Changeset 2628 for trunk

Timestamp:

Oct 14, 2011 11:48:46 AM (13 years ago)

Author:

gah

Message:

 

Location:

trunk

Files:

• gui/scripts/molvisviewer.tcl (modified) (14 diffs)
• packages/vizservers/pymolproxy/pymolproxy.c (modified) (1 diff)

trunk/gui/scripts/molvisviewer.tcl

@@ -65 +65 @@
     private variable _cacheid ""
     private variable _cacheimage ""
-
-    private variable _delta1 10
-    private variable _delta2 2
 
     private common _settings  ;         # Array of settings for all known 
@@ -82 +79 @@
     private variable _width
     private variable _height
-    private variable _restore 1;        # Restore camera settings
+    private variable _reset 1;  # Restore camera settings
     private variable _cell 0;           # Restore camera settings
+    private variable _flush 1
 
     constructor { hostlist args } {
@@ -183 +181 @@
     set _state(client) 1
     set _hostlist $hostlist
-    set _restore 1
+    set _reset 1
 
     array set _view {
@@ -401 +399 @@
 }
 
-itcl::body Rappture::MolvisViewer::BuildSettingsTab {} {
-    set fg [option get $itk_component(hull) font Font]
-
-    set inner [$itk_component(main) insert end \
-        -title "Settings" \
-        -icon [Rappture::icon wrench]]
-    $inner configure -borderwidth 4
-
-    label $inner.drawinglabel -text "Molecule Representation" \
-        -font "Arial 9 bold"
-
-    label $inner.pict -image $_settings($this-modelimg)
-
-    radiobutton $inner.bstick -text "balls and sticks" \
-        -command [itcl::code $this Representation ballnstick all] \
-        -variable Rappture::MolvisViewer::_settings($this-model) \
-        -value ballnstick -font "Arial 9" -pady 0 
-    Rappture::Tooltip::for $inner.bstick \
-        "Display atoms (balls) and connections (sticks) "
-
-    radiobutton $inner.spheres -text "spheres" \
-        -command [itcl::code $this Representation spheres all] \
-        -variable Rappture::MolvisViewer::_settings($this-model) \
-        -value spheres -font "Arial 9" -pady 0
-    Rappture::Tooltip::for $inner.spheres \
-        "Display atoms as spheres. Do not display bonds."
-
-    radiobutton $inner.sticks -text "sticks" \
-        -command [itcl::code $this Representation sticks all] \
-        -variable Rappture::MolvisViewer::_settings($this-model) \
-        -value sticks -font "Arial 9" -pady 0
-    Rappture::Tooltip::for $inner.sticks \
-        "Display bonds as sticks. Do not display atoms."
-
-    radiobutton $inner.lines -text "lines" \
-        -command [itcl::code $this Representation lines all] \
-        -variable [itcl::scope _settings($this-model)] \
-        -value lines -font "Arial 9" -pady 0
-    Rappture::Tooltip::for $inner.lines \
-        "Display bonds as lines. Do not display atoms."
-
-    radiobutton $inner.cartoon -text "cartoon" \
-        -command [itcl::code $this Representation cartoon all] \
-        -variable [itcl::scope _settings($this-model)] \
-        -value cartoon -font "Arial 9" -pady 0
-    Rappture::Tooltip::for $inner.cartoon \
-        "Display cartoon representation of bonds (sticks)."
-
-    scale $inner.spherescale -width 10 -font "Arial 9 bold" \
-        -from 0.1 -to 2.0 -resolution 0.05 -label "Sphere Scale" \
-        -showvalue true -orient horizontal \
-        -command [itcl::code $this SphereScale] \
-        -variable Rappture::MolvisViewer::_settings($this-spherescale)
-    $inner.spherescale set $_settings($this-spherescale)
-    Rappture::Tooltip::for $inner.spherescale \
-        "Adjust scale of atoms (spheres or balls). 1.0 is the full VDW radius."
-
-    scale $inner.stickradius -width 10 -font "Arial 9 bold" \
-        -from 0.1 -to 1.0 -resolution 0.025 -label "Stick Radius" \
-        -showvalue true -orient horizontal \
-        -command [itcl::code $this StickRadius] \
-        -variable Rappture::MolvisViewer::_settings($this-stickradius)
-    Rappture::Tooltip::for $inner.stickradius \
-        "Adjust scale of bonds (sticks)."
-    $inner.stickradius set $_settings($this-stickradius)
-
-    checkbutton $inner.labels -text "Show labels on atoms" \
-        -command [itcl::code $this labels update] \
-        -variable [itcl::scope _settings($this-showlabels)] \
-        -font "Arial 9 bold"
-    Rappture::Tooltip::for $inner.labels \
-        "Display atom symbol and serial number."
-
-    checkbutton $inner.rock -text "Rock model back and forth" \
-        -command [itcl::code $this Rock toggle] \
-        -variable Rappture::MolvisViewer::_settings($this-rock) \
-        -font "Arial 9 bold"
-    Rappture::Tooltip::for $inner.rock \
-        "Rotate the object back and forth around the y-axis."
-
-    checkbutton $inner.ortho -text "Orthoscopic projection" \
-        -command [itcl::code $this OrthoProjection update] \
-        -variable Rappture::MolvisViewer::_settings($this-ortho) \
-         -font "Arial 9 bold"
-    Rappture::Tooltip::for $inner.ortho \
-        "Toggle between orthoscopic/perspective projection modes."
-
-    checkbutton $inner.cartoontrace -text "Cartoon Trace" \
-        -command [itcl::code $this CartoonTrace update] \
-        -variable [itcl::scope _settings($this-cartoontrace)] \
-        -font "Arial 9 bold"
-    Rappture::Tooltip::for $inner.cartoontrace \
-        "Set cartoon representation of bonds (sticks)."
-
-    checkbutton $inner.cell -text "Parallelepiped" \
-        -command [itcl::code $this Cell toggle] \
-        -font "Arial 9 bold"
-    $inner.cell select
-
-    label $inner.spacer
-    blt::table $inner \
-        0,0 $inner.drawinglabel -anchor w -columnspan 4 \
-        1,1 $inner.pict -anchor w -rowspan 5 \
-        1,2 $inner.bstick -anchor w -columnspan 2 \
-        2,2 $inner.spheres -anchor w -columnspan 2 \
-        3,2 $inner.sticks -anchor w -columnspan 2 \
-        4,2 $inner.lines -anchor w -columnspan 2 \
-        5,2 $inner.cartoon -anchor w -columnspan 2 \
-        6,0 $inner.labels -anchor w -columnspan 4 -pady {1 0} \
-        7,0 $inner.rock -anchor w -columnspan 4 -pady {1 0} \
-        8,0 $inner.ortho -anchor w -columnspan 4 -pady {1 0} \
-        9,0 $inner.cartoontrace -anchor w -columnspan 4 -pady {1 0} \
-        10,0 $inner.cell -anchor w -columnspan 4 -pady {1 0} \
-        11,1 $inner.spherescale -fill x -columnspan 4 -pady {1 0} \
-        12,1 $inner.stickradius -fill x -columnspan 4 -pady {1 0} \
-
-    blt::table configure $inner c0 -resize expand -width 2
-    blt::table configure $inner c1 c2 -resize none
-    blt::table configure $inner c3 -resize expand
-    blt::table configure $inner r* -resize none
-    blt::table configure $inner r13 -resize expand
-}
-
 # ----------------------------------------------------------------------
 # DESTRUCTOR
@@ -532 +407 @@
     image delete $_image(plot)
     array unset _settings $this-*
+}
+
+
+# ----------------------------------------------------------------------
+# USAGE: add <dataobj> ?<settings>?
+#
+# Clients use this to add a data object to the plot.  The optional
+# <settings> are used to configure the plot.  Allowed settings are
+# -color, -brightness, -width, -linestyle, and -raise. Only
+# -brightness and -raise do anything.
+# ----------------------------------------------------------------------
+itcl::body Rappture::MolvisViewer::add { dataobj {options ""}} {
+    array set params {
+        -color          auto
+        -brightness     0
+        -width          1
+        -raise          0
+        -linestyle      solid
+        -description    ""
+        -param          ""
+    }
+
+    foreach {opt val} $options {
+        if {![info exists params($opt)]} {
+            error "bad settings \"$opt\": should be [join [lsort [array names params]] {, }]"
+        }
+        set params($opt) $val
+    }
+
+    set pos [lsearch -exact $dataobj $_dlist]
+
+    if {$pos < 0} {
+        if {![Rappture::library isvalid $dataobj]} {
+            error "bad value \"$dataobj\": should be Rappture::library object"
+        }
+
+        if { !$_settings($this-showlabels-initialized) } {
+            set showlabels [$dataobj get components.molecule.about.emblems]
+            if { $showlabels != "" && [string is boolean $showlabels] } {
+                set _settings($this-showlabels) $showlabels
+            } 
+        }
+
+        lappend _dlist $dataobj
+        if { $params(-brightness) >= 0.5 } {
+            set _dobj2transparency($dataobj) "ghost"
+        } else {
+            set _dobj2transparency($dataobj) "normal"
+        }
+        set _dobj2raise($dataobj) $params(-raise)
+        debug "setting parameters for $dataobj\n"
+
+        if { [isconnected] } {
+            $_dispatcher event -idle !rebuild
+        }
+    }
+}
+
+# ----------------------------------------------------------------------
+# USAGE: delete ?<dataobj> <dataobj> ...?
+#
+# Clients use this to delete a dataobj from the plot. If no dataobjs
+# are specified, then all dataobjs are deleted.
+# ----------------------------------------------------------------------
+itcl::body Rappture::MolvisViewer::delete { args } {
+    if {[llength $args] == 0} {
+        set args $_dlist
+    }
+
+    # delete all specified dataobjs
+    set changed 0
+    set _flush 1
+    foreach dataobj $args {
+        set pos [lsearch -exact $_dlist $dataobj]
+        if {$pos >= 0} {
+            set _dlist [lreplace $_dlist $pos $pos]
+            if { [info exists _obj2models($dataobj)] } {
+                foreach model $_obj2models($dataobj) {
+                    array unset _active $model
+                }
+            }
+            array unset _obj2models $dataobj
+            array unset _dobj2transparency $dataobj
+            array unset _dobj2color $dataobj
+            array unset _dobj2width $dataobj
+            array unset _dobj2dashes $dataobj
+            array unset _dobj2raise $dataobj
+            set changed 1
+        }
+    }
+
+    # if anything changed, then rebuild the plot
+    if {$changed} {
+        if { [isconnected] } {
+            $_dispatcher event -idle !rebuild
+        }
+    }
+}
+
+# ----------------------------------------------------------------------
+# USAGE: get
+#
+# Clients use this to query the list of objects being plotted, in
+# order from bottom to top of this result.
+# ----------------------------------------------------------------------
+itcl::body Rappture::MolvisViewer::get {} {
+    # put the dataobj list in order according to -raise options
+    set dlist $_dlist
+    foreach obj $dlist {
+        if {[info exists _dobj2raise($obj)] && $_dobj2raise($obj)} {
+            set i [lsearch -exact $dlist $obj]
+            if {$i >= 0} {
+                set dlist [lreplace $dlist $i $i]
+                lappend dlist $obj
+            }
+        }
+    }
+    return $dlist
 }
 
@@ -608 +601 @@
         return 0
     }
-    set _restore 1 
+    set _reset 1 
     set result [VisViewer::Connect $hosts]
     if { $result } {
@@ -707 +700 @@
 
 
+itcl::body Rappture::MolvisViewer::BuildSettingsTab {} {
+    set fg [option get $itk_component(hull) font Font]
+
+    set inner [$itk_component(main) insert end \
+        -title "Settings" \
+        -icon [Rappture::icon wrench]]
+    $inner configure -borderwidth 4
+
+    label $inner.drawinglabel -text "Molecule Representation" \
+        -font "Arial 9 bold"
+
+    label $inner.pict -image $_settings($this-modelimg)
+
+    radiobutton $inner.bstick -text "balls and sticks" \
+        -command [itcl::code $this Representation ballnstick all] \
+        -variable Rappture::MolvisViewer::_settings($this-model) \
+        -value ballnstick -font "Arial 9" -pady 0 
+    Rappture::Tooltip::for $inner.bstick \
+        "Display atoms (balls) and connections (sticks) "
+
+    radiobutton $inner.spheres -text "spheres" \
+        -command [itcl::code $this Representation spheres all] \
+        -variable Rappture::MolvisViewer::_settings($this-model) \
+        -value spheres -font "Arial 9" -pady 0
+    Rappture::Tooltip::for $inner.spheres \
+        "Display atoms as spheres. Do not display bonds."
+
+    radiobutton $inner.sticks -text "sticks" \
+        -command [itcl::code $this Representation sticks all] \
+        -variable Rappture::MolvisViewer::_settings($this-model) \
+        -value sticks -font "Arial 9" -pady 0
+    Rappture::Tooltip::for $inner.sticks \
+        "Display bonds as sticks. Do not display atoms."
+
+    radiobutton $inner.lines -text "lines" \
+        -command [itcl::code $this Representation lines all] \
+        -variable [itcl::scope _settings($this-model)] \
+        -value lines -font "Arial 9" -pady 0
+    Rappture::Tooltip::for $inner.lines \
+        "Display bonds as lines. Do not display atoms."
+
+    radiobutton $inner.cartoon -text "cartoon" \
+        -command [itcl::code $this Representation cartoon all] \
+        -variable [itcl::scope _settings($this-model)] \
+        -value cartoon -font "Arial 9" -pady 0
+    Rappture::Tooltip::for $inner.cartoon \
+        "Display cartoon representation of bonds (sticks)."
+
+    scale $inner.spherescale -width 10 -font "Arial 9 bold" \
+        -from 0.1 -to 2.0 -resolution 0.05 -label "Sphere Scale" \
+        -showvalue true -orient horizontal \
+        -command [itcl::code $this SphereScale] \
+        -variable Rappture::MolvisViewer::_settings($this-spherescale)
+    $inner.spherescale set $_settings($this-spherescale)
+    Rappture::Tooltip::for $inner.spherescale \
+        "Adjust scale of atoms (spheres or balls). 1.0 is the full VDW radius."
+
+    scale $inner.stickradius -width 10 -font "Arial 9 bold" \
+        -from 0.1 -to 1.0 -resolution 0.025 -label "Stick Radius" \
+        -showvalue true -orient horizontal \
+        -command [itcl::code $this StickRadius] \
+        -variable Rappture::MolvisViewer::_settings($this-stickradius)
+    Rappture::Tooltip::for $inner.stickradius \
+        "Adjust scale of bonds (sticks)."
+    $inner.stickradius set $_settings($this-stickradius)
+
+    checkbutton $inner.labels -text "Show labels on atoms" \
+        -command [itcl::code $this labels update] \
+        -variable [itcl::scope _settings($this-showlabels)] \
+        -font "Arial 9 bold"
+    Rappture::Tooltip::for $inner.labels \
+        "Display atom symbol and serial number."
+
+    checkbutton $inner.rock -text "Rock model back and forth" \
+        -command [itcl::code $this Rock toggle] \
+        -variable Rappture::MolvisViewer::_settings($this-rock) \
+        -font "Arial 9 bold"
+    Rappture::Tooltip::for $inner.rock \
+        "Rotate the object back and forth around the y-axis."
+
+    checkbutton $inner.ortho -text "Orthoscopic projection" \
+        -command [itcl::code $this OrthoProjection update] \
+        -variable Rappture::MolvisViewer::_settings($this-ortho) \
+         -font "Arial 9 bold"
+    Rappture::Tooltip::for $inner.ortho \
+        "Toggle between orthoscopic/perspective projection modes."
+
+    checkbutton $inner.cartoontrace -text "Cartoon Trace" \
+        -command [itcl::code $this CartoonTrace update] \
+        -variable [itcl::scope _settings($this-cartoontrace)] \
+        -font "Arial 9 bold"
+    Rappture::Tooltip::for $inner.cartoontrace \
+        "Set cartoon representation of bonds (sticks)."
+
+    checkbutton $inner.cell -text "Parallelepiped" \
+        -command [itcl::code $this Cell toggle] \
+        -font "Arial 9 bold"
+    $inner.cell select
+
+    label $inner.spacer
+    blt::table $inner \
+        0,0 $inner.drawinglabel -anchor w -columnspan 4 \
+        1,1 $inner.pict -anchor w -rowspan 5 \
+        1,2 $inner.bstick -anchor w -columnspan 2 \
+        2,2 $inner.spheres -anchor w -columnspan 2 \
+        3,2 $inner.sticks -anchor w -columnspan 2 \
+        4,2 $inner.lines -anchor w -columnspan 2 \
+        5,2 $inner.cartoon -anchor w -columnspan 2 \
+        6,0 $inner.labels -anchor w -columnspan 4 -pady {1 0} \
+        7,0 $inner.rock -anchor w -columnspan 4 -pady {1 0} \
+        8,0 $inner.ortho -anchor w -columnspan 4 -pady {1 0} \
+        9,0 $inner.cartoontrace -anchor w -columnspan 4 -pady {1 0} \
+        10,0 $inner.cell -anchor w -columnspan 4 -pady {1 0} \
+        11,1 $inner.spherescale -fill x -columnspan 4 -pady {1 0} \
+        12,1 $inner.stickradius -fill x -columnspan 4 -pady {1 0} \
+
+    blt::table configure $inner c0 -resize expand -width 2
+    blt::table configure $inner c1 c2 -resize none
+    blt::table configure $inner c3 -resize expand
+    blt::table configure $inner r* -resize none
+    blt::table configure $inner r13 -resize expand
+}
+
 # ----------------------------------------------------------------------
 # USAGE: Rebuild
@@ -725 +841 @@
     set _cell 0
 
-    if { $_restore } {
+    if { $_reset } {
         set _rocker(server) 0
         set _cacheid 0
@@ -933 +1049 @@
         set flush 0
     }
-    if { $_restore } {
+    if { $_reset } {
         # Set or restore viewing parameters.  We do this for the first
         # model and assume this works for everything else.
@@ -948 +1064 @@
 
         SendCmd "raw -defer {zoom complete=1}"
-        set _restore 0
+        set _reset 0
     }
     if { $changed } {
@@ -967 +1083 @@
         $inner.cell configure -state disabled
     }
-    if { $flush } {
+    if { $_flush || $flush } {
         global readyForNextFrame
         set readyForNextFrame 0;        # Don't advance to the next frame
                                         # until we get an image.
         SendCmd "ppm";                  # Flush the results.
+        set _flush 0
     }
     set _buffering 0;                   # Turn off buffering.
@@ -1461 +1578 @@
 
 
-# ----------------------------------------------------------------------
-# USAGE: add <dataobj> ?<settings>?
-#
-# Clients use this to add a data object to the plot.  The optional
-# <settings> are used to configure the plot.  Allowed settings are
-# -color, -brightness, -width, -linestyle, and -raise. Only
-# -brightness and -raise do anything.
-# ----------------------------------------------------------------------
-itcl::body Rappture::MolvisViewer::add { dataobj {options ""}} {
-    array set params {
-        -color          auto
-        -brightness     0
-        -width          1
-        -raise          0
-        -linestyle      solid
-        -description    ""
-        -param          ""
-    }
-
-    foreach {opt val} $options {
-        if {![info exists params($opt)]} {
-            error "bad settings \"$opt\": should be [join [lsort [array names params]] {, }]"
-        }
-        set params($opt) $val
-    }
-
-    set pos [lsearch -exact $dataobj $_dlist]
-
-    if {$pos < 0} {
-        if {![Rappture::library isvalid $dataobj]} {
-            error "bad value \"$dataobj\": should be Rappture::library object"
-        }
-
-        if { !$_settings($this-showlabels-initialized) } {
-            set showlabels [$dataobj get components.molecule.about.emblems]
-            if { $showlabels != "" && [string is boolean $showlabels] } {
-                set _settings($this-showlabels) $showlabels
-            } 
-        }
-
-        lappend _dlist $dataobj
-        if { $params(-brightness) >= 0.5 } {
-            set _dobj2transparency($dataobj) "ghost"
-        } else {
-            set _dobj2transparency($dataobj) "normal"
-        }
-        set _dobj2raise($dataobj) $params(-raise)
-        debug "setting parameters for $dataobj\n"
-
-        if { [isconnected] } {
-            $_dispatcher event -idle !rebuild
-        }
-    }
-}
-
 #
 # ResetView
@@ -1541 +1603 @@
     SendCmd "zoom $_view(zoom)"
 }
-
-# ----------------------------------------------------------------------
-# USAGE: get
-#
-# Clients use this to query the list of objects being plotted, in
-# order from bottom to top of this result.
-# ----------------------------------------------------------------------
-itcl::body Rappture::MolvisViewer::get {} {
-    # put the dataobj list in order according to -raise options
-    set dlist $_dlist
-    foreach obj $dlist {
-        if {[info exists _dobj2raise($obj)] && $_dobj2raise($obj)} {
-            set i [lsearch -exact $dlist $obj]
-            if {$i >= 0} {
-                set dlist [lreplace $dlist $i $i]
-                lappend dlist $obj
-            }
-        }
-    }
-    return $dlist
-}
-
-# ----------------------------------------------------------------------
-# USAGE: delete ?<dataobj> <dataobj> ...?
-#
-# Clients use this to delete a dataobj from the plot. If no dataobjs
-# are specified, then all dataobjs are deleted.
-# ----------------------------------------------------------------------
-itcl::body Rappture::MolvisViewer::delete { args } {
-    if {[llength $args] == 0} {
-        set args $_dlist
-    }
-
-    # delete all specified dataobjs
-    set changed 0
-    foreach dataobj $args {
-        set pos [lsearch -exact $_dlist $dataobj]
-        if {$pos >= 0} {
-            set _dlist [lreplace $_dlist $pos $pos]
-            if { [info exists _obj2models($dataobj)] } {
-                foreach model $_obj2models($dataobj) {
-                    array unset _active $model
-                }
-            }
-            array unset _obj2models $dataobj
-            array unset _dobj2transparency $dataobj
-            array unset _dobj2color $dataobj
-            array unset _dobj2width $dataobj
-            array unset _dobj2dashes $dataobj
-            array unset _dobj2raise $dataobj
-            set changed 1
-        }
-    }
-
-    # if anything changed, then rebuild the plot
-    if {$changed} {
-        if { [isconnected] } {
-            $_dispatcher event -idle !rebuild
-        }
-    }
-}
-
-# ----------------------------------------------------------------------
-# OPTION: -device
-# ----------------------------------------------------------------------
-itcl::configbody Rappture::MolvisViewer::device {
-    if {$itk_option(-device) != "" } {
-
-        if {![Rappture::library isvalid $itk_option(-device)]} {
-            error "bad value \"$itk_option(-device)\": should be Rappture::library object"
-        }
-        $this delete
-        $this add $itk_option(-device)
-    } else {
-        $this delete
-    }
-
-    if { [isconnected] } {
-        $_dispatcher event -idle !rebuild
-    }
-}
-
 
 
@@ -2096 +2076 @@
     return $vertices
 }
+
+
+# ----------------------------------------------------------------------
+# OPTION: -device
+# ----------------------------------------------------------------------
+itcl::configbody Rappture::MolvisViewer::device {
+    if {$itk_option(-device) != "" } {
+
+        if {![Rappture::library isvalid $itk_option(-device)]} {
+            error "bad value \"$itk_option(-device)\": should be Rappture::library object"
+        }
+        $this delete
+        $this add $itk_option(-device)
+    } else {
+        $this delete
+    }
+
+    if { [isconnected] } {
+        $_dispatcher event -idle !rebuild
+    }
+}
+

trunk/packages/vizservers/pymolproxy/pymolproxy.c

@@ -2203 +2203 @@
                 Debug("STDOUT>%.*s", nBytes, line);
                 Debug("Done with pymol stdout\n");
+                INFO("EOF on pymol server");
+                goto error;             /* Pymol server died unexpectedly. */
             } else if (nBytes == BUFFER_CONTINUE) {
                 Debug("Done with pymol stdout\n");
-                goto error;             /* Pymol server died unexpectedly. */
+                INFO("Need to read more from Pymol server, repolling.");
+                continue;
             } else {
                 ERROR("can't read pymol stdout (nBytes=%d): %s\n", nBytes,