Changeset 1795 for branches

Timestamp:

Jul 8, 2010 2:09:35 PM (14 years ago)

Author:

gah

Message:

 

Location:

branches/blt4/gui/scripts

Files:

• analyzer.tcl (modified) (3 diffs)
• molvisviewer.tcl (modified) (2 diffs)

branches/blt4/gui/scripts/analyzer.tcl

@@ -71 +71 @@
     protected method _simOutput {message}
     protected method _resultTooltip {}
+    protected method _isPdbTrajectory {data}
+    protected method _isLammpsTrajectory {data}
+    protected method _pdbToSequence {xmlobj path id child data}
+    protected method _lammpsToSequence {xmlobj path id child data}
+    protected method _trajToSequence {xmlobj {path ""}}
 
     private variable _tool ""          ;# belongs to this tool
@@ -523 +528 @@
 
     lappend _runs $xmlobj
+
+    # detect molecule elements that contain trajectory data and convert
+    # to sequences.
+    _trajToSequence $xmlobj output
 
     # go through the analysis and find all result sets
@@ -1132 +1141 @@
 itcl::body Rappture::Analyzer::_fixNotebook {} {
     switch -- $itk_option(-notebookpage) {
-        about {
-            $itk_component(notebook) current about
-        }
-        simulate {
-            $itk_component(notebook) current simulate
-        }
-        analyze {
-            $itk_component(notebook) current analyze
-        }
-        default {
-            error "bad value \"$itk_option(-notebookpage)\": should be about, simulate, analyze"
-        }
+        about {
+            $itk_component(notebook) current about
+        }
+        simulate {
+            $itk_component(notebook) current simulate
+        }
+        analyze {
+            $itk_component(notebook) current analyze
+        }
+        default {
+            error "bad value \"$itk_option(-notebookpage)\": should be about, simulate, analyze"
+        }
+    }
+}
+
+# ----------------------------------------------------------------------
+# USAGE: _isPdbTrajectory <data>
+#
+# Used internally to determine whether pdb or lammps data represents a
+# trajectory rather than a single frame
+# ----------------------------------------------------------------------
+itcl::body Rappture::Analyzer::_isPdbTrajectory {data} {
+    if { [llength $data]  == 0 } {
+        return 0
+    }
+    set nModels 0
+    foreach line $data {
+        if { [string match "MODEL*" $line] }  {
+            incr nModels
+            if { $nModels > 1 } {
+                # Stop if more than one model found.  No need to count them
+                # all.
+                return 1
+            }
+        }
+    }
+    return 0
+}
+
+# ----------------------------------------------------------------------
+# USAGE: _isLammpsTrajectory <data>
+#
+# Used internally to determine whether pdb or lammps data represents a
+# trajectory rather than a single frame
+# ----------------------------------------------------------------------
+itcl::body Rappture::Analyzer::_isLammpsTrajectory { data } {
+    if { [llength $data]  == 0 } {
+        return 0
+    }
+    set nModels 0
+    foreach line $data {
+        if { [regexp {^[\t ]*ITEM:[ \t]+TIMESTEP} $line] } {
+            incr nModels
+            if { $nModels > 1 } {
+                # Stop if more than one model found.  No need to count them
+                # all.
+                return 1
+            }
+        }
+    }
+    return 0
+}
+
+# ----------------------------------------------------------------------
+# USAGE: _trajtosequence <xmlobj> ?<path>?
+#
+    # If the molecule element is a trajectory, delete the original
+    # and create a sequence of individual molecules.
+# Used internally to detect any molecule output elements that contain
+# trajectory data.  Trajectories will be converted into sequences of
+# individual molecules.  All other elements will be unaffected. Scans
+# the entire xml tree if a starting path is not specified.
+# ----------------------------------------------------------------------
+itcl::body Rappture::Analyzer::_pdbToSequence {xmlobj path id child data} {
+
+    set seqLabel [$xmlobj get ${child}.about.label]
+    set descr    [$xmlobj get ${child}.about.description]
+    set formula  [$xmlobj get ${child}.components.molecule.formula]
+    $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 { [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 molPath ${framePath}.structure.components.molecule
+                $xmlobj put ${molPath}.lammps $frameContents
+                $xmlobj put ${molPath}.lammpstypemap $typemap
+                
+                incr frameNum
+                set frameContents ""
+            }
+            set inModel 1
+        } elseif { [scan $line "%d %d %f %f %f" a b c d e] == 5 } {
+            if { !$inModel } {
+                puts stderr "found \"$line\" without previous \"ITEM: ATOMS\""
+                set inModel 1
+            }
+            append frameContents $line\n
+        }
+    }
+    if { $frameContents != "" } {
+        set framePath ${seqPath}.element($frameNum)
+        $xmlobj put ${framePath}.index $frameNum
+        
+        set molPath ${framePath}.structure.components.molecule
+        $xmlobj put ${molPath}.lammps $frameContents
+        $xmlobj put ${molPath}.lammpstypemap $typemap
+    }
+}
+
+# ----------------------------------------------------------------------
+# USAGE: _trajtosequence <xmlobj> ?<path>?
+#
+#       Check for PDB and LAMMPS trajectories in molecule data and rewrite 
+#       the individual models as a sequence of molecules.  Used internally 
+#       to detect any molecule output elements that contain trajectory data.
+#       Trajectories will be converted into sequences of individual molecules.
+#       All other elements will be unaffected. Scans the entire xml tree if a
+#       starting path is not specified.  
+#
+# ----------------------------------------------------------------------
+itcl::body Rappture::Analyzer::_trajToSequence {xmlobj {path ""}} {
+    puts stderr "path=$path"
+    # Remove leading dot from path, if present.
+    if { [string index $path 0] == "." } {
+        set path [string range $path 1 end]
+    }
+    # Otherwise check each child.
+    foreach child [$xmlobj children $path] {
+        set current ${path}.${child}
+        if { [string match "structure*" $child] } {
+            # Look for trajectory if molecule element found.  Check both pdb
+            # data and lammps data.
+            set type [$xmlobj element -as type $current]
+            set id   [$xmlobj element -as id $current]
+            set pdbdata    [$xmlobj get ${current}.components.molecule.pdb]
+            set lammpsdata [$xmlobj get ${current}.components.molecule.lammps]
+            if { $pdbdata != "" && $lammpsdata != "" } {
+                puts stderr \
+                    "found both <pdb> and <lammps> elements: picking pdb"
+            }
+            set pdbdata [split $pdbdata \n]
+            set lammpsdata [split $lammpsdata \n]
+            if { [_isPdbTrajectory $pdbdata] } {
+                _pdbToSequence $xmlobj $path $id $current $pdbdata
+            } elseif { [_isLammpsTrajectory $lammpsdata] } {
+                _lammpsToSequence $xmlobj $path $id $current $lammpsdata
+            }
+            continue
+        }
+        # Recurse over all child nodes.
+        _trajToSequence $xmlobj $current
     }
 }

branches/blt4/gui/scripts/molvisviewer.tcl

@@ -780 +780 @@
                 set _dataobjs($model-$state)  1
             }
+
+            # lammps dump file overwrites pdb file (change this?)
+            set lammpstypemap [$dataobj get components.molecule.lammpstypemap]
+            set lammpsdata [$dataobj get components.molecule.lammps]
+            if {"" != $lammpsdata} {
+                set data3 ""
+                set modelcount 0
+                foreach lammpsline [split $lammpsdata "\n"] {
+                    if {[scan $lammpsline "%d %d %f %f %f" id type x y z] == 5} {
+                        set recname  "ATOM  "
+                        set altLoc   ""
+                        set resName  ""
+                        set chainID  ""
+                        set Seqno    ""
+                        set occupancy  1
+                        set tempFactor 0
+                        set recID      ""
+                        set segID      ""
+                        set element    ""
+                        set charge     ""
+                        if { "" == $lammpstypemap} {
+                            set atom $type 
+                        } else {
+                            set atom [lindex $lammpstypemap [expr {$type - 1}]]
+                            if { "" == $atom} {
+                              set atom $type
+                            }
+                        }
+                        set pdbline [format "%6s%5d %4s%1s%3s %1s%5s   %8.3f%8.3f%8.3f%6.2f%6.2f%8s\n" $recname $id $atom $altLoc $resName $chainID $Seqno $x $y $z $occupancy $tempFactor $recID]
+                        append data3 $pdbline
+                    }
+                    # only read first model 
+                    if {[regexp "^ITEM: ATOMS" $lammpsline]} {
+                      incr modelcount
+                      if {$modelcount > 1} {
+                        break
+                      }
+                    }
+                }
+                if {"" != $data3} {
+                    set _pdbdata $data3
+                    SendCmd "loadpdb -defer \"$data3\" $model $state"
+                    set _dataobjs($model-$state) 1
+                }
+            }
         }
         if { ![info exists _model($model-transparency)] } {
@@ -1266 +1311 @@
         set _settings($this-modelimg) [Rappture::icon $option]
     }
-    set inner [$itk_component(main) panel "View Settings"]
+    set tab [$itk_component(main) panel "View Settings"]
+    set inner $tab.ss.frame
     $inner.pict configure -image $_settings($this-modelimg)