forked from lijiext/lammps
57 lines
1.5 KiB
Tcl
57 lines
1.5 KiB
Tcl
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# small script to extract bonding info from a lammps data file
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# so that VMD will display the correct bonds for CG-MD.
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# (c) 2007 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
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proc lmpbondsfromdata {mol filename} {
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# create an empty bondlist
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set na [molinfo $mol get numatoms]; # number of atoms
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set nb 0; # number of bonds
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set bl {}; # bond list
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for {set i 0} {$i < $na} {incr i} {
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lappend bl {}
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}
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# open lammps data file
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if {[catch {open $filename r} fp]} {
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puts stderr "could not open file $filename"
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return -1
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}
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# read file line by line until we hit the Bonds keyword
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while {[gets $fp line] >= 0} {
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# pick number of bonds
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regexp {^\s*(\d+)\s+bonds} $line dummy nb
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if { [regexp {^\s*Bonds} $line] } {
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puts "nbonds= $nb\n now reading Bonds section"
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break
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}
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}
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# skip one line
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gets $fp line
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# read the bonds file
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for {set i 0} {$i < $nb} {incr i} {
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gets $fp line
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# grep bond numbers from entry and adjust to VMD numbering style
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regexp {^\s*\d+\s+\d+\s+(\d+)\s+(\d+)} $line dummy ba bb
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incr ba -1
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incr bb -1
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set bn [lindex $bl $ba]
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lappend bn $bb
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set bl [lreplace $bl $ba $ba $bn]
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set bn [lindex $bl $bb]
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lappend bn $ba
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set bl [lreplace $bl $bb $bb $bn]
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}
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close $fp
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set sel [atomselect $mol all]
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$sel setbonds $bl
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$sel delete
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}
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