A Toy Model of Chemical Reaction Networks - TBI - Universität Wien
A Toy Model of Chemical Reaction Networks - TBI - Universität Wien
A Toy Model of Chemical Reaction Networks - TBI - Universität Wien
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3.3. CHEMICAL STRUCTURE REPRESENTATION 23<br />
H<br />
1s<br />
H<br />
1s<br />
H<br />
1s<br />
2sp 2 2sp 2<br />
C<br />
2sp 2 p<br />
1s<br />
H<br />
2sp 2<br />
C<br />
2sp 2<br />
N<br />
2sp 2 2sp 2 2sp 2<br />
2sp 2<br />
2sp 2 2sp 2<br />
p<br />
p<br />
2sp 2 2sp 2<br />
C<br />
2sp 2 p<br />
2sp 2<br />
O<br />
p<br />
1s<br />
H<br />
Figure 3.5: Orbital graph <strong>of</strong> propenamide H 2 C = CH − C(= O) − NH 2 . Direct,<br />
semi-direct σ-overlaps, and π-overlaps are represented by solid black,<br />
dashed, and solid gray lines.<br />
3.3 <strong>Chemical</strong> structure representation<br />
As the <strong>Toy</strong> <strong>Model</strong> only needs to store a graph to represent a molecule completely,<br />
an appropriate structure representation format has to be selected.<br />
A particularly convenient encoding is the Graph Meta Language (GML)<br />
[90]. It is a simple and flexible file format for graphs, designed to represent<br />
arbitrary data types as ASCII files. The BNF notation for GML is:<br />
GML ::= List<br />
List ::= (whitespace* Key whitespace+ Value)*<br />
Value ::= Integer | Real | String | [ List ]<br />
Key ::= [ ’a’-’z’ ’A’-’Z’ ] [ ’a’-’z’ ’A’-’Z’ ’0’-’9’ ]*<br />
Integer ::= sign digit+<br />
Real ::= sign digit* . digit* mantissa<br />
String ::= ’"’ instring ’"’<br />
sign ::= empty | + | -
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