Changeset 1830 for trunk

Timestamp:

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

Author:

gah

Message:

 

Location:

trunk

Files:

• gui/scripts/analyzer.tcl (modified) (11 diffs)
• packages/vizservers/pymolproxy/pymolproxy.c (modified) (4 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
+        }
     }
 }

trunk/packages/vizservers/pymolproxy/pymolproxy.c

@@ -57 +57 @@
 #include <fcntl.h>
 #include <getopt.h>
-#include <net/if.h>
-#include <netinet/in.h>
 #include <poll.h>
-#include <signal.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include <sys/ioctl.h>
-#include <sys/select.h>
-#include <sys/socket.h>
 #include <sys/stat.h>
 #include <sys/time.h>
@@ -102 +96 @@
 
 static FILE *flog;
-static int debug = 0;
+static int debug = FALSE;
 static FILE *scriptFile;
-static int savescript = 0;
+static int savescript = FALSE;
 
 typedef struct Image {
@@ -1025 +1019 @@
            const char *argv[])
 {
-    const char *pdbdata, *name;
-    PymolProxy *proxyPtr = clientData;
-    int state = 1;
-    int i, defer = 0, push = 0, varg = 1;
+    const char *data, *name;
+    char *allocated;
+    PymolProxy *proxyPtr = clientData;
+    int state, defer, push;
     int nBytes;
-
-    if (proxyPtr == NULL)
+    int i, j;
+
+    if (proxyPtr == NULL){
         return TCL_ERROR;
-    clear_error(proxyPtr);
-    pdbdata = name = NULL;              /* Suppress compiler warning. */
-    nBytes = 0;                         /* Suppress compiler warning. */
-    for(i = 1; i < argc; i++) {
-        if ( strcmp(argv[i],"-defer") == 0 )
-            defer = 1;
-        else if (strcmp(argv[i],"-push") == 0)
-            push = 1;
-        else if (varg == 1) {
-            nBytes = atoi(argv[i]);
-            varg++;
-        } else if (varg == 2) {
-            name = argv[i];
-            varg++;
-        } else if (varg == 3) {
-            state = atoi( argv[i] );
-            varg++;
+    }
+    clear_error(proxyPtr);
+    defer = push = FALSE;
+    for(i = j = 1; i < argc; i++) {
+        if (strcmp(argv[i],"-defer") == 0) {
+            defer = TRUE;
+        } else if (strcmp(argv[i],"-push") == 0) {
+            push = TRUE;
+        } else {
+            if (j < i) {
+                argv[j] = argv[i];
+            }
+            j++;
+        }
+    }
+    argc = j;
+    if (argc < 4) {
+        Tcl_AppendResult(interp, "wrong # arguments: should be \"", argv[0],
+                         " <data>|follows <model> <state> ?<nBytes>?\"",
+                         (char *)NULL);
+        return TCL_ERROR;
+    }
+    data = argv[1];
+    name = argv[2];
+    if (Tcl_GetInt(interp, argv[3], &state) != TCL_OK) {
+        return TCL_ERROR;
+    }
+    nBytes = -1;
+    if (strcmp(data, "follows") == 0) {
+        if (argc != 5) {
+            Tcl_AppendResult(interp, "wrong # arguments: should be \"", argv[0],
+                         " follows <model> <state> <nBytes>\"", (char *)NULL);
+            return TCL_ERROR;
+        }
+        if (Tcl_GetInt(interp, argv[4], &nBytes) != TCL_OK) {
+            return TCL_ERROR;
+        }
+        if (nBytes < 0) {
+            Tcl_AppendResult(interp, "bad value for # bytes \"", argv[4],
+                         "\"", (char *)NULL);
+            return TCL_ERROR;
         }
     }
@@ -1061 +1080 @@
     /* Does not invalidate cache? */
 
+    allocated = NULL;
+    if (nBytes >= 0) {
+        allocated = malloc(sizeof(char) * nBytes);
+        if (allocated == NULL) {
+            Tcl_AppendResult(interp, "can't allocate buffer for pdbdata.",
+                             (char *)NULL);
+            return TCL_ERROR;
+        }
+        if (GetBytes(&proxyPtr->client, allocated, nBytes) != BUFFER_OK) {
+            Tcl_AppendResult(interp, "can't read pdbdata from client.",
+                             (char *)NULL);
+            free(allocated);
+            return TCL_ERROR;
+        }
+        data = allocated;
+    } else {
+        nBytes = strlen(data);
+    }
     {
         char fileName[200];
         FILE *f;
-        char *data;
         ssize_t nWritten;
 
-        data = malloc(sizeof(char) * nBytes);
-        if (data == NULL) {
-            trace("can't allocate %d bytes for \"pdbdata\" buffer", nBytes);
-            return  TCL_ERROR;
-        }
-        if (GetBytes(&proxyPtr->client, data, nBytes) != BUFFER_OK) {
-            trace("can't read %d bytes for \"pdbdata\" buffer", nBytes);
-            free(data);
-            return  TCL_ERROR;
-        }
+        proxyPtr->status = TCL_ERROR;
         sprintf(fileName, "/tmp/pymol%d.pdb", getpid());
         f = fopen(fileName, "w");
         if (f == NULL) {
-            trace("can't open `%s': %s", fileName, strerror(errno));
-            perror("pymolproxy");
-            free(data);
-            return TCL_ERROR;
+            Tcl_AppendResult(interp, "can't create temporary file \"",
+                             fileName, "\": ", Tcl_PosixError(interp),
+                             (char *)NULL);
+            goto error;
         } 
         nWritten = fwrite(data, sizeof(char), nBytes, f);
         if (nBytes != nWritten) {
-            trace("short write %d wanted %d bytes", nWritten, nBytes);
-            perror("pymolproxy");
+            Tcl_AppendResult(interp, "can't write PDB data to \"",
+                             fileName, "\": ", Tcl_PosixError(interp),
+                             (char *)NULL);
+            fclose(f);
+            goto error;
         }
         fclose(f);
-        free(data);
         Pymol(proxyPtr, "load %s,%s,%d\n", fileName, name, state);
+        proxyPtr->status = TCL_OK;
+    }
+ error:
+    if (allocated != NULL) {
+        free(allocated);
     }
     return proxyPtr->status;