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. On a related note, I removed the experimental 'bondorder' command because its functionality is superseded by 'connect' Miguel connect changes --------------- * The script compiler no longer requires that the expressions be at the end of the statement.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. * 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 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 # create new aromatic bonds # do not modify any existing carbon-carbon bonds connect create aromatic (carbon) 1.5 (carbon); ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
