# Bulk-fetch all bonds, filter out H1-H2 bonds in SWM4, reassign in one shot

# Get the set of H1/H2 atom indices in SWM4 residues
set sel [atomselect top "resname SWM4 and name H1 H2"]
set target_indices [$sel get index]
$sel delete

# Build a lookup array for O(1) membership test
array unset is_target
foreach idx $target_indices {
    set is_target($idx) 1
}

# Get ALL atoms and ALL bonds in one call
set all [atomselect top "all"]
set all_bonds [$all getbonds]

# Build new bond lists, stripping target-target bonds
set new_bonds {}
set modified 0
set removed 0
set i 0

foreach blist $all_bonds {
    if {[info exists is_target($i)]} {
        # This atom is an H1/H2 in SWM4 — filter its bonds
        set filtered {}
        foreach b $blist {
            if {![info exists is_target($b)]} {
                lappend filtered $b
            } else {
                incr removed
            }
        }
        lappend new_bonds $filtered
        if {[llength $filtered] != [llength $blist]} {
            set modified 1
        }
    } else {
        lappend new_bonds $blist
    }
    incr i
}

# Reassign all bonds at once
if {$modified} {
    $all setbonds $new_bonds
}
$all delete

# Each bond counted from both ends
puts "Deleted [expr {$removed / 2}] H1-H2 bonds in SWM4 residues."