ADDED   mttroot/mtt/bin/trans/m/adjbond.m
Index: mttroot/mtt/bin/trans/m/adjbond.m
==================================================================
--- /dev/null
+++ mttroot/mtt/bin/trans/m/adjbond.m
@@ -0,0 +1,27 @@
+function [index,distance] = adjbond(point,arrow_end,other_end);
+% adjbond:  Determines the bond closest to the point 
+%  [index,distance] = adjbond(point,arrow_end,other_end);
+
+
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %% Version control history
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %% $Id$
+% %% $Log$
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+[n,m] = size(other_end);
+one = ones(n,1);
+arrow_distance = length2d(one*point - arrow_end);
+min_arrow_distance = min(arrow_distance);
+
+other_distance = length2d(one*point - other_end);
+min_other_distance = min(other_distance);
+
+min_distance = min([arrow_distance; other_distance]);
+
+adjacent = [arrow_distance, other_distance] == min_distance*[one one];
+[index,n] = getindex(adjacent,1);
+distance = min_distance;
+

ADDED   mttroot/mtt/bin/trans/m/adjcomp.m
Index: mttroot/mtt/bin/trans/m/adjcomp.m
==================================================================
--- /dev/null
+++ mttroot/mtt/bin/trans/m/adjcomp.m
@@ -0,0 +1,33 @@
+function indices = adjcomp(arrow_end,other_end,components);
+% adjcomp: Determines the two components at each end of the bond
+
+
+
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %% Version control history
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %% $Id$
+% %% $Log$
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+[n,m] = size(components);
+one = ones(n,1);
+
+arrow_distance = length2d(one*arrow_end - components(:,1:2));
+min_arrow_distance = min(arrow_distance);
+
+other_distance = length2d(one*other_end - components(:,1:2));
+min_other_distance = min(other_distance);
+
+arrow_adjacent = arrow_distance==min_arrow_distance*one;
+other_adjacent = other_distance==min_other_distance*one;
+[index,n] = getindex([arrow_adjacent,other_adjacent],1);
+
+if index(1,2)==1
+  indices = index(1:2,1)';
+else
+  indices = index(2:-1:1,1)';
+end;
+
+

ADDED   mttroot/mtt/bin/trans/m/getindex.m
Index: mttroot/mtt/bin/trans/m/getindex.m
==================================================================
--- /dev/null
+++ mttroot/mtt/bin/trans/m/getindex.m
@@ -0,0 +1,46 @@
+function [index, n, otherindex, m] = getindex(array,value);
+% Finds the n indices of the elements of array equal to value
+% otherindex contains indeces of the the m other  elements.
+
+
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %% Version control history
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %% $Id$
+% %% $Log$
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+[N,M] = size(array);
+n=0; m=0;
+for i=1:N
+  for j = 1:M
+    if array(i,j)==value
+      n=n+1;
+      index(n,:) = [i j];
+    else
+      m=m+1;
+      otherindex(m,:) = [i j];
+    end;
+  end;
+end;
+
+
+if (M==1)&(n>0)
+  index = index(:,1);
+end;
+
+if (M==1)&(m>0)
+  otherindex = otherindex(:,1);
+end;
+
+% Octave doesn't like empty matrices
+if n==0
+  index=0;
+end;
+
+if m==0
+  otherindex=0;
+end;
+
+
+