In Quixote we are writing a semantic infrastructure for computational chemistry. That means we have to create precise and consistent annotation for components. The community “knows the semantics” so often they aren’t explicit. But the problem is that if the semantics aren’t clear, or if they could be misinterpreted, then it’s impossible to write programs that behave consistently. Here we are interpreting a logfile [the voluminous output that is designed to be read by humans and not machines] and I want to know what it means. So I’m asking for your help. Now before you all tell me to RTFM it’s not common to describe every part of a logfile in the manual so I haven’t gone looking.
So here’s a chunk I was marking up using an element of knowledge and intuition (== guesswork). I had a sudden worry I’d guessed wrong. So I’m asking readers to help me annotate this chunk (the file is about 100 times larger). In particular do we all understand the same things?
Task: Please annotate the columns in the two tables as fully as necessary (i.e. Write a description of what each means in sufficient detail that it could be used by someone in – say – the Blue Obelisk community but who wasn’t familiar with the precise code). Where there are precise terms agreed in the community please use those. [BTW I have no particular comment on the level of semantics in this code compared to others.]
No. Tag Charge X Y Z
—- —————- ———- ————– ————– ————–
1 c 6.0000 1.00000000 3.00000000 5.00000000
2 f 9.0000 1.00000000 3.00000000 6.38300000
3 h 1.0000 2.02800000 3.00000000 4.65000000
4 h 1.0000 0.48600000 3.89000000 4.65000000
5 h 1.0000 0.48600000 2.11000000 4.65000000
Atomic Mass
-----------
c 12.000000
f 18.998400
h 1.007825
UPDATE: I’ll give my own answer later (this is NOT trivial) but I’d prefer others to contribute because then *I* learn something