...
In summary:
There are 4 operations that you can perform:
delete - deletes bonds
modify - modify existing bonds only
create - create new bonds only
modifyOrCreate - modify or create as needed
...
You may specify two distances, a minDistance and maxDistance. Default
minDistance is 0.1 angstroms. Default maxDistance is 1 meter. If only
one
distance is specified then it is interpreted as the maxDistance.
Two sets are required to make the connections. If only one set is
specified then the other set defaults to 'selected'. If no sets are
specified then both sets default to 'selected'.
The following should all make sense:
connect delete (*) (*) # delete all bonds
select *; connect delete;
connect delete single (carbon) (hydrogen)
connect delete (carbon) double (carbon) # if you prefer
# existing carbon-carbon bonds within 1.2 angstroms become double
connect modify (carbon) 1.2 (carbon) double
connect; #rerun autobond code
didn't respect current selection
this is a logic brake, while
select atomno=1
connect delete
is substituted by
connect delete (*) (selected)
only deletes bonds from atom #1 to other
select atomno=1
connect
is substituted by
connect {CONNECT record and autobound algorithm} (*) (*)
and not
connect AUTO (*) (selected)
as expected (by me naively)
I think it would be more clear with an additional operator AUTObound
where naively I had expected that AUTObound is the default if no
distance parameter is given, that
connect
resolves to:
connect AUTO
connect AUTO (*)
connect AUTO (*) (selected)
Regards, Jan
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