Changeset 1807 for branches/blt4/packages/vizservers/pymolproxy/pymolproxy.c

Timestamp:

Jul 14, 2010, 3:54:10 PM (14 years ago)

Author:

gah

Message:

 

File:

• branches/blt4/packages/vizservers/pymolproxy/pymolproxy.c (modified) (9 diffs)

branches/blt4/packages/vizservers/pymolproxy/pymolproxy.c

@@ -1038 +1038 @@
 }
 
+/* 
+ * LoadPDBCmd --
+ *
+ *      Load a PDB file into pymol.  There is no good way to load PDB data
+ *      into pymol without using a file.  This causes problems in that we
+ *      don't know when pymol is done with the file.  So there's always
+ *      a bit of mess left around. We use the same file for every file
+ *      so there's a chance that pymol is still using a file while we're
+ *      overwriting it.  
+ *
+ *      The command expects the number of bytes in the pdb data, the 
+ *      name, and the state.
+ */
 static int
 LoadPDBCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
@@ -1046 +1059 @@
     int state = 1;
     int i, defer = 0, push = 0, varg = 1;
-    
+    int nBytes;
+
     if (proxyPtr == NULL)
         return TCL_ERROR;
     clear_error(proxyPtr);
-    pdbdata = name = NULL;      /* Suppress compiler warning. */
+    pdbdata = name = NULL;              /* Suppress compiler warning. */
+    nBytes = 0;                         /* Suppress compiler warning. */
     for(i = 1; i < argc; i++) {
         if ( strcmp(argv[i],"-defer") == 0 )
@@ -1057 +1072 @@
             push = 1;
         else if (varg == 1) {
-            pdbdata = argv[i];
+            nBytes = atoi(argv[i]);
             varg++;
         } else if (varg == 2) {
@@ -1067 +1082 @@
         }
     }
-    
     if (!defer || push) {
         proxyPtr->flags |= UPDATE_PENDING;
@@ -1080 +1094 @@
         char fileName[200];
         FILE *f;
-        size_t nBytes;
         ssize_t nWritten;
-
+        char *data;
+
+        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);
+            return  TCL_ERROR;
+        }
         sprintf(fileName, "/tmp/pymol%d.pdb", getpid());
         f = fopen(fileName, "w");
@@ -1089 +1112 @@
             perror("pymolproxy");
         }
-        nBytes = strlen(pdbdata);
-        nWritten = fwrite(pdbdata, sizeof(char), nBytes, f);
+        nWritten = fwrite(data, sizeof(char), nBytes, f);
         if (nBytes != nWritten) {
             trace("short write %d wanted %d bytes", nWritten, nBytes);
@@ -1844 +1866 @@
 
     child = fork();
-        
     if (child < 0) {
         fprintf(stderr, "can't fork process: %s\n", strerror(errno));
@@ -1943 +1964 @@
     } else if (status == 0) {
         trace("attempting to signal (SIGTERM) pymol server.");
-        kill(-child, SIGTERM); // kill process group
+        kill(-child, SIGTERM);          // Kill process group
         alarm(5);
         status = waitpid(child, &result, 0);
@@ -1950 +1971 @@
         while ((status == -1) && (errno == EINTR)) {
             trace("Attempting to signal (SIGKILL) pymol server.");
-            kill(-child, SIGKILL); // kill process group
+            kill(-child, SIGKILL);      // Kill process group
             alarm(10);
             status = waitpid(child, &result, 0);