Re: [Jmol-users] connect 0.0 5.5 DELETE (*) (*); end of expression expected

[Jan <jo...@gm...>]

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 its functionality is superseded by 'connect'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.