leah blogs

Today I experimented with ppchTeX, a macro package for plain TeX, LaTeX and ConTeXt to typeset chemical formulas.

It’s stucture is very interesting; it uses an arcane syntax which in fact is a domain specific language. I’ll show some examples here.

First, Ethene (CH₂CH₂).

The code of this looks like this (there is some stuff around it, but this is the code unique to this certain formula):

\chemical[ONE,SB46,DB1,Z0146,MOV1,SB28,Z28][C,C,H,H,H,H]

This reads like a simple program:

• ONE: This is the command to introduce an “node” inside the formula.

• SB46: Draw a Single Bond on position 4 and 6 of the current node. This is bottom-left and top-left.

• DB1: Draw a Double Bond on position 1 of the current node. This is right-middle.

• Z0146: Add the name of the atoms at position 0 (the middle of the node), 1, 4 and 6. These get the names from the data attached to the call; i.e. the current node gets named C, just like the right node, and the two left ones get H.

• MOV1: Move to the node at position 1, that is, the right node.

• SB28 and Z28: Draw the upper-right and bottom-right bonds, and name them accordingly.

This sounds quite compilicated, but once you got how to look at the formula, its quite easy to write.

Now, a bit more complicated example, two acetic acid molecules connected by hydrogen bonds. The code:

\chemical[ONE,Z05,SB25,DB8][C,H_3C]
\chemical[PB:Z2,ONE,Z01,SB1,PE][O,H]
\chemical[PB:Z8,ONE,Z0,HB1,PE][O]
\chemical[SUB1,ONE,18OFF1,Z01,SB16,DB4][C,CH_3]
\chemical[PB:Z4,ONE,Z0,HB5,PE][O]
\chemical[PB:Z6,ONE,Z05,SB5,PE][O,H]

I’ll only explain the stuff not covered above:

• PB:pos…PE: Start a subdiagram at position pos.

• SUB1: move one structure in relation to another in the direction given.

• 18OFF1: do 18 small steps in direction 1 (right).

Now, a quite tricky one, Guanine:

\chemical[FIVE,SB235,DB14,SR4,Z1245,RZ4][C,C,C,N,H]
\chemical[PB:Z3,ONE,Z0,SB3,CZ3,PE][N,H]
\chemical[ADJ1,SIX,SB1356,DB2,Z1236,DR6,RZ6][N,C,N,C,O]
\chemical[ADJ1,SIX,SB35,Z6][H,H]
\chemical[PB:Z3,ONE,Z0,SB28,CZ28,PE][N,H,H]

• FIVE draws a five-ring.
• RZ draws substituents using names from the data given.
• ADJ1 moves another structure in the direction given adjacent to a bond.

Yeah, that’s it. Lots of fun and a source of endless frustration… :-)

NP: Grateful Dead—Mountains Of The Moon