I think I'm done with the documentation for 10.2. If you have time,
please look over http://www.stolaf.edu/people/hansonr/jmol/docs
As I predicted, documentation writing informs coding. I'm very glad to
have had the time to do this prior to 10.2 release. Thank you Miguel
(when you return), for giving us that extra two weeks. Specifically, I
have tightened up the syntax for connect and polyhedra. You can see both
of them in action at
http://www.stolaf.edu/people/hansonr/jmol/test/10.2/new.htm
No new functionality here, but the syntax for these two commands is
considerably stricter and I hope all agree makes good sense.
From http://www.stolaf.edu/people/hansonr/jmol/docs:
connect
(v. 10.2 -- new)
/The *connect* command allows real-time bond manipulation, allowing the
user or application to connect and disconnect specific atom sets. The
general syntax is as follows:
*connect [minimum and maximum distances] [source and target atom sets]
[bond type] [modify/create option] *
//(*connect* by itself deletes all bonds and then creates bonds based on
Jmol default bond-generating algorithms, all as single bonds, without
respect to what bonding patterns might have been indicated in the model
file.)
/
The thing to notice here is the order of parameters -- distances first,
atom sets next, ONE optional bond type, then ONE optional modify/create option.
If you have a problem with this, tell me now.
I've added error traps in Eval.connect() to enforce this, and yes, it is not
quite the way we had been talking about earlier. (However, it IS the way it was
preliminarily documented.) Believe me, it is FAR easier to explain the command
and verify that it is entered correctly this way than to say,
"order doesn't really matter."
/
/
polyhedra
(v. 10.2 -- greatly expanded)
/Jmol will form a wide variety of polyhedral structures. The *polyhedra*
command can be used for either construction of new polyhedra or
modification of existing polyhedra.
*Polyhedron construction* Used for construction of new polyhedra,
parameters fall into five subsets:
*polyhedra [number of vertices] [basis] [selection sets] [display
options] [design parameters]*
...
//*Polyhedron modification* The *polyhedra* command can also be used to
modify already-constructed polyhedra. Used in this way, the command can
take only one atom set expression, and it must not indicate the number
of vertices or the basis. If the atom set expression is omitted,
"(selected)" is assumed.
To turn on, turn off, or delete selected polyhedra, use *polyhedra ON*,
*polyhedra OFF*, or *polyhedra DELETE*, respectively. Any of the display
options (FLAT, COLLAPSED, EDGES, FRONTEDGES, or NOEDGES) can also be
similarly modified. To color a set of polyhedra a particular color or to
make them translucent, first select the set of centers of the polyhedra
to modify, then use the color polyhedra
<http://www.stolaf.edu/people/hansonr/jmol/docs/#colormodelobject> command.
/
So here again we have a well-defined and enforced order for the syntax:
First, if generating, enough information to base the generating on,
either a number of vertices or the word BONDS or a radius, or a valid
combination of two of these three. Then the atom sets, then display option
such as COLLAPSED EDGES, then one or more design parameter options. In that order.
If modifying, just a single optional atom set and then one or more display options
or one of ON, OFF, or DELETE.
Hope this isn't being too strict. It makes the documentation
much more straightforward.
Bob
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