Changeset 1957

Timestamp:

Nov 17, 2010 7:51:18 AM (14 years ago)

Author:

gah

Message:

add unit cell to molvisviewer

Location:

trunk

Files:

• configure (modified) (2 diffs)
• configure.in (modified) (1 diff)
• examples/zoo/Makefile.in (modified) (1 diff)
• examples/zoo/cell (deleted)
• examples/zoo/parallelepiped (added)
• examples/zoo/parallelepiped/Makefile.in (added)
• examples/zoo/parallelepiped/parallelepiped.tcl (added)
• examples/zoo/parallelepiped/tool.xml (added)
• gui/scripts/molvisviewer.tcl (modified) (6 diffs)

trunk/configure

@@ -9636 +9636 @@
 
 
-ac_config_files="$ac_config_files Makefile packages/Makefile src/Makefile src/core/Makefile src/core2/Makefile src/objects/Makefile src/objects/RpHash.h gui/Makefile gui/apps/Makefile gui/apps/about gui/apps/encodedata gui/apps/rappture gui/apps/rappture-csh.env gui/apps/rappture.env gui/apps/rappture.use gui/apps/rerun gui/apps/simsim gui/apps/xmldiff gui/pkgIndex.tcl gui/scripts/Makefile instant/Makefile instant/irappture lang/Makefile lang/java/Makefile lang/java/rappture/Makefile lang/perl/Makefile lang/perl/Makefile.PL lang/python/Makefile lang/python/setup.py lang/matlab/Makefile lang/octave/Makefile lang/octave/octave2/Makefile lang/octave/octave3/Makefile lang/ruby/Makefile lang/ruby/build.rb lang/tcl/Makefile lang/tcl/pkgIndex.tcl lang/tcl/src/Makefile lang/tcl/scripts/Makefile lang/tcl/tests/Makefile lib/Makefile examples/3D/Makefile examples/Makefile examples/app-fermi/2.0/Makefile examples/app-fermi/Makefile examples/app-fermi/cee/Makefile examples/app-fermi/fortran/Makefile examples/app-fermi/java/Makefile examples/app-fermi/matlab/Makefile examples/app-fermi/matlab/compiled/Makefile examples/app-fermi/matlab/uncompiled/Makefile examples/app-fermi/octave/Makefile examples/app-fermi/octave/2/Makefile examples/app-fermi/octave/3/Makefile examples/app-fermi/perl/Makefile examples/app-fermi/python/Makefile examples/app-fermi/ruby/Makefile examples/app-fermi/tcl/Makefile examples/app-fermi/wrapper/Makefile examples/app-fermi/wrapper/cee/Makefile examples/app-fermi/wrapper/perl/Makefile examples/app-fermi/wrapper/python/Makefile examples/app-fermi/wrapper/tcl/Makefile examples/c-example/Makefile examples/canvas/Makefile examples/demo.bash examples/flow/Makefile examples/flow/demo1/Makefile examples/flow/demo2/Makefile examples/flow/demo3/Makefile examples/graph/Makefile examples/objects/Makefile examples/objects/axis/Makefile examples/objects/contour/Makefile examples/objects/curve/Makefile examples/objects/dxWriter/Makefile examples/objects/floatBuffer/Makefile examples/objects/histogram/Makefile examples/objects/library/Makefile examples/objects/number/Makefile examples/objects/path/Makefile examples/objects/plot/Makefile examples/objects/scatter/Makefile examples/objects/string/Makefile examples/objects/tree/Makefile examples/objects/xmlparser/Makefile examples/zoo/Makefile examples/zoo/binary/Makefile examples/zoo/boolean/Makefile examples/zoo/cell/Makefile examples/zoo/choice/Makefile examples/zoo/cloud/Makefile examples/zoo/cloud/matlab/Makefile examples/zoo/curve/Makefile examples/zoo/enable/Makefile examples/zoo/field/Makefile examples/zoo/group/Makefile examples/zoo/image/Makefile examples/zoo/image/docs/Makefile examples/zoo/image/examples/Makefile examples/zoo/integer/Makefile examples/zoo/integer2/Makefile examples/zoo/loader/Makefile examples/zoo/loader/examples/Makefile examples/zoo/loadrun/Makefile examples/zoo/log/Makefile examples/zoo/note/Makefile examples/zoo/note/docs/Makefile examples/zoo/number/Makefile examples/zoo/number2/Makefile examples/zoo/periodicelement/Makefile examples/zoo/phase/Makefile examples/zoo/sequence/Makefile examples/zoo/sequence/examples/Makefile examples/zoo/string/Makefile examples/zoo/structure/Makefile examples/zoo/structure/examples/Makefile examples/zoo/table/Makefile examples/zoo/unirect2d/Makefile test/Makefile test/src/Makefile"
+ac_config_files="$ac_config_files Makefile packages/Makefile src/Makefile src/core/Makefile src/core2/Makefile src/objects/Makefile src/objects/RpHash.h gui/Makefile gui/apps/Makefile gui/apps/about gui/apps/encodedata gui/apps/rappture gui/apps/rappture-csh.env gui/apps/rappture.env gui/apps/rappture.use gui/apps/rerun gui/apps/simsim gui/apps/xmldiff gui/pkgIndex.tcl gui/scripts/Makefile instant/Makefile instant/irappture lang/Makefile lang/java/Makefile lang/java/rappture/Makefile lang/perl/Makefile lang/perl/Makefile.PL lang/python/Makefile lang/python/setup.py lang/matlab/Makefile lang/octave/Makefile lang/octave/octave2/Makefile lang/octave/octave3/Makefile lang/ruby/Makefile lang/ruby/build.rb lang/tcl/Makefile lang/tcl/pkgIndex.tcl lang/tcl/src/Makefile lang/tcl/scripts/Makefile lang/tcl/tests/Makefile lib/Makefile examples/3D/Makefile examples/Makefile examples/app-fermi/2.0/Makefile examples/app-fermi/Makefile examples/app-fermi/cee/Makefile examples/app-fermi/fortran/Makefile examples/app-fermi/java/Makefile examples/app-fermi/matlab/Makefile examples/app-fermi/matlab/compiled/Makefile examples/app-fermi/matlab/uncompiled/Makefile examples/app-fermi/octave/Makefile examples/app-fermi/octave/2/Makefile examples/app-fermi/octave/3/Makefile examples/app-fermi/perl/Makefile examples/app-fermi/python/Makefile examples/app-fermi/ruby/Makefile examples/app-fermi/tcl/Makefile examples/app-fermi/wrapper/Makefile examples/app-fermi/wrapper/cee/Makefile examples/app-fermi/wrapper/perl/Makefile examples/app-fermi/wrapper/python/Makefile examples/app-fermi/wrapper/tcl/Makefile examples/c-example/Makefile examples/canvas/Makefile examples/demo.bash examples/flow/Makefile examples/flow/demo1/Makefile examples/flow/demo2/Makefile examples/flow/demo3/Makefile examples/graph/Makefile examples/objects/Makefile examples/objects/axis/Makefile examples/objects/contour/Makefile examples/objects/curve/Makefile examples/objects/dxWriter/Makefile examples/objects/floatBuffer/Makefile examples/objects/histogram/Makefile examples/objects/library/Makefile examples/objects/number/Makefile examples/objects/path/Makefile examples/objects/plot/Makefile examples/objects/scatter/Makefile examples/objects/string/Makefile examples/objects/tree/Makefile examples/objects/xmlparser/Makefile examples/zoo/Makefile examples/zoo/binary/Makefile examples/zoo/boolean/Makefile examples/zoo/parallelepiped/Makefile examples/zoo/choice/Makefile examples/zoo/cloud/Makefile examples/zoo/cloud/matlab/Makefile examples/zoo/curve/Makefile examples/zoo/enable/Makefile examples/zoo/field/Makefile examples/zoo/group/Makefile examples/zoo/image/Makefile examples/zoo/image/docs/Makefile examples/zoo/image/examples/Makefile examples/zoo/integer/Makefile examples/zoo/integer2/Makefile examples/zoo/loader/Makefile examples/zoo/loader/examples/Makefile examples/zoo/loadrun/Makefile examples/zoo/log/Makefile examples/zoo/note/Makefile examples/zoo/note/docs/Makefile examples/zoo/number/Makefile examples/zoo/number2/Makefile examples/zoo/periodicelement/Makefile examples/zoo/phase/Makefile examples/zoo/sequence/Makefile examples/zoo/sequence/examples/Makefile examples/zoo/string/Makefile examples/zoo/structure/Makefile examples/zoo/structure/examples/Makefile examples/zoo/table/Makefile examples/zoo/unirect2d/Makefile test/Makefile test/src/Makefile"
 
 cat >confcache <<\_ACEOF
@@ -10433 +10433 @@
     "examples/zoo/binary/Makefile") CONFIG_FILES="$CONFIG_FILES examples/zoo/binary/Makefile" ;;
     "examples/zoo/boolean/Makefile") CONFIG_FILES="$CONFIG_FILES examples/zoo/boolean/Makefile" ;;
-    "examples/zoo/cell/Makefile") CONFIG_FILES="$CONFIG_FILES examples/zoo/cell/Makefile" ;;
+    "examples/zoo/parallelepiped/Makefile") CONFIG_FILES="$CONFIG_FILES examples/zoo/parallelepiped/Makefile" ;;
     "examples/zoo/choice/Makefile") CONFIG_FILES="$CONFIG_FILES examples/zoo/choice/Makefile" ;;
     "examples/zoo/cloud/Makefile") CONFIG_FILES="$CONFIG_FILES examples/zoo/cloud/Makefile" ;;

trunk/configure.in

@@ -859 +859 @@
     examples/zoo/binary/Makefile
     examples/zoo/boolean/Makefile
-    examples/zoo/cell/Makefile
+    examples/zoo/parallelepiped/Makefile
     examples/zoo/choice/Makefile
     examples/zoo/cloud/Makefile

trunk/examples/zoo/Makefile.in

@@ -33 +33 @@
                 number2 \
                 phase \
+                parallelepiped \
                 periodicelement \
                 sequence \

trunk/gui/scripts/molvisviewer.tcl

@@ -135 +135 @@
     private method Representation {option {model "all"} }
     private method CartoonTrace {option {model "all"}}
+    private method ComputeParallelepipedVertices { dataobj }
     private method Cell {option}
     private method Rock {option}
-
 }
 
@@ -495 +495 @@
         "Set cartoon representation of bonds (sticks)."
 
-    checkbutton $inner.cell -text "Cell" \
+    checkbutton $inner.cell -text "Parallelepiped" \
         -command [itcl::code $this Cell toggle] \
         -font "Arial 9 bold"
@@ -845 +845 @@
                 }
                 set _dataobjs($model-$state) 1
-            }
+            }
         }
         if { ![info exists _model($model-transparency)] } {
@@ -862 +862 @@
             set _active($model) $dataobj
         }
-        set values [$dataobj get components.cell.values]
-        if { $values != "" } {
-            regsub -all {,} $values { } values
-            set rows {}
-            foreach { x y z } $values {
-                lappend rows "    \[ $x, $y, $z \]"
-            }
-            set rows [join $rows ",\\\n"]
-            SendCmd "raw -defer {verts = \[$rows\]\n}"
+        set vector [$dataobj get components.parallelepiped.vector]
+        if { $vector != "" } {
+            set vertices [ComputeParallelepipedVertices $dataobj]
+            SendCmd "raw -defer {verts = \[$vertices\]\n}"
             SendCmd "raw -defer {run \$PYMOL_PATH/rappture/box.py\n}"
             SendCmd "raw -defer {draw_box(verts)\n}"
@@ -876 +871 @@
         }
     }
-
+        
     # enable/disable models as required (0=off->off, 1=on->off, 2=off->on,
     # 3=on->on)
@@ -2012 +2007 @@
 }
 
+itcl::body Rappture::MolvisViewer::snap { w h } {
+    if { $w <= 0 || $h <= 0 } {
+        set w [image width $_image(plot)]
+        set h [image height $_image(plot)]
+    } 
+    set tag "$_state(client),$_rocker(client)"
+    if { $_image(id) != "$tag" } {
+        while { ![info exists _imagecache($tag)] } {
+            update idletasks
+            update
+            after 100
+        }
+        if { [info exists _imagecache($tag)] } {
+            $_image(plot) configure -data $_imagecache($tag)
+            set _image(id) "$tag"
+        }
+    }
+    set img [image create picture -width $w -height $h]
+    $img resample $_image(plot)
+    return $img
+}
+
+# FIXME: Handle 2D vectors
+itcl::body Rappture::MolvisViewer::ComputeParallelepipedVertices { dataobj } {
+    # Create a vector for every 3D point
+    blt::vector point0(3) point1(3) point2(3) point3(3) point4(3) point5(3) \
+        point6(3) point7(3) origin(3) scale(3)
+
+    set count 0
+    set parent [$dataobj element -as object "components.parallelepiped"]
+    foreach child [$parent children] {
+        if { ![string match "vector*" $child] } {
+            continue
+        }
+        incr count
+        set vector  [$parent get $child]
+        regexp -all {,} $vector {} vector
+        point$count set $vector
+    }
+    itcl::delete object $parent
+    if { $count < 1 || $count > 3 } {
+        error "bad number of vectors supplied to parallelepiped"
+    }
+    set values [$dataobj get components.parallelepiped.scale]
+    set n [llength $values]
+    scale set { 1.0 1.0 1.0 }
+    if { $n == 1 } {
+        set scale(0:2) [lindex $values 0]
+    } elseif { $n == 2 } {
+        set scale(0:1) [lindex $values 0]
+    } elseif { $n == 3 } {
+        scale set $values
+    }
+    set values [$dataobj get components.parallelepiped.origin]
+    set n [llength $values]
+    origin set { 0.0 0.0 0.0 }
+    if { $n == 1 } {
+        set origin(0) [lindex $values 0]
+    } elseif { $n == 2 } {
+        set origin(0) [lindex $values 0]
+        set origin(1) [lindex $values 1]
+    } elseif { $n == 3 } {
+        origin set $values
+    }
+    point0 set { 0.0 0.0 0.0 }
+    point4 expr {point2 + point1}
+    point5 expr {point4 + point3}
+    point6 expr {point2 + point3}
+    point7 expr {point1 + point3}
+
+    # Generate vertices as a string for PyMOL
+    set vertices ""
+    blt::vector x
+    foreach n { 0 1 0 2 0 3 1 4 2 4 2 6 1 7 3 7 5 7 4 5 3 6 5 } {
+        x expr "(point${n} * scale) + origin"
+        set values [x print 0 end]
+        append vertices "\[ [join $values {, }] \], \\\n"
+    }
+    x expr "(point6 * scale) + origin"
+    set values [x print 0 end]
+    append vertices "\[ [join $values {, }] \]  \\\n"
+    blt::vector destroy point0 point1 point2 point3 point4 point5 point6 \
+        point7 x origin scale
+    return $vertices
+}