Bob,
I'm making some progress on your suggestion to check and branch during the
addition of atoms (below). One problem that I'm having is comparing points,
so I thought that better check with you. If I have two points defined, a and
b, shouldn't the following syntax produce a true or false based on xyz
identity of the points?
If ({a} == {b}){do stuff;};continue on to other stuff;
I can send you the specific code, but I thought I'd ask about my basic
understanding of point math and logic first. My problem is that the above
seems to be true for points that are not the same.
To give some context to the above: Your atom addition code solves the
chirality problem for interior atoms, but if the interior atom is trigonal
or linear, then the new atom is placed exactly on top of the clicked atom.
Given your computation of the added atoms coordinates, this is
understandable. Connect, however, will not bond these atoms. The subsequent
minimize ejects the new atom from the molecule. I'm trying to catch cases
where a clicked atom and an added atom have the same coordinates. If I can
catch these, I can branch to an addition that deals with the problem.
Otis
>
>> Your second suggestion is really slick, and I learned a lot picking it
>> apart. Unfortunately, it leads to linear chain growth from time to time, and
>> that starts getting into problems. Ethane growth seems to be linear
>> consistently - i.e. C-C-C. If you build off of C2, you start to add
>> superimposed atoms, as per your Jmol math.
>>
>> Right -- you could check for that and do something different then.
>
>
>> The _atomPick X+0, Y+.1, Z+.1 that I used seems to do two things: 1) the
>> atoms are close enough to bond; 2) the atoms are offset enough for minimize
>> to push the new atom away.
>>
>>
> I just thought it was very odd to have the groups already present invert
> chirality completely.
>
>
>
--
Otis Rothenberger
http://chemagic.org
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