Changeset 1801 for branches/blt4/gui

Timestamp:

Jul 12, 2010, 8:03:19 PM (14 years ago)

Author:

gah

Message:

 

File:

• branches/blt4/gui/scripts/analyzer.tcl (modified) (4 diffs)

branches/blt4/gui/scripts/analyzer.tcl

@@ -1205 +1205 @@
 
 # ----------------------------------------------------------------------
-# 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
@@ -1221 +1221 @@
     $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 numLines [llength $data]
+    for { set i 0 } { $i < $numLines } { incr i } {
+        set line [lindex $data $i]
+        set line [string trim $line]
+        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 $formula
+            incr frameNum
+        }
+    }
+}
+
+itcl::body Rappture::Analyzer::_lammpsToSequence {xmlobj path id child data} {
+
+    set seqLabel [$xmlobj get ${child}.about.label]
+    set descr    [$xmlobj get ${child}.about.description]
+    set typemap  [$xmlobj get ${child}.components.molecule.lammpstypemap]
+    $xmlobj remove $child
+
+    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
@@ -1234 +1276 @@
             continue;                   # Skip blank lines
         }
-        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 $formula
-    }
-}
-
-itcl::body Rappture::Analyzer::_lammpsToSequence {xmlobj path id child data} {
-
-    set seqLabel [$xmlobj get ${child}.about.label]
-    set descr    [$xmlobj get ${child}.about.description]
-    set typemap  [$xmlobj get ${child}.components.molecule.lammpstypemap]
-    $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 frameNum 0
-    set frameContents ""
-    set inModel 0
-    foreach line $data {
-        set line [string trim $line]
-        if { $line == "" } {
-            continue;                   # Skip blank lines
-        }
         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
@@ -1311 +1298 @@
     }
     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
+        set molecule ${frame}.structure.components.molecule
+        $xmlobj put ${molecule}.lammps $frameContents
+        $xmlobj put ${molecule}.lammpstypemap $typemap
     }
 }