VMD-L Mailing List

From: Olaf Lenz (olenz_at_fias.uni-frankfurt.de)
Date: Fri Jul 27 2007 - 01:28:09 CDT

-----BEGIN PGP SIGNED MESSAGE-----
Hash: RIPEMD160

Hi Arneh!

Arneh Babakhani wrote:
> Is there such a thing as 'bondselect', analogous to atomselect (where
> you can select bonds of a certain length, or orientation)????
>
> Or alternatively, how can I just cycle through all of bonds and delete
> the ones that are greater than a certain threshold length?

There is no such thing as bondselect. However, I have written a script
that does simply delete bonds that are longer than a maximal length.
Just call

        remove_long_bonds 3

to remove all bonds that are longer than 3 in the top molecule.

##################################################
############## Remove long bonds #################
##################################################
proc remove_long_bonds { max_length } {
    for { set i 0 } { $i < [ molinfo top get numatoms ] } { incr i } {
        set bead [ atomselect top "index $i" ]
        set bonds [ lindex [$bead getbonds] 0 ]

        if { [ llength bonds ] > 0 } {
            set bonds_new {}
            set xyz [ lindex [$bead get {x y z}] 0 ]

            foreach j $bonds {
                set bead_to [ atomselect top "index $j" ]
                set xyz_to [ lindex [$bead_to get {x y z}] 0 ]
                if { [ vecdist $xyz $xyz_to ] < $max_length } {
                    lappend bonds_new $j
                }
            }
            $bead setbonds [ list $bonds_new ]
        }
    }
}

Cheers
        Olaf

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.2 (GNU/Linux)
Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org

iD8DBQFGqZB5tQ3riQ3oo/oRAwzFAJ9QapiNmgx4NBXcndvAf/8jwvx02wCfTEOi
Jp+BUuyZGEU+V+wKfcGmfYg=
=NU/O
-----END PGP SIGNATURE-----