Miguel wrote:
Jan wrote of 'connect' problems.
connect 0.0 5.5 DELETE (*) (*)
produces an end of expression expected error
[snip]
Jan,
I have reintroduced the connect functionality developed by Bob.
Please run your tests again.
I made some changes that are summarized below.
things look good this time, but after a delete all bonds a prior
hbonds on
has no effect on the visibility of newly created hbonds (they are
invisible).
On a related note, I removed the experimental 'bondorder' command because
its functionality is superseded by 'connect'
Miguel
connect changes
---------------
* The script compiler no longer requires that the expressions be at the
end of the statement. This gives more flexibility on the order in which
things are written. This may be useful because it allows one to place the
distance (or distances) between the atom sets.
* 'delete' can take a bond type. If no bond type is specified then delete
will remove all bonds that meet the criteria specified by the distances
and the sets.
very nice, I like
connect delete hbonds
* you can specify whether you want to 'modify' existing bonds, 'create'
new bonds, or 'modifyOrCreate'. This gives a little more flexibility and
replaces the 'static' keyword that Bob implemented.
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
connect modify double (carbon) (carbon)
connect create single (carbon) (carbon)
The bond types you can specify are:
single
double
triple
aromatic
hbond
default bond type is 'single' for modifying/creating bonds. 'delete' will
delete all bonds unless a bond type is specified.
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
# create new aromatic bonds
# do not modify any existing carbon-carbon bonds
connect create aromatic (carbon) 1.5 (carbon);
Regards, Jan
--
'backbone 25' now seems the border at which the expected 'backbone on'
graph shows up.
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