Changeset 1830 for trunk/gui/scripts/analyzer.tcl

Timestamp:

Jul 17, 2010, 1:54:59 PM (14 years ago)

Author:

gah

Message:

 

File:

• trunk/gui/scripts/analyzer.tcl (modified) (11 diffs)

trunk/gui/scripts/analyzer.tcl

@@ -24 +24 @@
 option add *Analyzer.simControlActiveBackground #ffffcc widgetDefault
 option add *Analyzer.simControlActiveOutline black widgetDefault
+option add *Analyzer.notebookpage "about" widgetDefault
 
 option add *Analyzer.font \
@@ -46 +47 @@
     itk_option define -simcontrolactivebackground simControlActiveBackground Background ""
     itk_option define -holdwindow holdWindow HoldWindow ""
-    itk_option define -notebookpage notebookPage NotebookPage "about"
+    itk_option define -notebookpage notebookPage NotebookPage ""
 
     constructor {tool args} { # defined below }
@@ -505 +506 @@
         foreach c [$inclobj children output] {
             switch -glob -- $c {
-                # we don't want to include these tags
+                # We don't want to include these tags.
                 include* - time* - status* - user* {
                     continue
@@ -521 +522 @@
     lappend _runs $xmlobj
 
-    # detect molecule elements that contain trajectory data and convert
+    # Detect molecule elements that contain trajectory data and convert
     # to sequences.
     _trajToSequence $xmlobj output
 
-    # go through the analysis and find all result sets
+    # Go through the analysis and find all result sets.
     set haveresults 0
     foreach item [_reorder [$xmlobj children output]] {
@@ -1197 +1198 @@
 
 # ----------------------------------------------------------------------
-# USAGE: _trajtosequence <xmlobj> ?<path>?
-#
-    # If the molecule element is a trajectory, delete the original
-    # and create a sequence of individual molecules.
+# USAGE: _pdbToSequence <xmlobj> ?<path>?
+#
+# If the molecule element is a trajectory, delete the original
+# and create a sequence of individual molecules.
 # Used internally to detect any molecule output elements that contain
 # trajectory data.  Trajectories will be converted into sequences of
@@ -1213 +1214 @@
     $xmlobj remove $child
 
-    set seqPath  $path.sequence($id)
-    $xmlobj put ${seqPath}.about.label $seqLabel
-    $xmlobj put ${seqPath}.about.description $descr
-    $xmlobj put ${seqPath}.index.label "Frame"
+    set sequence  $path.sequence($id)
+    $xmlobj put ${sequence}.about.label $seqLabel
+    $xmlobj put ${sequence}.about.description $descr
+    $xmlobj put ${sequence}.index.label "Frame"
 
     set frameNum 0
-    set frameContents ""
-    set inModel 0
-    foreach line $data {
+    set numLines [llength $data]
+    for { set i 0 } { $i < $numLines } { incr i } {
+        set line [lindex $data $i]
         set line [string trim $line]
-        if { $line == "" } {
-            continue;                   # Skip blank lines
+        set contents {}
+        if { [string match "MODEL*" $line] } {
+            # Save the contents until we get an ENDMDL record.
+            for {} { $i < $numLines } { incr i } {
+                set line [lindex $data $i]
+                set line [string trim $line]
+                if { $line == "" } {
+                    continue;           # Skip blank lines.
+                }
+                if { [string match "ENDMDL*" $line] } {
+                    break;
+                }
+                append contents $line\n
+            }
+            set frame ${sequence}.element($frameNum)
+            $xmlobj put ${frame}.index $frameNum
+            
+            set molecule ${frame}.structure.components.molecule
+            $xmlobj put ${molecule}.pdb $contents
+            $xmlobj put ${molecule}.formula $formula
+            incr frameNum
         }
-        if { [string match "MODEL*" $line] } {
-            if { $inModel && $frameContents != "" } {
-                # Dump the current contents into the last model
-
-                set framePath ${seqPath}.element($frameNum)
-                $xmlobj put ${framePath}.index $frameNum
-                
-                set molPath ${framePath}.structure.components.molecule
-                $xmlobj put ${molPath}.pdb $frameContents
-                $xmlobj put ${molPath}.formula $formula
-                
-                incr frameNum
-                set frameContents ""
-            }
-            set inModel 1
-        } elseif {[string match "ATOM*" $line] } {
-            if { !$inModel } {
-                puts stderr "found \"$line\" without previous MODEL line"
-                set inModel 1
-            }
-            append frameContents $line\n
-        }
-    }
-    if { $frameContents != "" } {
-        # Dump the current contents into the last model
-
-        set framePath ${seqPath}.element($frameNum)
-        $xmlobj put ${framePath}.index $frameNum
-        
-        set molPath ${framePath}.structure.components.molecule
-        $xmlobj put ${molPath}.pdb $frameContents
-        $xmlobj put ${molPath}.formula $formula
-    }
-}
-
+    }
+}
+
+# ----------------------------------------------------------------------
+# USAGE: _lammpsToSequence <xmlobj> ?<path>?
+#
+# If the molecule element is a trajectory, delete the original
+# and create a sequence of individual molecules.
+# Used internally to detect any molecule output elements that contain
+# trajectory data.  Trajectories will be converted into sequences of
+# individual molecules.  All other elements will be unaffected. Scans
+# the entire xml tree if a starting path is not specified.
+# ----------------------------------------------------------------------
 itcl::body Rappture::Analyzer::_lammpsToSequence {xmlobj path id child data} {
 
@@ -1268 +1266 @@
     $xmlobj remove $child
 
-    set seqPath ${path}.sequence($id)
-    $xmlobj put ${seqPath}.about.label $seqLabel
-    $xmlobj put ${seqPath}.about.description $descr
-    $xmlobj put ${seqPath}.index.label "Frame"
+    set sequence ${path}.sequence($id)
+    $xmlobj put ${sequence}.about.label $seqLabel
+    $xmlobj put ${sequence}.about.description $descr
+    $xmlobj put ${sequence}.index.label "Frame"
 
     set frameNum 0
@@ -1283 +1281 @@
         if {[regexp {^[\t ]*ITEM:[ \t]+ATOMS} $line] } {
             if { $inModel && $frameContents != "" } {
-                set framePath ${seqPath}.element($frameNum)
-                $xmlobj put ${framePath}.index $frameNum
+                set frame ${sequence}.element($frameNum)
+                $xmlobj put ${frame}.index $frameNum
                 
-                set molPath ${framePath}.structure.components.molecule
-                $xmlobj put ${molPath}.lammps $frameContents
-                $xmlobj put ${molPath}.lammpstypemap $typemap
+                set molecule ${frame}.structure.components.molecule
+                $xmlobj put ${molecule}.lammps $frameContents
+                $xmlobj put ${molecule}.lammpstypemap $typemap
                 
                 incr frameNum
@@ -1303 +1301 @@
     }
     if { $frameContents != "" } {
-        set framePath ${seqPath}.element($frameNum)
-        $xmlobj put ${framePath}.index $frameNum
+        set frame ${sequence}.element($frameNum)
+        $xmlobj put ${frame}.index $frameNum
         
-        set molPath ${framePath}.structure.components.molecule
-        $xmlobj put ${molPath}.lammps $frameContents
-        $xmlobj put ${molPath}.lammpstypemap $typemap
-    }
-}
-
-# ----------------------------------------------------------------------
-# USAGE: _trajtosequence <xmlobj> ?<path>?
+        set molecule ${frame}.structure.components.molecule
+        $xmlobj put ${molecule}.lammps $frameContents
+        $xmlobj put ${molecule}.lammpstypemap $typemap
+    }
+}
+
+# ----------------------------------------------------------------------
+# USAGE: _trajToSequence <xmlobj> ?<path>?
 #
 #       Check for PDB and LAMMPS trajectories in molecule data and rewrite 
@@ -1333 +1331 @@
         set current ${path}.${child}
         if { [string match "structure*" $child] } {
+            set isTraj [$xmlobj get ${current}.components.molecule.trajectory]
+            if { !$isTraj } {
+                continue;               # Not a trajectory.
+            }
             # Look for trajectory if molecule element found.  Check both pdb
             # data and lammps data.
@@ -1352 +1354 @@
             continue
         }
+        if 0 {
         # Recurse over all child nodes.
         _trajToSequence $xmlobj $current
+        }
     }
 }