, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Tl |
| R | R, He, Ne, Ar, Kr, Xe, Rn, Ac, Th, Pa, U, Np, Pu, Am, Cm, Bk, Cf, Es, Fm, Md, No, Lr, Db, Jl |
Cyclic
Acyclic atoms are preceded by a hyphen "-" mark.
Example
Phenol
