Chemical structures with plain TeX

Peter Flynn peter at
Sat Jul 6 16:22:15 CEST 2019

On 6 July 2019 08:11:09 "Taylor, P" <P.Taylor at> wrote:

> Phil is NOT "pissed off".  He is sad (very sad, so sad that he weeps)
> that even today, in the 21st century, we still communicate algorithms in
> such impenetrable prose.

I would distinguish between the communication.of information in an informal 
setting like this list, between people with a strong technical background, 
where a compact format (code) and specialist language (jargon) are 
justified; and a more formal setting like books or journals, for people 
not.necessarily familiar with the detail, where a more descriptive approach 
is better. I use the first here, on c.t.t, and in Twitter, but the second 
in my books and web pages, where I hope I have explained everything in 
accessible prose.

> R Shreevatsa demonstrated in a follow-up
> message that the same algorithm can be expressed in language that is
> accessible to mere mortals, even those with no familiarity whatsoever
> with his preferred language of expression .

I turned down learning Python many years ago and have not so far regretted 
that decision 😃 I suppose I have a firmly-rooted objection to having to 
open a  new file, writing the procedure, saving it, and then executing it, 
instead of just typing the commands and having IG execute there and then. 
It's probably just the way I think.

> Peter's formulation, while
> arguably elegant, is cryptic beyond belief.

True, although not beyond belief. We're in different fields — for most 
people in my field , what I typed would be immediately obvious.

> And if Peter's were to
> fail,for some unknown reason, how would one go about debugging it ?

By removing the error redirects to expose the errors. It happens 
occasionally, for example, that some pseudo-HTML source is so grossly 
malformed that even Tidy is unable to make sense of it. At which point I 
give up, as I don't deal professionally with that level of error.

> By
> deliberately piping the output of one program into the input of another,
> eschewing temporary files, no trace is left of the intermediate results,

That's correct and deliberate. I've already tested it, and I trust Karl to 
serve only well-formed HTML, so in this case an error is very unlikely. But 
if you apply the same principles to some other web source whose curators 
lack skill or care, you would need to test it and add more code to work 
around the errors. But the same would apply to Python or any other code 

> so one cannot go back to inspect these in an attempt to identify the
> source of the error.

Yes it's possible, just hit up-arrow to retrieve the last command, edit it 
to remove the redirects, and hit Enter to re-run it.

> Yes, I do not deny for one second that I loathe and detest Unix,

Perfectly acceptable. I don't either loathe or detest VMS, although I found 
it horribly tedious and long-winded. I come closest with Windows,  which I 
despise rather than hate,  as it's devoid of any shred of common-sense. But 
both serve their purpose in their own way, and I still have clients using them.

> but
> that was not the motivation for posting my message — I was genuinely
> saddened (OK, I didn't actually weep, that was a slight exaggeration)
> that such a potentially useful solution to such an important (within the
> universe of discourse) problem should be transmitted as such (sorry, I
> cannot find a better phrase) complete and utter gibberish.

I'm sorry you found it incomprehensible, but it's the world in, 
where I earn my keep and do my research, and in this environment I will 
keep using it because it's the default for anyone doing document engineering.

My view is that if you are dealing in any significant way with text 
documents, especially on the web, you should be prepared to.invest a little 
time and effort in learning and using Linux (or MacOSX), as it's the only 
system with a broad enough set of facilities to handle document and 
information fast and consistently.

>> This is not a good precondition for a fruitful discussion.
> As the British Parliamentary system so clearly demonstrates.

That's a whole other can of worms. Protracted political suicide isn't my 
kick, I'm.afraid.

> ** Phil (more in sorrow than in anger).

When/If I get round to writing the book on how to weak with this stuff, the 
code will just be examples: there copious textual explanation and 
you will get a proof copy 😃


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