Changeset 3850 for trunk/gui/src

Timestamp:

Aug 2, 2013 7:51:39 PM (11 years ago)

Author:

gah

Message:

added code for computing bonds: seems to add more bonds than pymol or vmd

File:

• trunk/gui/src/RpPdbToVtk.c (modified) (10 diffs)

trunk/gui/src/RpPdbToVtk.c

@@ -220 +220 @@
             // perform distance test, but ignore pairs between atoms
             // with nearly identical coords
-            if (ds2 < 0.001) {
+            if (ds2 < 0.16) {
                 continue;
             }
@@ -252 +252 @@
     int elemIndex, symbolIndex;
     int count;
-    char *p;
+    const char *p;
 
     symbolIndex = elemIndex = -1;
@@ -463 +463 @@
 
 static int 
-SerialToOrdinal(Tcl_Interp *interp, Tcl_HashTable *tablePtr, const char *string,
-              int *ordPtr)
+SerialToAtom(Tcl_Interp *interp, Tcl_HashTable *tablePtr, const char *string,
+                PdbAtom **atomPtrPtr)
 {
     int serial;
-    PdbAtom *atomPtr;
     long lserial;
     Tcl_HashEntry *hPtr;
@@ -485 +484 @@
         return TCL_ERROR;
     }
-    atomPtr = Tcl_GetHashValue(hPtr);
-    *ordPtr = atomPtr->ordinal;
+    *atomPtrPtr = Tcl_GetHashValue(hPtr);
     return TCL_OK;
 }
@@ -508 +506 @@
     int bondFlags;
 
-    bondFlags = BOND_NONE;
+    bondFlags = BOND_BOTH;
     lineNum = nextOrdinal = 0;
     if ((objc != 2) && (objc != 4)) {
@@ -612 +610 @@
             nextOrdinal++;
         } else if ((c == 'C') && (strncmp(line, "CONECT", 6) == 0)) {
-            int a, i, n;
+            PdbAtom *atom1Ptr;
+            int i, n;
             char buf[200];
 
@@ -630 +629 @@
                 goto error;
             }
-            if (SerialToOrdinal(interp, &atomTable, buf, &a) != TCL_OK) {
+            if (SerialToAtom(interp, &atomTable, buf, &atom1Ptr) != TCL_OK) {
                 goto error;
             }
@@ -636 +635 @@
             for (n = 11, i = 0; i < 4; i++, n += 5) {
                 ConnectKey key;
-                int b;
+                PdbAtom *atom2Ptr;
+
                 if (n >= lineLength) {
                     break;              
@@ -645 +645 @@
                     break;              /* No more entries */
                 }
-                if (SerialToOrdinal(interp, &atomTable, buf, &b) != TCL_OK) {
+                if (SerialToAtom(interp, &atomTable, buf, &atom2Ptr) !=TCL_OK) {
                     goto error;
                 }
-                if (a > b) {
-                    key.from = b;
-                    key.to = a;
+                if (atom1Ptr->ordinal > atom2Ptr->ordinal) {
+                    key.from = atom2Ptr->ordinal;
+                    key.to = atom1Ptr->ordinal;
                 } else {
-                    key.from = a;
-                    key.to = b;
+                    key.from = atom1Ptr->ordinal;
+                    key.to = atom2Ptr->ordinal;
                 }
                 Tcl_CreateHashEntry(&conectTable, (char *)&key, &isNew);
@@ -690 +690 @@
         sprintf(mesg, "\n");
         Tcl_AppendToObj(objPtr, mesg, -1);
+    }
+    for (hPtr = Tcl_FirstHashEntry(&atomTable, &iter); hPtr != NULL;
+         hPtr = Tcl_NextHashEntry(&iter)) {
+        PdbAtom *atomPtr;
+
+        atomPtr = Tcl_GetHashValue(hPtr);
+        fprintf(stderr, "%d %s %d connections\n", atomPtr->ordinal,
+                elements[atomPtr->number].symbol, atomPtr->numConnections);
     }
     sprintf(mesg, "POINT_DATA %d\n", atomTable.numEntries);