This is a two-part question. You can answer "(1) Yes (2) No", "(1) No
(2) No" or "(1) irrelevant (2) Yes"
(1): Is "auto" the right word?
The reason I ask is that it's taken us quite some time to realize what
this does, and that leads me to wonder if something is amiss.
My thinking:
Taking a look at this code:
private final static String[] connectOperationStrings =
{ "delete", "modify", "create", "modifyOrCreate", "auto" };
we see that there are five possible operations that the connect command
can do. None of us, even Miguel, were realizing that "auto" is in this
set -- that you can't "modify auto" any more than you can "delete
create". You get one operation only.
I believe the confusion may lie with the fact that "auto" is an adverb
and the rest are action verbs. Thus, you can "delete" or "modify"
something, but you can't "auto" it. Sometimes it just takes time to
realize things like this. My suggetion, proposal, question, is this:
Should this list read:
private final static String[] connectOperationStrings =
{ "delete", "modify", "create", "modifyOrCreate", "calculate" };
? Would that be more obvious? Seems to me "calculate" is the operation
actually being performed.
connect calculate hbonds (*) (*)
connect calculate (*) (*)
?
(2) Second point along these lines. Various people have pointed out that
defaults should have names as well. Here the default seems to me to be
"covalent":
connect calculate hbonds (*) (*)
connect calculate covalent (*) (*)
In Jmol, "hbond" and "hbonds" are equivalent. But because connect is
being used for two separate operations -- one in which "hbonds" is
simply indicating what sort of thing to calculate, the other what sort
of bond to produce (subtle difference), and because this calculate
function doesn't use, for example, the minimum/maximum distance
business, I propose splitting it off to a new command:
calculate hbonds (*) (*)
calculate covalent (*) (*)
Now we have a clearly distinguishable action. I'm always thinking
documentation: "The calculate command generates either hydrogen bonds or
covalent bonds based on algorithms involving atom type and distance...."
This will avoid all confusion with "connect modify". And there would be
no suggestion of
calculate 1.0 1.3 covalent (*) (*)
which otherwise would be "conceivable" with
connect 1.0 1.3 auto (*) (*)
which also doesn't make any sense.
Bob
Bob Hanson wrote:
Let' see exactly what the processor does here:
connect modify auto (*) (*)
First, "modify" is ignored. The covalent "autobonding" functionality
does not ever replace existing bonds. So since in this case the bonds
are already double, they are left intact. If some had been deleted,
then they would show up again, but if none were deleted, none are
changed.
That is, the "auto" functionality in its current state cannot be used
to modify bond order. All it is meant to do is add bonds that don't
already exist. "Create" is implicit.
To use "connect" to replace current bonding patterns with
Jmol-calculated single bonds you would invoke:
connect delete (*) (*)
connect auto (*) (*)
The same goes for hydrogen bonds. The "auto" functionality there
cannot be used to modify existing bonds, only create bonds. For that
you would need:
connect hbonds delete (*) (*)
connect hbonds auto (*) (*)
Bob
programming note: This is because both methods end up ultimately at
Atom.bondMutually(Atom, short, Frame), and that method never changes
an existing bond.
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