--- trunk/SHAPES/PDBReader.cpp	2004/07/20 17:07:01	1359
+++ trunk/SHAPES/PDBReader.cpp	2004/07/20 20:02:15	1360
@@ -4,18 +4,23 @@ PDBReader::~PDBReader(void) {
 }
 
 PDBReader::~PDBReader(void) {
-  gzclose(PDBfile);
+  fclose(PDBfile);
 }
 
 
-void PDBReader::setPDBfile(const char *fname) {
-  PDBfile = gzopen(fname, "r");
-  if (PDBfile == Z_NULL) { 
+void PDBReader::setPDBfileName(const char *fname) {
+  PDBfile = fopen(fname, "r");
+  if (PDBfile == NULL) { 
     printf("Could not open PDB file %s\n", fname);
     exit(-1);
-  }
+  } else 
+    setPDBfile(PDBfile);
 }
 
+void PDBReader::setPDBfile(FILE* myFile) {
+  PDBfile = myFile;
+}
+
 vector<VDWAtom*> PDBReader::getAtomList() {
 
   char numstr[9];
@@ -31,10 +36,10 @@ vector<VDWAtom*> PDBReader::getAtomList() {
   ta = getTotAtoms();
   theAtoms.reserve(ta);
 
-  gzrewind(PDBfile);
+  rewind(PDBfile);
 
-  while (!gzeof(PDBfile)) {
-    gzgets(PDBfile, buf, 150);
+  while (!feof(PDBfile)) {
+    fgets( buf, 150, PDBfile);
     if (!strcmp(buf, "END") || 
 	!strncmp(buf, "END ", 4) || 
 	!strncmp(buf, "TER ", 4) || 
@@ -84,9 +89,9 @@ unsigned int PDBReader::getTotAtoms(void) {
 unsigned int PDBReader::getTotAtoms(void) {
   char buf[150];
   unsigned int ta = 0;
-  gzrewind(PDBfile);
-  while (!gzeof(PDBfile)) {
-    gzgets(PDBfile,buf,150);
+  rewind(PDBfile);
+  while (!feof(PDBfile)) {
+    fgets(buf,150,PDBfile);
     if (!strcmp(buf, "END") ||
         !strncmp(buf, "END ", 4) ||
         !strncmp(buf, "TER ", 4) ||