| version 1.4 | version 1.5 |
|---|
| |
| variable paxis | variable paxis |
| variable COM | variable COM |
| variable I | variable I |
| | variable priority_axis |
| } | } |
| | |
| # package require Orient | # package require Orient |
| |
| | |
| #replace sel with point list | #replace sel with point list |
| proc Orient::sel_mass { size } { | proc Orient::sel_mass { size } { |
| puts "VND MASS..." | #puts "VND MASS..." |
| variable assigned_weights | variable assigned_weights |
| set assigned_weights {} | set assigned_weights {} |
| #length of values | #length of values |
| |
| set y $yarg | set y $yarg |
| set z $zarg | set z $zarg |
| set m $assigned_weights | set m $assigned_weights |
| puts "[llength $m]" | |
| set comx 0 | set comx 0 |
| set comy 0 | set comy 0 |
| set comz 0 | set comz 0 |
| |
| } | } |
| | |
| # draws the three principal axes | # draws the three principal axes |
| proc vmd_draw_principalaxes {xarg yarg zarg mol} { | proc vmd_draw_principalaxes {xarg yarg zarg mol flip} { |
| variable paxis | variable paxis |
| variable COM | variable COM |
| variable I | variable I |
| variable a1 | variable a1 |
| | variable priority_axis |
| | |
| set x $xarg | set x $xarg |
| set y $yarg | set y $yarg |
| set z $zarg | set z $zarg |
| | |
| | set flip_priority_axis $flip |
| | |
| set I [Orient::calc_principalaxes $x $y $z] | set I [Orient::calc_principalaxes $x $y $z] |
| set ::NeuronVND::princ_axes $I | set ::NeuronVND::princ_axes $I |
| | |
| |
| #set minmax [measure minmax $sel] remove because VMD only | #set minmax [measure minmax $sel] remove because VMD only |
| #set ranges [vecsub [lindex $minmax 1] [lindex $minmax 0]] | #set ranges [vecsub [lindex $minmax 1] [lindex $minmax 0]] |
| set ranges [vecsub $maxT $minT] | set ranges [vecsub $maxT $minT] |
| puts "ranges = $ranges" | # puts "ranges = $ranges" |
| set scale [expr .7*[Orient::max [lindex $ranges 0] \ | set scale [expr .7*[Orient::max [lindex $ranges 0] \ |
| [lindex $ranges 1] \ | [lindex $ranges 1] \ |
| [lindex $ranges 2]]] | [lindex $ranges 2]]] |
| |
| set COM [Orient::sel_com $x $y $z] | set COM [Orient::sel_com $x $y $z] |
| set ::NeuronVND::princ_axes_com $COM | set ::NeuronVND::princ_axes_com $COM |
| vmd_draw_vector $mol $COM [vecscale $scale $a1] | vmd_draw_vector $mol $COM [vecscale $scale $a1] |
| graphics $mol color blue | |
| vmd_draw_vector $mol $COM [vecscale $scale $a2] | |
| graphics $mol color green | graphics $mol color green |
| vmd_draw_vector $mol $COM [vecscale $scale $a3] | vmd_draw_vector $mol $COM [vecscale $scale $a2] |
| | |
| | |
| set items [list [list x [lindex $ranges 0]] [list y [lindex $ranges 1]] [list z [lindex $ranges 2]]] | |
| set ordered [lsort -real -index 1 $items] | |
| | |
| set xindex [lsearch $ordered x] | |
| set yindex [lsearch $ordered y] | |
| set zindex [lsearch $ordered z] | |
| | |
| | |
| if {$xindex == 0} { | |
| set a1weight "3" | |
| } elseif {$xindex == 1} { | |
| set a1weight "2" | |
| } elseif {$xindex == 2} { | |
| set a1weight "3" | |
| } | |
| | |
| if {$yindex == 2} { | graphics $mol color 24 |
| set a2weight "1" | #Biological Constraint Check to See if We have to Flip the Axis for 3D Reconstruction |
| } elseif {$yindex == 1} { | set ::NeuronVND::priority_axis $a3 |
| set a2weight "2" | if {$flip_priority_axis == 1} { |
| } elseif {$yindex == 0} { | #set $a3 [vecscale -1 $a3] |
| set a2weight "3" | set flippy -1 |
| } | set text "1" |
| if {$zindex == 1} { | } else { |
| set a3weight "2" | set flippy 1 |
| } elseif {$zindex == 0} { | set text "1" |
| set a3weight "3" | |
| } elseif {$zindex == 2} { | |
| set a3weight "1" | |
| } | } |
| | |
| set a1weight "3" | vmd_draw_vector $mol $COM [vecscale [expr $flippy * $scale] $a3] |
| set a2weight "1" | #setup data and order ascending |
| set a3weight "2" | #a1 is x, a2 is z, a3 is y |
| graphics $mol color white | graphics $mol color white |
| graphics $mol text [vecadd $COM [vecscale $scale2 $a1]] "$a1weight" | graphics $mol text [vecadd $COM [vecscale $scale2 $a1]] "3" |
| graphics $mol text [vecadd $COM [vecscale $scale2 $a2]] "$a2weight" | graphics $mol text [vecadd $COM [vecscale $scale2 $a2]] "2" |
| graphics $mol text [vecadd $COM [vecscale $scale2 $a3]] "$a3weight" | graphics $mol text [vecadd $COM [vecscale [expr $flippy * $scale2] $a3]] "$text" |
| set paxis [list $a1 $a2 $a3] | set paxis [list $a1 $a2 $a3] |
| return $paxis | return $paxis |
| } | } |
| |
| puts "Computing the inertia tensor..." | puts "Computing the inertia tensor..." |
| # get the I | # get the I |
| set I [Orient::sel_it $x $y $z $COM] | set I [Orient::sel_it $x $y $z $COM] |
| puts "I before the $I" | |
| puts "Drawing the principal components..." | puts "Drawing the principal components..." |
| La::mevsvd_br I evals | La::mevsvd_br I evals |
| # now $I holds in its columns the principal axes | # now $I holds in its columns the principal axes |
| |
| set a2 "[lindex $I 4] [lindex $I 7] [lindex $I 10]" | set a2 "[lindex $I 4] [lindex $I 7] [lindex $I 10]" |
| set a3 "[lindex $I 5] [lindex $I 8] [lindex $I 11]" | set a3 "[lindex $I 5] [lindex $I 8] [lindex $I 11]" |
| set calculated_axis [list $a1 $a2 $a3] | set calculated_axis [list $a1 $a2 $a3] |
| puts "this is the calculated_axis I after SVD" | |
| foreach elem $calculated_axis { | set ::NeuronVND::priority_axis $a3 |
| puts "$elem\n" | |
| } | |
| return $::Orient::calculated_axis | return $::Orient::calculated_axis |
| } | } |
| | |
| |
| # plotpoints $calced_list | # plotpoints $calced_list |
| } | } |
| | |
| | #this file is not called |
| proc Orient::draw_alignment_axis {xarg yarg zarg amol} { | proc Orient::draw_alignment_axis {xarg yarg zarg amol} { |
| set COM $::Orient::COM | set COM $::Orient::COM |
| #initial principal axes tensor | #initial principal axes tensor |
| set I $::Orient::calculated_axis | set I $::Orient::calculated_axis |
| Orient::vnd_orient | Orient::vnd_orient |
| | variable priority_axis |
| puts "$COM" | |
| puts "$I" | |
| | |
| set newa1 "" | set newa1 "" |
| set newa2 "" | set newa2 "" |
| set newa3 "" | set newa3 "" |
| | set minmax "" |
| | |
| | |
| set x $xarg | set x $xarg |
| |
| [lindex $ranges 1] \ | [lindex $ranges 1] \ |
| [lindex $ranges 2]]] | [lindex $ranges 2]]] |
| set scale2 [expr 1.02 * $scale] | set scale2 [expr 1.02 * $scale] |
| | |
| set rot_m $::Orient::calculated_list | set rot_m $::Orient::calculated_list |
| | |
| set newa1 [coordtrans [lindex $rot_m 0] [lindex $I 0]] | set newa1 [coordtrans [lindex $rot_m 0] [lindex $I 0]] |
| set newa2 [coordtrans [lindex $rot_m 1] [lindex $I 1]] | set newa2 [coordtrans [lindex $rot_m 1] [lindex $I 1]] |
| set newa3 [coordtrans [lindex $rot_m 2] [lindex $I 2]] | set newa3 [coordtrans [lindex $rot_m 2] [lindex $I 2]] |
| | |
| #Need to make this chunk more efficient in finding the largest axis and labeling it "1" | #set items [list [list xpriori [lindex $ranges 0]] [list ypriori [lindex $ranges 1]] [list zpriori [lindex $ranges 2]]] |
| set items [list [list x [lindex $ranges 0]] [list y [lindex $ranges 1]] [list z [lindex $ranges 2]]] | #set ordered [lsort -real -index 1 $items] |
| set ordered [lsort -real -index 1 $items] | |
| | #puts "testingggg under draw_aligment _ axis $ordered" |
| set xindex [lsearch $ordered x] | #set xpriori, ypriori, zpriori variables here. |
| set yindex [lsearch $ordered y] | #set [lindex $ordered 0 0] 3 |
| set zindex [lsearch $ordered z] | #set [lindex $ordered 1 0] 2 |
| if {$xindex == 0} { | #set [lindex $ordered 2 0] 1 |
| set a1weight "3" | |
| } elseif {$xindex == 1} { | #switch [lindex $ordered 2 0] { |
| set a1weight "2" | # "xpriori" {set priority_axis "[lindex $I 0]"} |
| } elseif {$xindex == 2} { | # "ypriori" {set priority_axis "[lindex $I 1]"} |
| set a1weight "3" | # "zpriori" {set priority_axis "[lindex $I 2]"} |
| } | #} |
| | |
| if {$yindex == 0} { | #set priority_axis $newa3 |
| set a2weight "3" | |
| } elseif {$yindex == 1} { | |
| set a2weight "2" | |
| } elseif {$yindex == 2} { | |
| set a2weight "3" | |
| } | |
| if {$zindex == 0} { | |
| set a3weight "3" | |
| } elseif {$zindex == 1} { | |
| set a3weight "2" | |
| } elseif {$zindex == 2} { | |
| set a3weight "3" | |
| } | |
| | |
| graphics $mol color 20 | graphics $mol color 20 |
| set COM [Orient::sel_com $x $y $z] | set COM [Orient::sel_com $x $y $z] |
| vmd_draw_vector $mol $COM [vecscale $scale $newa1] | vmd_draw_vector $mol $COM [vecscale $scale $newa1] |
| vmd_draw_vector $mol $COM [vecscale $scale $newa2] | vmd_draw_vector $mol $COM [vecscale $scale $newa2] |
| vmd_draw_vector $mol $COM [vecscale $scale $newa3] | vmd_draw_vector $mol $COM [vecscale $scale $newa3] |
| | |
| set a1weight "2" | |
| set a2weight "3" | |
| set a3weight "1" | |
| graphics $mol color white | graphics $mol color white |
| #now just drawing straight from calculated axis | #now just drawing straight from calculated axis |
| graphics $mol text [vecadd $COM [vecscale $scale2 $newa1]] "$a1weight" | graphics $mol text [vecadd $COM [vecscale $scale2 $newa1]] "$xpriori stupiid " |
| graphics $mol text [vecadd $COM [vecscale $scale2 $newa2]] "$a2weight" | graphics $mol text [vecadd $COM [vecscale $scale2 $newa2]] "$ypriori stupid y" |
| graphics $mol text [vecadd $COM [vecscale $scale2 $newa3]] "$a3weight" | graphics $mol text [vecadd $COM [vecscale $scale2 $newa3]] "$zpriori stupid z" |
| set alignment_vector [list $newa1 $newa2 $newa3] | set alignment_vector [list $newa1 $newa2 $newa3] |
| return $alignment_vector | return $alignment_vector |
| | |
| } | } |
| | |
| #prototype for drawing the alignment axis or "final position" | #prototype for drawing the alignment axis or "final position" |
| |
| set yvec { 0 1 0} | set yvec { 0 1 0} |
| set zvec { 0 0 1} | set zvec { 0 0 1} |
| set vec2list [list $xvec $yvec $zvec] | set vec2list [list $xvec $yvec $zvec] |
| puts "$vec2list" | |
| variable calculated_list | variable calculated_list |
| set calculated_list "" | set calculated_list "" |
| | |
| |
| set sine [veclength $rotvec] | set sine [veclength $rotvec] |
| set cosine [vecdot $ivec1 $ivec2] | set cosine [vecdot $ivec1 $ivec2] |
| set angle [expr atan2($sine,$cosine)] | set angle [expr atan2($sine,$cosine)] |
| puts "rotvec $rotvec" | #puts "rotvec $rotvec" |
| puts "sine $sine" | # puts "sine $sine" |
| puts "cosine $cosine" | # puts "cosine $cosine" |
| puts "angle $angle" | # puts "angle $angle" |
| puts "-------------------------------" | # puts "-------------------------------" |
| lappend calculated_list [trans center $COM axis $rotvec $angle rad] | lappend calculated_list [trans center $COM axis $rotvec $angle rad] |
| } | } |
| #set calculated_list [transmult [lindex $calculated_list 0] [lindex $calculated_list 1] [lindex $calculated_list 2]] | #set calculated_list [transmult [lindex $calculated_list 0] [lindex $calculated_list 1] [lindex $calculated_list 2]] |
| puts "done calculating rotation matrix $calculated_list" | #puts "done calculating rotation matrix $calculated_list" |
| } | } |
| | |
| proc vmd_draw_arrow {mol start end} { | proc vmd_draw_arrow {mol start end} { |
| set scaling [expr [veclength [vecsub $end $start]]/100] | set scaling [expr [veclength [vecsub $end $start]]/100] |
| # an arrow is made of a cylinder and a cone | # an arrow is made of a cylinder and a cone |
| set middle [vecadd $start [vecscale 0.8 [vecsub $end $start]]] | set middle [vecadd $start [vecscale 0.8 [vecsub $end $start]]] |
| graphics $mol cylinder $start $middle radius [expr 2*$scaling] | graphics $mol cylinder $start $middle radius [expr 1.4*$scaling] |
| #i added this | #i added this |
| #graphics $mol line $start [vecadd $start {100 100 100}] width 2 style solid | #graphics $mol line $start [vecadd $start {100 100 100}] width 2 style solid |
| puts [list cone $middle $end radius [expr 5*$scaling]] | #puts [list cone $middle $end radius [expr 5*$scaling]] |
| graphics $mol cone $middle $end radius [expr 5*$scaling] | graphics $mol cone $middle $end radius [expr 5*$scaling] |
| } | } |
| | |
| |
| } | } |
| return $maxval | return $maxval |
| } | } |
| | |
| | puts "Done loading orient.tcl modified by jason" |