vmd中以dynamic bonds形式识别不了氢原子与氢原子成键，是软件的bug吗 - 计算化学公社

# Pickbond
# Author: Justin Gullingsrud
# Date: 11 January, 2001
# Compatible VMD versions: Post-1.6; i.e, anything built after the above
# date ;-) You can rewrite the delbond and addbond procs below to reflect
# the current state of VMD's bond changing API; it's undergone a bit of flux.
# This is a script to allow users to add or delete bonds by picking atoms
# with the mouse. Type "pickbond add" at the text console, and now picking
# pairs of atoms will result a new bond being created between them.
# "pickbond del" will cause bonds between picked pairs of atoms to be
# deleted. "pickbond stop" ceases all pickbond behavior.
proc delbond { molid atom1 atom2 } {
if { $atom1 > $atom2 } {
set tmp $atom1
set atom1 $atom2
set atom2 $tmp
}
set sel [atomselect $molid "index $atom1 $atom2"]
lassign [$sel getbonds] bond1 bond2
set id [lsearch -exact $bond1 $atom2]
if { $id != -1 } {
set bond1 [lreplace $bond1 $id $id ]
}
set id [lsearch -exact $bond2 $atom1]
if { $id != -1 } {
set bond2 [lreplace $bond2 $id $id ]
}
$sel setbonds [list $bond1 $bond2]
$sel delete
}
proc addbond { molid atom1 atom2 } {
if {$atom1 == $atom2 } {
#error "cannot bond an atom to itself"
return
}
if { $atom1 > $atom2 } {
set tmp $atom1
set atom1 $atom2
set atom2 $tmp
}
set sel [atomselect $molid "index $atom1 $atom2"]
lassign [$sel getbonds] bond1 bond2
set id [lsearch -exact $bond1 $atom2]
if { $id == -1 } {
lappend bond1 $atom2
}
set id [lsearch -exact $bond2 $atom1]
if { $id == -1 } {
lappend bond2 $atom1
}
$sel setbonds [list $bond1 $bond2]
$sel delete
}
# set this proc to trace on vmd_pick_atom
set pickbond_molid -1
set pickbond_atom1 -1
set pickbond_proc addbond
proc pickbond_trace { name1 name2 op } {
global pickbond_proc pickbond_molid pickbond_atom1 vmd_pick_mol vmd_pick_atom
if { $pickbond_molid == -1 } {
# this is the first atom
set pickbond_molid $vmd_pick_mol
set pickbond_atom1 $vmd_pick_atom
} else {
# we have two atoms: call the proc
catch {$pickbond_proc $pickbond_molid $pickbond_atom1 $vmd_pick_atom}
set pickbond_molid -1
set pickbond_atom1 -1
}
}
#
# pickbond [add | del | stop ]
#
proc pickbond { op } {
global pickbond_molid pickbond_atom1 pickbond_proc
set pickbond_molid -1
set pickbond_atom1 -1
uplevel {trace vdelete vmd_pick_atom w pickbond_trace}
if { $op == "add" } {
set pickbond_proc addbond
uplevel {trace variable vmd_pick_atom w pickbond_trace}
} elseif { $op == "del" } {
set pickbond_proc delbond
uplevel {trace variable vmd_pick_atom w pickbond_trace}
} elseif { $op == "stop" } {
puts "No more pickbond"
} else {
error "Unknown option: choose one of add, del, or stop"
}
}

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