diff --git a/doc/CpptrajManual.pdf b/doc/CpptrajManual.pdf
index b882f583bc..eb693da4e6 100644
Binary files a/doc/CpptrajManual.pdf and b/doc/CpptrajManual.pdf differ
diff --git a/doc/DocumentChecksums.txt b/doc/DocumentChecksums.txt
index 770ffa8977..1bfbe455d4 100644
--- a/doc/DocumentChecksums.txt
+++ b/doc/DocumentChecksums.txt
@@ -1,3 +1,3 @@
 f6f8cb1a79951d80a9d2656fd9c30f55  CpptrajDevelopmentGuide.lyx
-cbbe066a99553d484a9113510c740f1a  cpptraj.lyx
+676d7874e4942cf94f91fee003cf3c28  cpptraj.lyx
 5d9b5b5ed47a3ded57b6464df99b3585  CpptrajManual.lyx
diff --git a/src/Action_AutoImage.cpp b/src/Action_AutoImage.cpp
index 38d3fe41ff..2a0091a706 100644
--- a/src/Action_AutoImage.cpp
+++ b/src/Action_AutoImage.cpp
@@ -473,7 +473,7 @@ Action::RetType Action_AutoImage::autoimage_by_vector(int frameNum, ActionFrame&
         Vec3 translated_coord_frac = mobile_unit_center_frac + image_vec;
         // Closest distance of mobile unit center to anchor center
         int ixyz[3];
-        Cpptraj::Dist2_Imaged_Frac( translated_coord_frac, anchor_center_frac, box.UnitCell(), box.FracCell(), ixyz );
+        Cpptraj::Dist2_Imaged_Frac( translated_coord_frac, anchor_center_frac, box.UnitCell(), ixyz );
         if (ixyz[0] != 0 || ixyz[1] != 0 || ixyz[2] != 0) {
           // The reflection is closer to the center, so move the mobile unit.
           translate_unit(fracCoords_, Vec3(ixyz[0], ixyz[1], ixyz[2]), *it);
diff --git a/src/Action_Distance.cpp b/src/Action_Distance.cpp
index e915ce5efc..224d5b4cc4 100644
--- a/src/Action_Distance.cpp
+++ b/src/Action_Distance.cpp
@@ -2,6 +2,7 @@
 #include "CpptrajStdio.h"
 #include "DistRoutines.h"
 #include "AssociatedData_NOE.h"
+#include <cmath>
 
 // CONSTRUCTOR
 Action_Distance::Action_Distance() :
@@ -168,7 +169,8 @@ Action::RetType Action_Distance::DoAction(int frameNum, ActionFrame& frm) {
       a1 = frm.Frm().VGeometricCenter( Mask1_ );
   }
 
-  double Dist = DIST(imageOpt_.ImagingType(), a1, a2_, frm.Frm().BoxCrd());
+  double Dist2 = DIST2(imageOpt_.ImagingType(), a1, a2_, frm.Frm().BoxCrd());
+  double Dist = sqrt(Dist2);
 
   dist_->Add(frameNum, &Dist);
 
diff --git a/src/Action_NMRrst.cpp b/src/Action_NMRrst.cpp
index 868077390a..3b74189708 100644
--- a/src/Action_NMRrst.cpp
+++ b/src/Action_NMRrst.cpp
@@ -551,7 +551,8 @@ Action::RetType Action_NMRrst::DoAction(int frameNum, ActionFrame& frm) {
         a2 = frm.Frm().VGeometricCenter( noe->dMask2_ );
       }
 
-      double Dist = DIST(imageOpt_.ImagingType(), a1, a2, frm.Frm().BoxCrd());
+      double Dist2 = DIST2(imageOpt_.ImagingType(), a1, a2, frm.Frm().BoxCrd());
+      double Dist = sqrt(Dist2);
 
       noe->dist_->Add(frameNum, &Dist);
     }
diff --git a/src/Action_PairDist.cpp b/src/Action_PairDist.cpp
index fd758db3f9..cf94240b53 100644
--- a/src/Action_PairDist.cpp
+++ b/src/Action_PairDist.cpp
@@ -143,7 +143,8 @@ Action::RetType Action_PairDist::Setup(ActionSetup& setup) {
 void Action_PairDist::BinHist( std::vector<double>& tmp,
                                const double* XYZ1, const double* XYZ2, Box const& box)
 {
-  double Dist = DIST(imageOpt_.ImagingType(), XYZ1, XYZ2, box);
+  double Dist2 = DIST2(imageOpt_.ImagingType(), XYZ1, XYZ2, box);
+  double Dist = sqrt(Dist2);
 
   unsigned long bin = (unsigned long) (Dist / delta_);
   // Resize on the fly if necessary
diff --git a/src/Action_Radial.cpp b/src/Action_Radial.cpp
index 74f2003351..ef7c3abff6 100644
--- a/src/Action_Radial.cpp
+++ b/src/Action_Radial.cpp
@@ -3,7 +3,7 @@
 #include "Action_Radial.h"
 #include "CpptrajStdio.h"
 #include "Constants.h" // FOURTHIRDSPI
-#include "DistRoutines.h"
+#include "Dcalc.h"
 #ifdef _OPENMP
 #  include <omp.h>
 #endif
@@ -483,45 +483,23 @@ void Action_Radial::calcRDF_singleMask(Frame const& frmIn) {
   int outer_max = OuterMask_.Nselected();
   int idx1;
 
-  double boxX = frmIn.BoxCrd().Param(Box::X);
-  double boxY = frmIn.BoxCrd().Param(Box::Y);
-  double boxZ = frmIn.BoxCrd().Param(Box::Z);
-  bool isOrtho = (imageOpt_.ImagingType() == ImageOption::ORTHO &&
-                  boxX != 0.0 && boxY != 0.0 && boxZ != 0.0);
-
   long unsigned* myRDF = &RDF_[0];
 # ifdef _OPENMP
 # pragma omp parallel private(idx1, myRDF)
   {
-    //mprintf("OPENMP: %i threads\n",omp_get_num_threads());
-    myRDF = &(rdf_thread_[omp_get_thread_num()][0]);
+  //mprintf("OPENMP: %i threads\n",omp_get_num_threads());
+  myRDF = &(rdf_thread_[omp_get_thread_num()][0]);
+  Cpptraj::Dcalc dcalc(frmIn, imageOpt_.ImagingType());
 # pragma omp for schedule(dynamic)
+# else
+  Cpptraj::Dcalc dcalc(frmIn, imageOpt_.ImagingType());
 # endif
   for (idx1 = 0; idx1 < outer_max; idx1++) {
     const double* xyz1 = frmIn.XYZ( OuterMask_[idx1] );
+    dcalc.SetXYZ1( xyz1 );
     for (int idx2 = idx1 + 1; idx2 < outer_max; idx2++) {
       const double* xyz2 = frmIn.XYZ( OuterMask_[idx2] );
-      double D2;
-      if (isOrtho) {
-        double x = xyz1[0] - xyz2[0];
-        double y = xyz1[1] - xyz2[1];
-        double z = xyz1[2] - xyz2[2];
-        x = std::fabs(x);
-        y = std::fabs(y);
-        z = std::fabs(z);
-        while (x > boxX) x -= boxX;
-        while (y > boxY) y -= boxY;
-        while (z > boxZ) z -= boxZ;
-        double D = boxX - x;
-        if (D < x) x = D;
-        D = boxY - y;
-        if (D < y) y = D;
-        D = boxZ - z;
-        if (D < z) z = D;
-        D2 = x*x + y*y + z*z;
-      }
-      else
-        D2 = DIST2(imageOpt_.ImagingType(), xyz1, xyz2, frmIn.BoxCrd());
+      double D2 = dcalc.Dist2(xyz2);
       if (D2 <= maximum2_) {
       // NOTE: Can we modify the histogram to store D^2?
         double dist = sqrt(D2);
@@ -542,42 +520,24 @@ void Action_Radial::calcRDF_twoMask(Frame const& frmIn) {
   int outer_max = OuterMask_.Nselected();
   int inner_max = InnerMask_.Nselected();
   int idx1;
-  double boxX = frmIn.BoxCrd().Param(Box::X);
-  double boxY = frmIn.BoxCrd().Param(Box::Y);
-  double boxZ = frmIn.BoxCrd().Param(Box::Z);
-  bool isOrtho = (imageOpt_.ImagingType() == ImageOption::ORTHO &&
-                boxX != 0.0 && boxY != 0.0 && boxZ != 0.0);
 
   long unsigned* myRDF = &RDF_[0];
 # ifdef _OPENMP
 # pragma omp parallel private(idx1, myRDF)
   {
-    //mprintf("OPENMP: %i threads\n",omp_get_num_threads());
-    myRDF = &(rdf_thread_[omp_get_thread_num()][0]);
+  //mprintf("OPENMP: %i threads\n",omp_get_num_threads());
+  myRDF = &(rdf_thread_[omp_get_thread_num()][0]);
+  Cpptraj::Dcalc dcalc(frmIn, imageOpt_.ImagingType());
 # pragma omp for
+# else
+  Cpptraj::Dcalc dcalc(frmIn, imageOpt_.ImagingType());
 # endif
   for (idx1 = 0; idx1 < outer_max; idx1++) {
     const double* xyz1 = frmIn.XYZ( OuterMask_[idx1] );
+    dcalc.SetXYZ1( xyz1 );
     for (int idx2 = 0; idx2 < inner_max; idx2++) {
       const double* xyz2 = frmIn.XYZ( InnerMask_[idx2] );
-      double D2;
-      if (isOrtho) {
-        double x = std::fabs(xyz1[0] - xyz2[0]);
-        double y = std::fabs(xyz1[1] - xyz2[1]);
-        double z = std::fabs(xyz1[2] - xyz2[2]);
-        while (x > boxX) x -= boxX;
-        while (y > boxY) y -= boxY;
-        while (z > boxZ) z -= boxZ;
-        double D = boxX - x;
-        if (D < x) x = D;
-        D = boxY - y;
-        if (D < y) y = D;
-        D = boxZ - z;
-        if (D < z) z = D;
-        D2 = x*x + y*y + z*z;
-      }
-      else
-        D2 = DIST2(imageOpt_.ImagingType(), xyz1, xyz2, frmIn.BoxCrd());
+      double D2 = dcalc.Dist2(xyz2);
       if (D2 <= maximum2_) {
       // NOTE: Can we modify the histogram to store D^2?
         double dist = sqrt(D2);
@@ -658,14 +618,19 @@ Action::RetType Action_Radial::DoAction(int frameNum, ActionFrame& frm) {
     {
     //mprintf("OPENMP: %i threads\n",omp_get_num_threads());
     mythread = omp_get_thread_num();
+    Cpptraj::Dcalc dcalc(frm.Frm(), imageOpt_.ImagingType());
 #   pragma omp for
+#   else
+    Cpptraj::Dcalc dcalc(frm.Frm(), imageOpt_.ImagingType());
 #   endif
     for (nmask1 = 0; nmask1 < outer_max; nmask1++) {
       atom1 = OuterMask_[nmask1];
+      dcalc.SetXYZ1( frm.Frm().XYZ(atom1) );
       for (nmask2 = 0; nmask2 < inner_max; nmask2++) {
         atom2 = InnerMask_[nmask2];
         if ( (*currentParm_)[atom1].MolNum() != (*currentParm_)[atom2].MolNum() ) {
-          D = DIST2( imageOpt_.ImagingType(), frm.Frm().XYZ(atom1), frm.Frm().XYZ(atom2), frm.Frm().BoxCrd());
+          //D = DIST2( imageOpt_.ImagingType(), frm.Frm().XYZ(atom1), frm.Frm().XYZ(atom2), frm.Frm().BoxCrd());
+          D = dcalc.Dist2( frm.Frm().XYZ(atom2) );
           if (D <= maximum2_) {
             // NOTE: Can we modify the histogram to store D^2?
             D = sqrt(D);
@@ -692,17 +657,22 @@ Action::RetType Action_Radial::DoAction(int frameNum, ActionFrame& frm) {
 #   pragma omp parallel private(nmask1,D,idx,mythread)
     {
     mythread = omp_get_thread_num();
+    Cpptraj::Dcalc dcalc(frm.Frm(), imageOpt_.ImagingType());
 #   pragma omp for
+#   else
+    Cpptraj::Dcalc dcalc(frm.Frm(), imageOpt_.ImagingType());
 #   endif
     for (nmask1 = 0; nmask1 < mask1_max; nmask1++)
     {
       AtomMask const& site1 = Sites1_[nmask1];
       Vec3 com1 = getCenter( frm.Frm(), site1 );
+      dcalc.SetXYZ1( com1.Dptr() );
       for (Marray::const_iterator site2 = Sites2_.begin(); site2 != Sites2_.end(); ++site2)
       {
         if (site1 != *site2) {
           Vec3 com2 = getCenter( frm.Frm(), *site2 );
-          D = DIST2(imageOpt_.ImagingType(), com1.Dptr(), com2.Dptr(), frm.Frm().BoxCrd());
+          //D = DIST2(imageOpt_.ImagingType(), com1.Dptr(), com2.Dptr(), frm.Frm().BoxCrd());
+          D = dcalc.Dist2( com2.Dptr() );
           if (D <= maximum2_) {
             D = sqrt(D);
             //mprintf("MASKLOOP: %10i %10i %10.4f\n",atom1,atom2,D);
@@ -734,11 +704,17 @@ Action::RetType Action_Radial::DoAction(int frameNum, ActionFrame& frm) {
 #   pragma omp parallel private(nmask2,atom2,D,idx,mythread)
     {
     mythread = omp_get_thread_num();
+    Cpptraj::Dcalc dcalc(frm.Frm(), imageOpt_.ImagingType());
+    dcalc.SetXYZ1( coord_center.Dptr() );
 #   pragma omp for
+#   else
+    Cpptraj::Dcalc dcalc(frm.Frm(), imageOpt_.ImagingType());
+    dcalc.SetXYZ1( coord_center.Dptr() );
 #   endif
     for (nmask2 = 0; nmask2 < mask2_max; nmask2++) {
       atom2 = InnerMask_[nmask2];
-      D = DIST2(imageOpt_.ImagingType(), coord_center.Dptr(), frm.Frm().XYZ(atom2), frm.Frm().BoxCrd());
+      D = dcalc.Dist2( frm.Frm().XYZ(atom2) );
+      //D = DIST2(imageOpt_.ImagingType(), coord_center.Dptr(), frm.Frm().XYZ(atom2), frm.Frm().BoxCrd());
       if (D <= maximum2_) {
         // NOTE: Can we modify the histogram to store D^2?
         D = sqrt(D);
diff --git a/src/Dcalc.h b/src/Dcalc.h
new file mode 100644
index 0000000000..a081b92ae0
--- /dev/null
+++ b/src/Dcalc.h
@@ -0,0 +1,144 @@
+#ifndef INC_CPPTRAJ_DCALC_H
+#define INC_CPPTRAJ_DCALC_H
+#include "Frame.h" // will bring in Vec3, Matrix_3x3, Box
+#include <limits> // std::numeric_limits
+#include <cmath> // std::fabs
+namespace Cpptraj {
+/** Class for implementing multiple distance calcs for a single frame. */
+class Dcalc {
+  public:
+    /// CONSTRUCTOR
+    Dcalc( Frame const& frmIn, ImageOption::Type itype) :
+      ucell_( frmIn.BoxCrd().UnitCell() ),
+      fcell_( frmIn.BoxCrd().FracCell() ),
+      boxX_( frmIn.BoxCrd().Param(Box::X) ),
+      boxY_( frmIn.BoxCrd().Param(Box::Y) ),
+      boxZ_( frmIn.BoxCrd().Param(Box::Z) ),
+      xyz1_(0),
+      itype_(ImageOption::NO_IMAGE)
+    {
+      if (boxX_ != 0.0 && boxY_ != 0.0 && boxZ_ != 0.0) {
+        itype_ = itype;
+      }
+    }
+    /// Set xyz1 - typically the coordinate from an outer loop
+    void SetXYZ1(const double* xyz1) {
+      xyz1_ = xyz1;
+      if (itype_ == ImageOption::NONORTHO) {
+        f1_ = fcell_ * Vec3(xyz1_);
+        wrap_frac(f1_);
+      }
+    }
+  private:
+    // ---------------------------------------------------------------
+    /// \return Dist^2 for xyz2 from previously set xyz1, orthogonal imaging
+    double Dist2_ortho(const double* xyz2) const
+    {
+      double x = xyz1_[0] - xyz2[0];
+      double y = xyz1_[1] - xyz2[1];
+      double z = xyz1_[2] - xyz2[2];
+      x = std::fabs(x);
+      y = std::fabs(y);
+      z = std::fabs(z);
+      while (x > boxX_) x -= boxX_;
+      while (y > boxY_) y -= boxY_;
+      while (z > boxZ_) z -= boxZ_;
+      double D = boxX_ - x;
+      if (D < x) x = D;
+      D = boxY_ - y;
+      if (D < y) y = D;
+      D = boxZ_ - z;
+      if (D < z) z = D;
+      return (x*x + y*y + z*z);
+    }
+    // ---------------------------------------------------------------
+    /// Bring each fractional coordinate back into the main unit cell (0 to 1)
+    static inline void wrap_frac(Vec3& frac) {
+      for (int idx = 0; idx != 3; idx++) {
+        while (frac[idx] < 0.0)
+          frac[idx] += 1.0;
+        while (frac[idx] > 1.0)
+          frac[idx] -= 1.0;
+      }
+    }
+    /// \return Dist^2 for xyz2 from previously set xyz1, non-orthogonal imaging
+    double Dist2_nonortho(const double* xyz2) const
+    {
+      // Wrap each coordinate in fractional coordinates back to the main unit cell
+      // (so each frac coord is between 0 and 1).
+      Vec3 f2 = fcell_ * Vec3(xyz2);
+      wrap_frac(f2);
+      // Calculate f2 to f1 in fractional space
+      Vec3 fdelta = f2 - f1_;
+      //fdelta.Print("fdelta");
+      // Set the min and max cell indices we need to look for based
+      // on the f1->f2 vector.
+      int imin[3];
+      int imax[3];
+      for (int idx = 0; idx != 3; idx++) {
+        if (fdelta[idx] < 0) {
+          imin[idx] = -1;
+          imax[idx] = 1;
+        } else {
+          imin[idx] = 0;
+          imax[idx] = 2;
+        }
+      }
+      // Calculate wrapped f2 back in Cartesian space
+      Vec3 c2 = ucell_.TransposeMult( f2 );
+      // Searching only images we are close to.
+      // Check each image of f1 to determine which distance is the smallest.
+      double minD2 = std::numeric_limits<double>::max();
+      for (int ix = imin[0]; ix != imax[0]; ix++) {
+        for (int iy = imin[1]; iy != imax[1]; iy++) {
+          for (int iz = imin[2]; iz != imax[2]; iz++) {
+            // Image in frac space
+            Vec3 f1img = f1_ + Vec3(ix, iy, iz);
+            // Image in Cartesian space
+            Vec3 c1img = ucell_.TransposeMult( f1img );
+            // Calculate distance in Cartesian space
+            double dx = (c1img[0] - c2[0]);
+            double dy = (c1img[1] - c2[1]);
+            double dz = (c1img[2] - c2[2]);
+            double D2 = (dx*dx) + (dy*dy) + (dz*dz);
+            if (D2 < minD2) {
+              minD2 = D2;
+            }
+          } // END loop over Z image indices
+        } // END loop over Y image indices
+      } // END loop over X image indices
+      //mprintf("minD %12.4f\n", sqrt(minD2));
+      return minD2;
+    }
+    // ---------------------------------------------------------------
+    /// \return Dist^2 for xyz2 from previously set xyz1, no imaging
+    double Dist2_noimage(const double* xyz2) const
+    {
+      double x = xyz1_[0] - xyz2[0];
+      double y = xyz1_[1] - xyz2[1];
+      double z = xyz1_[2] - xyz2[2];
+      //double D = x*x + y*y + z*z;
+      //fprintf(stdout,"Mask1=%8.3f %8.3f %8.3f Mask2=%8.3f %8.3f %8.3f D=%8.3f\n",
+      //        a1[0],a1[1],a1[2],a2[0],a2[1],a2[2],D);
+      return (x*x + y*y + z*z);
+     }
+  public:
+    /// \return Dist^2 for xyz2 from previously set xyz1
+    double Dist2(const double* xyz2) const {
+      switch (itype_) {
+        case ImageOption::ORTHO : return Dist2_ortho(xyz2);
+        case ImageOption::NONORTHO : return Dist2_nonortho(xyz2);
+        case ImageOption::NO_IMAGE : return Dist2_noimage(xyz2);
+      }
+      return -1.0;
+    }
+  private:
+    Matrix_3x3 const& ucell_;
+    Matrix_3x3 const& fcell_;
+    Vec3 f1_;
+    double boxX_, boxY_, boxZ_;
+    const double* xyz1_;
+    ImageOption::Type itype_;
+};
+}
+#endif
diff --git a/src/DistRoutines.cpp b/src/DistRoutines.cpp
index b83891d00e..4dbfa37335 100644
--- a/src/DistRoutines.cpp
+++ b/src/DistRoutines.cpp
@@ -1,6 +1,7 @@
-#include <cmath> // sqrt
 #include "DistRoutines.h"
-#include "Box.h"
+#include "Dist_Imaged.h"
+#include "Matrix_3x3.h"
+#include <cmath> // sqrt
 
 /** \param a1 First set of XYZ coordinates.
   * \param a2 Second set of XYZ coordinates.
@@ -346,7 +347,8 @@ double DIST2_ImageNonOrtho(Vec3 const& a1, Vec3 const& a2,
                            Matrix_3x3 const& ucell, Matrix_3x3 const& recip) 
 { 
   int ixyz[3];
-  return DIST2_ImageNonOrthoRecip(recip * a2, recip * a1, -1.0, ixyz, ucell);
+  //return DIST2_ImageNonOrthoRecip(recip * a2, recip * a1, -1.0, ixyz, ucell);
+  return Cpptraj::Dist2_Imaged_Cart(a1, a2, ucell, recip, ixyz);
 }
 
 /** \param a1 First set of XYZ coordinates.
@@ -359,51 +361,18 @@ double DIST2_ImageNonOrtho(const double* a1, const double* a2,
                            Matrix_3x3 const& ucell, Matrix_3x3 const& recip)
 {
   int ixyz[3];
-  Vec3 f1( ((recip[0]*a1[0]) + (recip[1]*a1[1]) + (recip[2]*a1[2])),
-           ((recip[3]*a1[0]) + (recip[4]*a1[1]) + (recip[5]*a1[2])),
-           ((recip[6]*a1[0]) + (recip[7]*a1[1]) + (recip[8]*a1[2]))  );
-  Vec3 f2( ((recip[0]*a2[0]) + (recip[1]*a2[1]) + (recip[2]*a2[2])),
-           ((recip[3]*a2[0]) + (recip[4]*a2[1]) + (recip[5]*a2[2])),
-           ((recip[6]*a2[0]) + (recip[7]*a2[1]) + (recip[8]*a2[2]))  );
-  return DIST2_ImageNonOrthoRecip(f1, f2, -1.0, ixyz, ucell);
+//  Vec3 f1( ((recip[0]*a1[0]) + (recip[1]*a1[1]) + (recip[2]*a1[2])),
+//           ((recip[3]*a1[0]) + (recip[4]*a1[1]) + (recip[5]*a1[2])),
+//           ((recip[6]*a1[0]) + (recip[7]*a1[1]) + (recip[8]*a1[2]))  );
+//  Vec3 f2( ((recip[0]*a2[0]) + (recip[1]*a2[1]) + (recip[2]*a2[2])),
+//           ((recip[3]*a2[0]) + (recip[4]*a2[1]) + (recip[5]*a2[2])),
+//           ((recip[6]*a2[0]) + (recip[7]*a2[1]) + (recip[8]*a2[2]))  );
+//  return DIST2_ImageNonOrthoRecip(f1, f2, -1.0, ixyz, ucell);
+  return Cpptraj::Dist2_Imaged_Cart(Vec3(a1), Vec3(a2), ucell, recip, ixyz);
 }
 
-// Frame::DIST2_ImageOrtho()
-/** Return the minimum orthorhombic imaged distance^2 between coordinates a1 
-  * and a2.
-  */
-
-/** Return the minimum orthorhombic imaged distance^2 between coordinates a1 
-  * and a2.
-  */
-double DIST2_ImageOrtho(Vec3 const& a1, Vec3 const& a2, Box const& box) {
-  return DIST2_ImageOrtho(a1.Dptr(), a2.Dptr(), box);
-}
-
-// Frame::DIST2_NoImage()
-/** Return distance^2 between coordinates in a1 and a2.
-  */
-
-/// \return Distance squared, no imaging.
-double DIST2_NoImage( Vec3 const& a1, Vec3 const& a2 ) {
-  Vec3 vec = a1 - a2;
-  return vec.Magnitude2();
-}
-
-/// \return Distance, no imaging.
+/** \return Distance, no imaging.*/
 double DIST_NoImage( Vec3 const& a1, Vec3 const& a2 ) {
   Vec3 vec = a1 - a2;
   return sqrt( vec.Magnitude2() );
 }
-
-/** \return Distance squared using either minimum-image convention or no imaging. */
-
-/** \return Distance squared using either minimum-image convention or no imaging. */
-double DIST2(ImageOption::Type itype, Vec3 const& a1, Vec3 const& a2, Box const& box) {
-  return DIST2(itype, a1.Dptr(), a2.Dptr(), box);
-}
-
-/** \return Distance using either minimum-image convention or no imaging. */
-double DIST(ImageOption::Type itype, Vec3 const& a1, Vec3 const& a2, Box const& box) {
-  return sqrt(DIST2(itype, a1.Dptr(), a2.Dptr(), box));
-}
diff --git a/src/DistRoutines.h b/src/DistRoutines.h
index 53d39fcd21..1abead4a8d 100644
--- a/src/DistRoutines.h
+++ b/src/DistRoutines.h
@@ -1,8 +1,10 @@
 #ifndef INC_DISTROUTINES_H
 #define INC_DISTROUTINES_H
 #include <cmath>
+#include "Vec3.h"
 #include "Box.h"
 #include "ImageOption.h"
+class Matrix_3x3;
 /*! \file DistRoutines.h
     \brief A collection of routines used to calculate distance.
  */
@@ -19,9 +21,14 @@ double DIST2_ImageNonOrtho(Vec3 const&, Vec3 const&, Matrix_3x3 const&, Matrix_3
 /// \return Distance squared between points in Cartesian space, general unit cell imaging.
 double DIST2_ImageNonOrtho(const double*, const double*, Matrix_3x3 const&, Matrix_3x3 const&);
 
-/// \return Distance squared, X-aligned and orthogonal imaging.
-inline double DIST2_ImageOrtho(const double* a1, const double* a2,
-                               Box const& box)
+/// \return Distance, no imaging.
+double DIST_NoImage( Vec3 const&, Vec3 const& );
+
+// ----- Inline Routines -------------------------
+/** \return the minimum orthorhombic imaged distance^2 between coordinates a1 
+  *         and a2.
+  */
+inline double DIST2_ImageOrtho(const double* a1, const double* a2, Box const& box)
 {
   const double boxX = box.Param(Box::X);
   const double boxY = box.Param(Box::Y);
@@ -47,35 +54,44 @@ inline double DIST2_ImageOrtho(const double* a1, const double* a2,
 
   return x*x + y*y + z*z;
 }
-/// \return Distance squared, X-aligned and orthogonal imaging.
-double DIST2_ImageOrtho(Vec3 const&, Vec3 const&, Box const&);
 
-/// \return Distance squared, no imaging.
-inline double DIST2_NoImage(const double* a1, const double* a2)
-{
+/** \return the minimum orthorhombic imaged distance^2 between coordinates a1 
+  *         and a2.
+  */
+inline double DIST2_ImageOrtho(Vec3 const& a1, Vec3 const& a2, Box const& box) {
+  return DIST2_ImageOrtho(a1.Dptr(), a2.Dptr(), box);
+}
+
+/// \return distance^2 between coordinates in a1 and a2.
+inline double DIST2_NoImage(const double* a1, const double* a2) {
   const double x = a1[0] - a2[0];
   const double y = a1[1] - a2[1];
   const double z = a1[2] - a2[2];
-  return x*x + y*y + z*z;
+  //double D = x*x + y*y + z*z;
+  //fprintf(stdout,"Mask1=%8.3f %8.3f %8.3f Mask2=%8.3f %8.3f %8.3f D=%8.3f\n",
+  //        a1[0],a1[1],a1[2],a2[0],a2[1],a2[2],D);
+  return (x*x + y*y + z*z);
 }
-/// \return Distance squared, no imaging
-double DIST2_NoImage( Vec3 const&, Vec3 const& );
-/// \return Distance, no imaging.
-double DIST_NoImage( Vec3 const&, Vec3 const& );
 
-/// \return Distance squared using minimum-image convention or no imaging.
-inline double DIST2(ImageOption::Type itype, const double* a1,
-                    const double* a2, Box const& box)
-{
+/// \return Distance squared, no imaging.
+inline double DIST2_NoImage( Vec3 const& a1, Vec3 const& a2 ) {
+  Vec3 vec = a1 - a2;
+  return vec.Magnitude2();
+}
+
+/** \return Distance squared using either minimum-image convention or no imaging. */
+inline double DIST2(ImageOption::Type itype, const double* a1, const double* a2, Box const& box) {
   if (itype == ImageOption::NO_IMAGE)
     return DIST2_NoImage(a1, a2);
   else if (itype == ImageOption::ORTHO)
     return DIST2_ImageOrtho(a1, a2, box);
-  else
+  else // NONORTHO
     return DIST2_ImageNonOrtho(a1, a2, box.UnitCell(), box.FracCell());
 }
-// \return Distance squared using minimum-image convention or no imaging.
-double DIST2(ImageOption::Type, Vec3 const&, Vec3 const&, Box const&);
-// \return Distance using minimum-image convention or no imaging.
-double DIST(ImageOption::Type, Vec3 const&, Vec3 const&, Box const&);
+
+/** \return Distance squared using either minimum-image convention or no imaging. */
+inline double DIST2(ImageOption::Type itype, Vec3 const& a1, Vec3 const& a2, Box const& box) {
+  return DIST2(itype, a1.Dptr(), a2.Dptr(), box);
+}
+
 #endif
diff --git a/src/Dist_Imaged.cpp b/src/Dist_Imaged.cpp
index efc75024d8..0d78f0a024 100644
--- a/src/Dist_Imaged.cpp
+++ b/src/Dist_Imaged.cpp
@@ -93,7 +93,7 @@ double Cpptraj::Dist2_Imaged(Vec3 const& xyz1, Vec3 const& xyz2,
   * TODO use in place of DIST2_ImageNonOrthoRecip()
   */
 double Cpptraj::Dist2_Imaged_Frac(Vec3 const& f1, Vec3 const& f2,
-                                  Matrix_3x3 const& ucell, Matrix_3x3 const& fcell,
+                                  Matrix_3x3 const& ucell,
                                   int* ixyz)
 {
   // Calculate f2 to f1 in fractional space
@@ -185,5 +185,5 @@ double Cpptraj::Dist2_Imaged_Cart(Vec3 const& xyz1, Vec3 const& xyz2,
   wrap_frac(f1);
   wrap_frac(f2);
 
-  return Dist2_Imaged_Frac(f1, f2, ucell, fcell, ixyz);
+  return Dist2_Imaged_Frac(f1, f2, ucell, ixyz);
 }
diff --git a/src/Dist_Imaged.h b/src/Dist_Imaged.h
index d1894376b2..341247f10a 100644
--- a/src/Dist_Imaged.h
+++ b/src/Dist_Imaged.h
@@ -6,7 +6,7 @@ namespace Cpptraj {
 /// Calculate minimum imaged distance (squared) between two coordinates in Cartesian space
 double Dist2_Imaged(Vec3 const&, Vec3 const&, Matrix_3x3 const&, Matrix_3x3 const&, int*);
 /// Calculate minimum imaged distance (squared) between two fractional coords in the primary cell
-double Dist2_Imaged_Frac(Vec3 const&, Vec3 const&, Matrix_3x3 const&, Matrix_3x3 const&, int*);
+double Dist2_Imaged_Frac(Vec3 const&, Vec3 const&, Matrix_3x3 const&, int*);
 /// Calculate minimum imaged distance (squared) between two coordinates in Cartesian space
 double Dist2_Imaged_Cart(Vec3 const&, Vec3 const&, Matrix_3x3 const&, Matrix_3x3 const&, int*);
 }
diff --git a/src/Topology.cpp b/src/Topology.cpp
index fe887bc984..11734e690a 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -698,6 +698,57 @@ int Topology::CommonSetup(bool molsearch, bool renumberResidues)
   // Determine # of extra points.
   DetermineNumExtraPoints();
 
+  // Check for duplicate atom names in residues
+//  Timer t_anamecheck;
+//  t_anamecheck.Start();
+  if (!atom_altloc_.empty() || lesparm_.HasLES()) {
+    // If alternate location IDs are present, append to name to check for true uniqueness
+    std::set<std::string> anames;
+    for (std::vector<Residue>::const_iterator res = residues_.begin(); res != residues_.end(); ++res)
+    {
+      // Skip solvent.
+      bool is_solvent = false;
+      if (!molecules_.empty()) is_solvent = molecules_[atoms_[res->FirstAtom()].MolNum()].IsSolvent();
+      if (!is_solvent) {
+        anames.clear();
+        for (int iat = res->FirstAtom(); iat != res->LastAtom(); iat++)
+        {
+          std::string aname(atoms_[iat].Name().Truncated());
+          if (!atom_altloc_.empty())
+            aname += atom_altloc_[iat];
+          if (lesparm_.HasLES())
+            aname.append( integerToString( lesparm_.Array()[iat].Copy() ) );
+          std::pair<std::set<std::string>::iterator, bool> ret = anames.insert( aname );
+          if (!ret.second) {
+            mprintf("Warning: '%s': In residue %s duplicate atom name detected: %s\n",
+                    c_str(), TruncResNameNum(res-residues_.begin()).c_str(), ret.first->c_str() );
+          }
+        }
+      }
+    }
+  } else {
+    std::set<NameType> anames;
+    for (std::vector<Residue>::const_iterator res = residues_.begin(); res != residues_.end(); ++res)
+    {
+      // Skip solvent.
+      bool is_solvent = false;
+      if (!molecules_.empty()) is_solvent = molecules_[atoms_[res->FirstAtom()].MolNum()].IsSolvent();
+      if (!is_solvent) {
+        anames.clear();
+        for (int iat = res->FirstAtom(); iat != res->LastAtom(); iat++)
+        {
+          std::pair<std::set<NameType>::iterator, bool> ret = anames.insert( atoms_[iat].Name() );
+          if (!ret.second) {
+            mprintf("Warning: '%s': In residue %s duplicate atom name detected: %s\n",
+                    c_str(), TruncResNameNum(res-residues_.begin()).c_str(), *(atoms_[iat].Name()) );
+          }
+        }
+      }
+    }
+  }
+//  t_anamecheck.Stop();
+//  t_anamecheck.WriteTiming(1, "Atom Name Check");
+
   return 0;
 }
 
diff --git a/src/Version.h b/src/Version.h
index 96e636a0a6..8104cb0dc1 100644
--- a/src/Version.h
+++ b/src/Version.h
@@ -12,7 +12,7 @@
  * Whenever a number that precedes <revision> is incremented, all subsequent
  * numbers should be reset to 0.
  */
-#define CPPTRAJ_INTERNAL_VERSION "V7.12.0"
+#define CPPTRAJ_INTERNAL_VERSION "V7.12.5"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index 466d8ad4d7..4c418b2919 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -69,7 +69,7 @@ Action_Principal.o : Action_Principal.cpp Action.h ActionState.h Action_Principa
 Action_Projection.o : Action_Projection.cpp Action.h ActionFrameCounter.h ActionState.h Action_Projection.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Modes.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Pucker.o : Action_Pucker.cpp Action.h ActionState.h Action_Pucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Action_Radgyr.o : Action_Radgyr.cpp Action.h ActionState.h Action_Radgyr.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
-Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_rdf.cuh
+Action_Radial.o : Action_Radial.cpp Action.h ActionState.h Action_Radial.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dcalc.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Gpu.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h cuda_kernels/kernel_rdf.cuh
 Action_RandomizeIons.o : Action_RandomizeIons.cpp Action.h ActionState.h Action_RandomizeIons.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_Remap.o : Action_Remap.cpp Action.h ActionState.h ActionTopWriter.h Action_Remap.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 Action_ReplicateCell.o : Action_ReplicateCell.cpp Action.h ActionFrameCounter.h ActionState.h ActionTopWriter.h Action_ReplicateCell.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h Unit.h Vec3.h
@@ -196,7 +196,7 @@ CmapParmHolder.o : CmapParmHolder.cpp CmapParmHolder.h Constants.h CpptrajStdio.
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_AddAtom.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_ConvertToFrac.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_EneDecomp.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SurfaceTension.h Action_SymmetricRmsd.h Action_Temperature.h Action_Test.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy/Ecalc_Nonbond.h Energy/EnergyDecomposer.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h EwaldOptions.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_Flush.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_Mutate.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParallelSetFrameNum.h ParameterTypes.h Parm/GB_Params.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_AddAtom.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_ConvertToFrac.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_EneDecomp.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_MinMaxDist.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SurfaceTension.h Action_SymmetricRmsd.h Action_Temperature.h Action_Test.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Project.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy/Ecalc_Nonbond.h Energy/EnergyDecomposer.h Energy/ErfcFxn.h Energy/EwaldParams.h Energy/PME_RecipParams.h Energy/VDW_LongRange_Correction.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h EwaldOptions.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Build.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Desc.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_Flush.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_Mutate.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_Source.h Exec_SplitCoords.h Exec_System.h Exec_TIMap.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h GridMover.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h InteractionData.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParallelSetFrameNum.h ParameterTypes.h Parm/GB_Params.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TIMatch.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
@@ -288,7 +288,7 @@ DataSet_unsignedInt.o : DataSet_unsignedInt.cpp AssociatedData.h CpptrajFile.h D
 Deprecated.o : Deprecated.cpp CpptrajStdio.h Deprecated.h DispatchObject.h
 DiffusionResults.o : DiffusionResults.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DiffusionResults.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h Unit.h Vec3.h
 DihedralSearch.o : DihedralSearch.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DihedralSearch.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
-DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
+DistRoutines.o : DistRoutines.cpp Box.h DistRoutines.h Dist_Imaged.h ImageOption.h Matrix_3x3.h Parallel.h Vec3.h
 Dist_Imaged.o : Dist_Imaged.cpp Dist_Imaged.h Matrix_3x3.h Parallel.h Vec3.h
 Energy.o : Energy.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h Energy.h Energy/Ene_Angle.h Energy/Ene_Bond.h Energy/Ene_LJ_12_6_4.h Energy/Ene_LJ_6_12.h Energy/Kernel_Harmonic.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 Energy/CMAP.o : Energy/CMAP.cpp ArrayIterator.h Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h Energy/CMAP.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h Unit.h Vec3.h
@@ -376,6 +376,7 @@ Exec_SortEnsembleData.o : Exec_SortEnsembleData.cpp Action.h ActionList.h Action
 Exec_Source.o : Exec_Source.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataIO.h DataIO_LeapRC.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Source.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_SplitCoords.o : Exec_SplitCoords.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SplitCoords.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_System.o : Exec_System.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_System.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
+Exec_TIMap.o : Exec_TIMap.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_TIMap.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TIMatch.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h Trajout_Single.h Unit.h Vec3.h
 Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Top.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h TopInfo.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h Unit.h Vec3.h
 Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CmapParmHolder.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Parm/AssignParams.h Parm/DihedralParmHolder.h Parm/GetParams.h Parm/ImproperParmHolder.h Parm/ParameterSet.h Parm/ParmEnum.h Parm/ParmHolder.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -420,7 +421,7 @@ KDE.o : KDE.cpp AssociatedData.h Constants.h CpptrajFile.h CpptrajStdio.h DataSe
 LeapInterface.o : LeapInterface.cpp ArgList.h Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h File_TempName.h Frame.h LeapInterface.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Topology.h Unit.h Vec3.h
 MapAtom.o : MapAtom.cpp Atom.h MapAtom.h NameType.h SymbolExporting.h
 MaskArray.o : MaskArray.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskArray.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h Unit.h Vec3.h
-MaskToken.o : MaskToken.cpp ArgList.h Atom.h CpptrajStdio.h DistRoutines.h ImageOption.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h
+MaskToken.o : MaskToken.cpp ArgList.h Atom.h Box.h CpptrajStdio.h DistRoutines.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h Residue.h Segment.h StringRoutines.h SymbolExporting.h Unit.h Vec3.h
 Matrix_3x3.o : Matrix_3x3.cpp Constants.h CpptrajStdio.h Matrix_3x3.h Parallel.h Vec3.h
 MdOpts.o : MdOpts.cpp ArgList.h Constants.h Constraints.h CpptrajStdio.h MdOpts.h ParameterTypes.h
 MetaData.o : MetaData.cpp CpptrajStdio.h FileName.h MetaData.h Range.h StringRoutines.h
@@ -519,6 +520,7 @@ Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h Box.h Constants.h
 StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileIO.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h PairList.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/LeastSquaresPlane.h Structure/RingFinder.h StructureCheck.h SymbolExporting.h Timer.h Topology.h Unit.h Vec3.h
 StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h Unit.h Vec3.h
 SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h Unit.h Vec3.h
+TIMatch.o : TIMatch.cpp Atom.h AtomMask.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h ModXNA_Info.h Molecule.h NameType.h Parallel.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TIMatch.h Topology.h Unit.h Vec3.h
 TextBlockBuffer.o : TextBlockBuffer.cpp BufferedLine.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h Parallel.h TextBlockBuffer.h
 TextFormat.o : TextFormat.cpp StringRoutines.h TextFormat.h
 Timer.o : Timer.cpp CpptrajStdio.h Timer.h