Changeset 3848 for trunk/gui/src/RpPdbToVtk.c

Timestamp:

Aug 2, 2013, 6:26:40 AM (11 years ago)

Author:

gah

Message:

clean up variable naming

File:

• trunk/gui/src/RpPdbToVtk.c (modified) (24 diffs)

trunk/gui/src/RpPdbToVtk.c

@@ -32 +32 @@
     double x, y, z;                     /* Coordinates of atom. */
     int number;                         /* Atomic number */
-    int index;                          /* Index of the atom in VTK. */
+    int ordinal;                        /* Index of the atom in VTK. */
 } PdbAtom;
 
@@ -175 +175 @@
 
 static void
-ComputeBonds(Tcl_HashTable *serialTablePtr, Tcl_HashTable *conectTablePtr)
+ComputeBonds(Tcl_HashTable *atomTablePtr, Tcl_HashTable *conectTablePtr)
 {
     PdbAtom **array;
@@ -184 +184 @@
 #define TOLERANCE 0.45                  /* Fuzz factor for comparing distances
                                          * (in angstroms) */
-    array = calloc(serialTablePtr->numEntries, sizeof(PdbAtom *));
+    array = calloc(atomTablePtr->numEntries, sizeof(PdbAtom *));
     if (array == NULL) {
         return;
     }
-    for (i = 0, hPtr = Tcl_FirstHashEntry(serialTablePtr, &iter); hPtr != NULL;
+    for (i = 0, hPtr = Tcl_FirstHashEntry(atomTablePtr, &iter); hPtr != NULL;
          hPtr = Tcl_NextHashEntry(&iter), i++) {
         PdbAtom *atomPtr;
@@ -195 +195 @@
         array[i] = atomPtr;
     }
-    for (i = 0; i < serialTablePtr->numEntries; i++) {
+    for (i = 0; i < atomTablePtr->numEntries; i++) {
         PdbAtom *atom1Ptr;
         double r1;
@@ -202 +202 @@
         atom1Ptr = array[i];
         r1 = elements[atom1Ptr->number].radius;
-        for (j = i+1; j < serialTablePtr->numEntries; j++) {
+        for (j = i+1; j < atomTablePtr->numEntries; j++) {
             PdbAtom *atom2Ptr;
             double ds2, cut;
@@ -214 +214 @@
             cut = (r1 + r2 + TOLERANCE);
             ds2 = (((atom1Ptr->x - atom2Ptr->x) * (atom1Ptr->x - atom2Ptr->x)) +
-                  ((atom1Ptr->y - atom2Ptr->y) * (atom1Ptr->y - atom2Ptr->y)) +
-                  ((atom1Ptr->z - atom2Ptr->z) * (atom1Ptr->z - atom2Ptr->z)));
+                   ((atom1Ptr->y - atom2Ptr->y) * (atom1Ptr->y - atom2Ptr->y)) +
+                   ((atom1Ptr->z - atom2Ptr->z) * (atom1Ptr->z - atom2Ptr->z)));
 
             // perform distance test, but ignore pairs between atoms
@@ -226 +226 @@
                 int isNew;
 
-                if (atom1Ptr->index > atom2Ptr->index) {
-                    key.from = atom2Ptr->index;
-                    key.to = atom1Ptr->index;
+                if (atom1Ptr->ordinal > atom2Ptr->ordinal) {
+                    key.from = atom2Ptr->ordinal;
+                    key.to = atom1Ptr->ordinal;
                 } else {
-                    key.from = atom1Ptr->index;
-                    key.to = atom2Ptr->index;
+                    key.from = atom1Ptr->ordinal;
+                    key.to = atom2Ptr->ordinal;
                 }
                 Tcl_CreateHashEntry(conectTablePtr, (char *)&key, &isNew);
@@ -343 +343 @@
 
 static PdbAtom *
-NewAtom(Tcl_Interp *interp, int index, const char *line, int lineLength)
+NewAtom(Tcl_Interp *interp, int ordinal, const char *line, int lineLength)
 {
     PdbAtom *atomPtr;
@@ -356 +356 @@
         return NULL;
     }
-    atomPtr->index = index;
+    atomPtr->ordinal = ordinal;
     strncpy(atomName, line + 12, 4);
     atomName[4] = '\0';
@@ -458 +458 @@
 
 static int 
-SerialToIndex(Tcl_Interp *interp, Tcl_HashTable *tablePtr, const char *string,
-              int *indexPtr)
+SerialToOrdinal(Tcl_Interp *interp, Tcl_HashTable *tablePtr, const char *string,
+              int *ordPtr)
 {
     int serial;
@@ -481 +481 @@
     }
     atomPtr = Tcl_GetHashValue(hPtr);
-    *indexPtr = atomPtr->index;
+    *ordPtr = atomPtr->ordinal;
     return TCL_OK;
 }
 
 /* 
- *  PdbToVtk string
+ *  PdbToVtk string ?-bonds none|both|auto|conect?
  */
 static int
@@ -492 +492 @@
            Tcl_Obj *const *objv) 
 {
-    Tcl_Obj *objPtr, *pointsObjPtr, *atomsObjPtr, *verticesObjPtr;
+    Tcl_Obj *objPtr, *pointsObjPtr, *atomsObjPtr;
     const char *p, *pend;
-    char *string;
+    const char *string;
     char mesg[2000];
-    int length, nextIndex;
-    Tcl_HashTable serialTable, conectTable;
+    int length, nextOrdinal;
+    Tcl_HashTable atomTable, conectTable;
     Tcl_HashEntry *hPtr;
     Tcl_HashSearch iter;
@@ -504 +504 @@
 
     bondFlags = BOND_NONE;
-    lineNum = nextIndex = 0;
+    lineNum = nextOrdinal = 0;
     if ((objc != 2) && (objc != 4)) {
         Tcl_AppendResult(interp, "wrong # arguments: should be \"",
@@ -538 +538 @@
         }
     }
-    Tcl_InitHashTable(&serialTable, TCL_ONE_WORD_KEYS);
+    Tcl_InitHashTable(&atomTable, TCL_ONE_WORD_KEYS);
     Tcl_InitHashTable(&conectTable, sizeof(ConnectKey) / sizeof(int));
     string = Tcl_GetStringFromObj(objv[1], &length);
     pointsObjPtr = Tcl_NewStringObj("", -1);
     atomsObjPtr = Tcl_NewStringObj("", -1);
-    verticesObjPtr = Tcl_NewStringObj("", -1);
     Tcl_IncrRefCount(pointsObjPtr);
     Tcl_IncrRefCount(atomsObjPtr);
-    Tcl_IncrRefCount(verticesObjPtr);
     objPtr = NULL;
     for (p = string, pend = p + length; p < pend; /*empty*/) {
@@ -587 +585 @@
             }
             lserial = (long)serialNum;
-            hPtr = Tcl_CreateHashEntry(&serialTable, (char *)lserial, &isNew);
+            hPtr = Tcl_CreateHashEntry(&atomTable, (char *)lserial, &isNew);
             if (!isNew) {
                 Tcl_AppendResult(interp, "line ", Itoa(lineNum), 
@@ -594 +592 @@
                 goto error;
             }
-            atomPtr = NewAtom(interp, nextIndex, line, lineLength);
+            atomPtr = NewAtom(interp, nextOrdinal, line, lineLength);
             if (atomPtr == NULL) {
                 goto error;
@@ -607 +605 @@
             Tcl_ListObjAppendElement(interp, atomsObjPtr, 
                                      Tcl_NewIntObj(atomPtr->number));
-            nextIndex++;
+            nextOrdinal++;
         } else if ((c == 'C') && (strncmp(line, "CONECT", 6) == 0)) {
             int a, i, n;
@@ -627 +625 @@
                 goto error;
             }
-            if (SerialToIndex(interp, &serialTable, buf, &a) != TCL_OK) {
+            if (SerialToOrdinal(interp, &atomTable, buf, &a) != TCL_OK) {
                 goto error;
             }
@@ -642 +640 @@
                     break;              /* No more entries */
                 }
-                if (SerialToIndex(interp, &serialTable, buf, &b) != TCL_OK) {
+                if (SerialToOrdinal(interp, &atomTable, buf, &b) != TCL_OK) {
                     goto error;
                 }
@@ -657 +655 @@
     }
     if (bondFlags & BOND_COMPUTE) {
-        ComputeBonds(&serialTable, &conectTable);
+        ComputeBonds(&atomTable, &conectTable);
     }
     objPtr = Tcl_NewStringObj("# vtk DataFile Version 2.0\n", -1);
@@ -663 +661 @@
     Tcl_AppendToObj(objPtr, "ASCII\n", -1);
     Tcl_AppendToObj(objPtr, "DATASET POLYDATA\n", -1);
-    sprintf(mesg, "POINTS %d float\n", serialTable.numEntries);
+    sprintf(mesg, "POINTS %d float\n", atomTable.numEntries);
     Tcl_AppendToObj(objPtr, mesg, -1);
     Tcl_AppendObjToObj(objPtr, pointsObjPtr);
@@ -684 +682 @@
         Tcl_AppendToObj(objPtr, mesg, -1);
     }
-    sprintf(mesg, "POINT_DATA %d\n", serialTable.numEntries);
+    sprintf(mesg, "POINT_DATA %d\n", atomTable.numEntries);
     Tcl_AppendToObj(objPtr, mesg, -1);
     sprintf(mesg, "SCALARS element int\n");
@@ -691 +689 @@
     Tcl_AppendToObj(objPtr, mesg, -1);
     Tcl_AppendObjToObj(objPtr, atomsObjPtr);
-    FreeAtoms(&serialTable);
+    FreeAtoms(&atomTable);
     Tcl_DeleteHashTable(&conectTable);
     Tcl_DecrRefCount(pointsObjPtr);
     Tcl_DecrRefCount(atomsObjPtr);
-    Tcl_DecrRefCount(verticesObjPtr);
     if (objPtr != NULL) {
         Tcl_SetObjResult(interp, objPtr);
@@ -702 +699 @@
  error:
     Tcl_DeleteHashTable(&conectTable);
-    FreeAtoms(&serialTable);
+    FreeAtoms(&atomTable);
     Tcl_DecrRefCount(pointsObjPtr);
     Tcl_DecrRefCount(atomsObjPtr);
-    Tcl_DecrRefCount(verticesObjPtr);
     return TCL_ERROR;
 }