Levels are stored in level sets. Level set has a simple ini-file format which includes:

1. Header

[LevelSet]
Name=KAtomic levels
Description=This is the additional collection of KAtomic levels.
Author=Mr. Foo Bar
AuthorEmail=foo@bar.mr
LevelCount=27

Fields Name and LevelCount are required

2. Levels description

Each level described by a separate ini-file group entry named [LevelNNN] where NNN is level number, for example:

[Level1]
Name=Water
atom_1=1-c
atom_2=3-cg
atom_3=1-g
feld_00=...............
feld_01=...............
feld_02=...............
feld_03=..###########..
feld_04=..#..#......#..
feld_05=..#.3#......#..
feld_06=..#.##......#..
feld_07=..#.#..#.####..
feld_08=..#....#.2..#..
feld_09=..###.#.....#..
feld_10=..#1....#...#..
feld_11=..###########..
feld_12=...............
feld_13=...............
feld_14=...............
mole_0=123

Explanation of level description format:
(could be improved, currently please read levels/default_levels.dat for examples)

atom_1=2-bdD

Here's how to decode that.
Atoms are the chars that go before dash,
Bonds are the chars that go after dash.

Atoms:
1=H
2=C
3=O
4=N
5=S
6=F
7=Cl
8=Br
9=P
0=J
o=Crystal
E,F,G,H,I,J,K,L - flasks with ranging fullness, E - being an empty flask, L - full flask.
A=horizontal connector
B=slash-like connector
C=vertical connector
D=backslash-like connector

Bonds:
a=single top
b=single top-right
c=single right
d=single bot-right
e=single bottom
f=single bot-left
g=single left
h=single top-left
A=double top
B=double right
C=double bottom
D=double left
E=triple top
F=triple right
G=triple bottom
H=triple left