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History

 

The original idea of the Baka Matrix came as a result of working on a project to model biochemical reactions with computer graphics.

 

The first approach to represent a molecular structure was to use graphs. Consider the molecular structure of propanoic acid. In the illustration below the structure is as from above the molecule so we can see the atoms in a flat layout. Each atom is given a number which is placed in a circle.

 

 

 

Simple Basis - Graph Storage in a Matrix.

 

Note:

Typically Chemists will draw a molecule without showing the letters for Carbon and no bonds for any hydrogen attached to a carbon. Propnanoic Acid would be normally be drawn like this:

 

 

 

If each node is put into a table so that the bonds are considered as edges and the atoms are listed as verci then the following diagram is produced.

 

 

 

1

2

3

4

5

6

7

8

9

10

11

1

 

1

 

 

 

 

 

1

1

1

 

2

1

 

1

 

 

 

1

 

 

 

1

3

 

1

 

1

1

 

 

 

 

 

 

4

 

 

1

 

 

 

 

 

 

 

 

5

 

 

1

 

 

1

 

 

 

 

 

6

 

 

 

 

1

 

 

 

 

 

 

7

 

1

 

 

 

 

 

 

 

 

 

8

1

 

 

 

 

 

 

 

 

 

 

9

1

 

 

 

 

 

 

 

 

 

 

10

1

 

 

 

 

 

 

 

 

 

 

11

 

1

 

 

 

 

 

 

 

 

 

 

 

 

There are several problems with this approach.

 

First of all there is a duplication of information. The upper right portion has the same information as the lower left portion in much the same way as a multipcation table.

 

There was also limitations to what kind of molecular structure graphs could represent.

Consider the following molecular structure.

 

 

 

 

This is much more complicated and would be very difficult to represent.

 

There is also not enough information about the bonds in the structure. The double Bond to Oxygen was not represented in a graph.

 

Clearly a new way was needed to represent a molecular structure.

 

 

 

0

1

2

3

4

5

6

7

8

9

M

0

 

 

 

 

 

 

 

 

 

 

Af

1

 

 

 

 

 

 

 

 

 

 

Pf

2

 

Pf1

Pf2

Pf3

Pf4

Pf5

Pf6

Pf7

Pf8

 

Xf

3

Xi

Xf1

Xf2

Xf3

Xf4

Xf5

Xf6

Xf7

Xf8

 

Yf

4

Yi

Yf1

Yf2

Yf3

Yf4

Yf5

Yf6

Yf7

Yf8

0

Ao

5

 

 

 

 

 

 

 

 

 

 

Po

6

 

 

 

 

 

 

 

 

 

PfL

Xs

7

Xo

Xs1

Xs2

Xs3

Xs4

Xs5

Xs6

Xs7

Xs8

XfL

Ys

8

Yo

Ys1

Ys2

Ys3

Ys4

Ys5

Ys6

Ys7

Ys8

YfL

Ab

9

Ao

Ab1

Ab2

Ab3

Ab4

Ab5

Ab6

Ab7

Ab8

AbL

Pb

10

Ie

 

 

 

 

 

 

 

 

 

Xb

11

 

 

 

 

 

 

 

 

 

 

Yb

12

 

 

 

 

 

 

 

 

 

 

 

 

 

M = Status Row For Molecule

Xi = Initial X Coordinate

Yi = Initial Y Coordinate

Po = Pointer from first Atom

Xo = X Coordinate of first Atom

Yo = Y Coordinate of first Atom

Ie  =  Index number of atom at the end

 

Xs = X Coordinate of a Skeletal Atom

 

 

P is a number which determines what directions there are bonds

 

a bond to Carbon on three sides such as the following:

 

1

 

Would be represented as

 

 

 

The following table shows the numeric representation used for each bond type.

 

0

Points To Nothing

 

1

2

 

3

4

 

5

 

6

 

7

 

8

 

9

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Early Works