zStackingOverlap

 zStackingOverlap(N1,N2) computes a measure of overlap between nucleotides
 N1 and N2, by projecting N2 onto the plane of N1.

0001 % zStackingOverlap(N1,N2) computes a measure of overlap between nucleotides
0002 % N1 and N2, by projecting N2 onto the plane of N1.
0003 
0004 function [SO] = zStackingOverlap(N1,N2)
0005 
0006 switch N1.Code,
0007   case 1,
0008 X = [[ -2.100463  0.000000  4.271447  1.920945  0.230436 -2.100463]; ...
0009      [  0.447145 -1.009320  1.317924  5.150733  4.699718  0.447145]]';
0010 t = [[    5    5    5]; ...
0011      [    2    4    2]; ...
0012      [    6    3    3]]';
0013   case 2,
0014 X = [[ -2.082733  0.000000  2.269450  1.203833 -0.527970 -2.036772 -2.082733]; ...
0015      [  0.123632 -1.010259 -0.120783  4.411996  4.602202  2.647095  0.123632]]';
0016 t = [[    6    6    4    4]; ...
0017      [    2    2    6    6]; ...
0018      [    7    3    3    5]]';
0019   case 3,
0020 X = [[ -2.101572  0.000000  4.872516  5.295175  3.613335  1.396986 -0.751391 -2.101572]; ...
0021      [  0.463584 -1.009529  0.097781  1.782283  3.374547  4.394213  2.120132  0.463584]]';
0022 t = [[    7    5    5    5    5]; ...
0023      [    2    7    3    7    3]; ...
0024      [    8    2    2    6    4]]';
0025   case 4,
0026 X = [[ -2.082780  0.000000  2.292490  2.092152  0.177156 -2.124577 -2.082780]; ...
0027      [  0.111836 -1.008947 -0.048394  2.445179  4.020060  2.616537  0.111836]]';
0028 t = [[    4    4    7    7]; ...
0029      [    5    2    4    4]; ...
0030      [    6    3    6    2]]';
0031 end
0032 
0033 S = N1.Fit(1,:);
0034 R = N1.Rot;
0035 L = length(N2.Fit(:,1));         % Number of base atoms
0036 Y = (N2.Fit   - ones(L,1)*S) * R; % rotated into position
0037 
0038 warning off
0039 
0040 d = tsearch(X(:,1),X(:,2),t,Y(:,1),Y(:,2));
0041 
0042 warning on
0043 
0044 SO = length(find(d < 100));
0045 
0046 %figure(2)
0047 %clf
0048 %plot(X(:,1),X(:,2),'k');
0049 %hold on
0050 %plot(Y(:,1),Y(:,2),'*');