git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1376 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/pymol_asphere/src/cartesian.cpp

@@ -169,12 +169,6 @@ TwoD<numtyp> TwoD<numtyp>::normal() {
 	return TwoD(y,x*numtyp(-1));
 }
 
-template<class numtyp>
-numtyp TwoD<numtyp>::dist(const TwoD<numtyp> &two) const {
-	TwoD diff=*this-two;
-	return numtyp(sqrt(double(diff.dot(diff))));
-}
-
 template<class numtyp>
 numtyp TwoD<numtyp>::dist2(const TwoD<numtyp> &two) const {
 	TwoD diff=*this-two;
@@ -293,26 +287,6 @@ template<class numtyp>
 ThreeD<numtyp>::ThreeD() {
 }
 
-template<class numtyp>
-numtyp & ThreeD<numtyp>::operator[](unsigned i) {
-  switch(i) {
-   case X: return x;
-   case Y: return y;
-   case Z: return z;
-  }
-  return x;
-}
-
-template<class numtyp>
-numtyp ThreeD<numtyp>::operator[](unsigned i) const {
-  switch(i) {
-   case X: return x;
-   case Y: return y;
-   case Z: return z;
-  }
-  return x;
-}
-
 template<class numtyp>
 void ThreeD<numtyp>::operator = (const ThreeD &two) {
   #ifdef NANCHECK
@@ -396,11 +370,6 @@ numtyp ThreeD<numtyp>::dot(const ThreeD<numtyp> &two) const {
 	return (x*two.x+y*two.y+z*two.z);
 }
 
-template<class numtyp>
-void ThreeD<numtyp>::operator *= (const numtyp &two) {
-  x*=two; y*=two; z*=two;
-}
-
 // Move coordinates into array
 template<class numtyp>
 void ThreeD<numtyp>::to_array(numtyp *array) {
@@ -499,27 +468,12 @@ numtyp ThreeD<numtyp>::norm2() const {
   return x*x+y*y+z*z;
 }
 
-template <class numtyp>
-numtyp ThreeD<numtyp>::dist(const ThreeD<numtyp> &two) {
-  return (*this-two).norm();
-}
-
 template <class numtyp>
 numtyp ThreeD<numtyp>::dist2(const ThreeD<numtyp> &two) {
 	ThreeD diff=*this-two;
 	return diff.dot(diff);
 }
 
-// For normalizing a vector
-template<class numtyp>
-void ThreeD<numtyp>::normalize() {
-  numtyp temp=norm();
-  #ifdef NANCHECK
-  assert(temp!=0);
-  #endif
-  *this/=temp;
-}
-
 // Return unit vector
 template<class numtyp>
 ThreeD<numtyp> ThreeD<numtyp>::unit() {

tools/pymol_asphere/src/cartesian.h

@@ -204,8 +204,23 @@ class ThreeD {
   friend ThreeD<numtyp> operator* <>(const numtyp, const ThreeD<numtyp> &two);
   friend ThreeD<numtyp> operator/ <>(const numtyp, const ThreeD<numtyp> &two);
 
-  numtyp &operator[](unsigned i);
+  inline numtyp &operator[](unsigned i) {
-  numtyp operator[](unsigned i) const;
+    switch(i) {
+    case X: return x;
+    case Y: return y;
+    case Z: return z;
+    }
+    return x;
+  }
+
+  inline numtyp operator[](unsigned i) const {
+    switch(i) {
+    case X: return x;
+    case Y: return y;
+    case Z: return z;
+    }
+    return x;
+  }
 
   bool operator == (const ThreeD<numtyp> &two) const;
   bool operator != (const ThreeD<numtyp> &two) const;
@@ -222,7 +237,10 @@ class ThreeD {
   void operator += (const ThreeD &two);
   void operator -= (const numtyp &two);
   void operator -= (const ThreeD &two);
-  void operator *= (const numtyp &two);
+  inline void operator *= (const numtyp &two) {
+    x*=two; y*=two; z*=two;
+  }
+
   void operator /= (const numtyp &two);
 
   /// Move coordinates into array
@@ -253,11 +271,20 @@ class ThreeD {
   /// Magnitude of vector
   numtyp hypot() const;
   /// Distance between two points
-  numtyp dist(const ThreeD<numtyp> &two);
+  inline numtyp dist(const ThreeD<numtyp> &two) {
+    return (*this-two).norm();
+  }
   /// Distance squared between two points
   numtyp dist2(const ThreeD<numtyp> &two);
   /// Converts \b *this to the unit vector
-  void normalize();
+  inline void normalize() {
+    numtyp temp=norm();
+    #ifdef NANCHECK
+    assert(temp!=0);
+    #endif
+    *this/=temp;
+  }
+
   /// Return the unit vector of \b *this
   ThreeD<numtyp> unit();
 

tools/pymol_asphere/src/glsurface.cpp

@@ -333,7 +333,8 @@ void GLSurface::write_vspheres(ofstream &out, const string &objname,
   writepymolheader(out);
   for (i=0; i<vertices.size(); i++) {
     // Output coords, colors, and normals of points
-//    if (vertices[i].transparency!=1)
+    if (vertices[i].transparency==0)
+      continue;
       out << "ALPHA," << vertices[i].transparency << ",";
     out << "COLOR,";
     for (k=X; k<=Z; k++)
@@ -353,7 +354,8 @@ void GLSurface::writespheres(ofstream &out, const string &objname) {
   writepymolheader(out);
   for (i=0; i<spheres.size(); i++) {
     // Output coords, colors, and normals of points
-//    if (vertices[i].transparency!=1)
+    if (vertices[i].transparency==0)
+      continue;
       out << "ALPHA," << vertices[spheres[i].i].transparency << ",";
     out << "COLOR,";
     for (k=X; k<=Z; k++)