Difference between revisions of "Multilevel Neighborhoods of Atoms"

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(Added reference)
(Added element mapping table)
 
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=== Element simplification ===
 
=== Element simplification ===
Elements are simplified into 32 groups.  Each group has a representative symbol used to stand for any element in that group. Some groups, such as H, C, N and O have only one element.  Group V however, contains V, Cr, Nb, Mo and Tc.
+
Elements are simplified into 32 groups.  Each group has a representative symbol used to stand for any element in that group.
 
+
{| border="1" cellpadding="5" cellspacing="0"
 +
|+ Mapping of elements to groups
 +
|- align="left"
 +
! 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 ===
 
=== Cyclic ===
 
Acyclic atoms are preceded by a hyphen "-" mark.
 
Acyclic atoms are preceded by a hyphen "-" mark.

Latest revision as of 23:13, 30 January 2010

Filename Extensions mna
Chemical MIME Type
Specification URL
Import No
Export Yes
Open Babel Version >2.2.3

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.

Mapping of elements to groups
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

References