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test_volmap.tcl
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mol new
mol addfile waterbox.psf type psf
mol addfile waterbox.dcd type dcd waitfor all
if { [molinfo top get numframes] < 2 } {
puts "ERROR) This test is meaningful only on trajectories (more than one frame)."
quit
}
if { 1 } {
# Test 1: time-varying selection
set sel [atomselect top "(not hydrogen) and (x > -2.0) and (x < 2.0) and (y > -2.0) and (y < 2.0) and (z > -2.0) and (z < 2.0)"]
set all [atomselect top "all"]
${all} set radius 1.0
${all} delete
set n_frames [molinfo top get numframes]
set n_waters [list]
for { set frame 0 } { ${frame} < ${n_frames} } { incr frame } {
${sel} frame ${frame}
${sel} update
lappend n_waters [${sel} num]
}
set n_waters_ave [expr [vecsum ${n_waters}] / ${n_frames}]
set res 0.25
volmap density \
${sel} \
-res ${res} -minmax [list [list -6.0 -6.0 -6.0] [list 6.0 6.0 6.0]] \
-allframes -combine avg \
-checkpoint 0 \
-o water_density.dx
set f [open "water_density.dx" "r"]
set integral 0.0
while { [gets ${f} line] != -1 } {
set words [split ${line}]
if { [string is double [lindex ${words} 0]] > 0 } {
foreach word ${words} {
set integral [expr ${integral} + ${word}]
}
}
}
close ${f}
set integral [expr ${integral}*(${res}*${res}*${res})]
puts "TEST1 results:"
puts [format "TEST1) Integral of density map = %.5f" ${integral}]
puts [format "TEST1) Average number of atoms = %.5f" ${n_waters_ave}]
${sel} delete
}
if { 2 } {
# Test 2: time-varying selection and custom weight with fixed property
set sel [atomselect top "(not hydrogen) and (x > -2.0) and (x < 2.0) and (y > -2.0) and (y < 2.0) and (z > -2.0) and (z < 2.0)"]
set all [atomselect top "all"]
${all} set occupancy 1.0
set n_frames [molinfo top get numframes]
set n_waters [list]
for { set frame 0 } { ${frame} < ${n_frames} } { incr frame } {
${sel} frame ${frame}
${sel} update
lappend n_waters [${sel} num]
}
set n_waters_ave [expr [vecsum ${n_waters}] / ${n_frames}]
set res 0.25
volmap density \
${sel} -weight occupancy \
-res ${res} -minmax [list [list -6.0 -6.0 -6.0] [list 6.0 6.0 6.0]] \
-allframes -combine avg \
-checkpoint 0 \
-o water_density.dx
set f [open "water_density.dx" "r"]
set integral 0.0
while { [gets ${f} line] != -1 } {
set words [split ${line}]
if { [string is double [lindex ${words} 0]] > 0 } {
foreach word ${words} {
set integral [expr ${integral} + ${word}]
}
}
}
close ${f}
set integral [expr ${integral}*(${res}*${res}*${res})]
puts "TEST2 results:"
puts [format "TEST2) Integral of density map = %.5f" ${integral}]
puts [format "TEST2) Average number of atoms = %.5f" ${n_waters_ave}]
${sel} delete
${all} delete
}
if { 3 } {
# Test 3: time-varying selection and time-varying custom weight (user)
set sel [atomselect top "(not hydrogen) and (x > -2.0) and (x < 2.0) and (y > -2.0) and (y < 2.0) and (z > -2.0) and (z < 2.0)"]
set all [atomselect top "all"]
${all} set occupancy 1.0
set n_frames [molinfo top get numframes]
set n_waters [list]
for { set frame 0 } { ${frame} < ${n_frames} } { incr frame } {
${sel} frame ${frame}
${sel} update
${sel} set user [vecmul [${sel} get x] [${sel} get x]]
lappend n_waters [vecsum [${sel} get user]]
}
set n_waters_ave [expr [vecsum ${n_waters}] / ${n_frames}]
set res 0.25
volmap density \
${sel} -weight user \
-res ${res} -minmax [list [list -6.0 -6.0 -6.0] [list 6.0 6.0 6.0]] \
-allframes -combine avg \
-checkpoint 0 \
-o water_density.dx
set f [open "water_density.dx" "r"]
set integral 0.0
while { [gets ${f} line] != -1 } {
set words [split ${line}]
if { [string is double [lindex ${words} 0]] > 0 } {
foreach word ${words} {
set integral [expr ${integral} + ${word}]
}
}
}
close ${f}
set integral [expr ${integral}*(${res}*${res}*${res})]
puts "TEST3 results:"
puts [format "TEST3) Integral of density map = %.5f" ${integral}]
puts [format "TEST3) Average value of \"user\" = %.5f" ${n_waters_ave}]
${sel} delete
${all} delete
}
if { 4 } {
# Test 4: time-varying selection and explicit weights
set sel [atomselect top "(not hydrogen) and (x > -2.0) and (x < 2.0) and (y > -2.0) and (y < 2.0) and (z > -2.0) and (z < 2.0)"]
set all [atomselect top "all"]
set weights_all [vecmul [${all} get y] [${all} get z]]
${all} set occupancy ${weights_all}
set n_frames [molinfo top get numframes]
set n_waters [list]
for { set frame 0 } { ${frame} < ${n_frames} } { incr frame } {
${sel} frame ${frame}
${sel} update
lappend n_waters [vecsum [${sel} get occupancy]]
}
set n_waters_ave [expr [vecsum ${n_waters}] / ${n_frames}]
set res 0.25
volmap density \
${sel} -weight ${weights_all} \
-res ${res} -minmax [list [list -6.0 -6.0 -6.0] [list 6.0 6.0 6.0]] \
-allframes -combine avg \
-checkpoint 0 \
-o water_density.dx
set f [open "water_density.dx" "r"]
set integral 0.0
while { [gets ${f} line] != -1 } {
set words [split ${line}]
if { [string is double [lindex ${words} 0]] > 0 } {
foreach word ${words} {
set integral [expr ${integral} + ${word}]
}
}
}
close ${f}
set integral [expr ${integral}*(${res}*${res}*${res})]
puts "TEST4 results:"
puts [format "TEST4) Integral of density map = %.5f" ${integral}]
puts [format "TEST4) Average value of (YxZ) = %.5f" ${n_waters_ave}]
${sel} delete
${all} delete
}
quit