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Multilevel Neighborhoods of Atoms (MNA) (mna)

Iteratively generated 2D descriptors suitable for QSAR

Multilevel Neighborhoods of Atoms (MNA) descriptors are 2D molecular fragments suitable for use in QSAR modelling [fpbg99]. The format outputs a complete descriptor fingerprint per molecule. Thus, a 27-atom (including hydrogen) molecule would result in 27 descriptors, one per line.

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.

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

Acyclic atoms are preceded by a hyphen “-” mark.

Here’s the multi-level neighborhood for the molecule represented by the SMILES string CC(=O)Cl:

# The contents of this file were derived from
# Title = acid chloride
-C(-H(-C)-H(-C)-H(-C)-C(-C-O-Cl))
-C(-C(-H-H-H-C)-O(-C)-Cl(-C))
-O(-C(-C-O-Cl))
-Cl(-C(-C-O-Cl))
-H(-C(-H-H-H-C))
-H(-C(-H-H-H-C))
-H(-C(-H-H-H-C))
[fpbg99]Dmitrii Filimonov, Vladimir Poroikov, Yulia Borodina, and Tatyana Gloriozova. Chemical Similarity Assessment through Multilevel Neighborhoods of Atoms: Definition and Comparison with the Other Descriptors. J. Chem. Inf. Comput. Sci. 1999, 39, 666-670. [Link]

Note

This is a write-only format.

Write Options

L <num> Levels (default = 2)