(* file geomanal/ramachandran.math  -- Make a Ramachandran plot *)

Off[General::spell1];
$DefaultFont={"Times-Roman",13};

                                     (* Change the name of the input file. *)
 (*===>*)  
  data=ReadList["ramachandran.list",{Number,Number,Number}];

  column1 = Transpose[data][[1]]; 
  column2 = Transpose[data][[2]]; 
  column3 = Transpose[data][[3]];

  number=Dimensions[column1][[1]];
  
            (* If it is a GLY residue, X-PLOR wrote a 0 and we make a "o"; *)
            (* otherwise we make an "x".                                   *)
  Data=Table[ Which[ column1[[i]]==1,
                     Text[FontForm[x, {"Plain", 6}],
                       { column2[[i]], column3[[i]] } ] ,
                   column1[[i]]==0,
                     Text[FontForm[o, {"Plain", 6}],
                       { column2[[i]], column3[[i]] } ] ],
           { i,  number }];

                   (* Make the "allowed" regions of the Ramachandran plot. *)
 Data=Join[Data,{
  Line[{{-156.5,91.3},{-70.4,91.3},{-54.7,112.8},{-54.7,173.2},
       {-136.95,173.2},{-136.9,155.8},{-156.5,135.6},{-156.5,91.3}}],
  Line[{{-180.,42.9},{-140.8,16.1},{-86.0,16.1},{-74.3,45.6},
       {-74.3,72.5},{-44.3,102.0},{-44.3,161.1},{-46.9,179.9}}],
  Line[{{-180.,-34.9},{-164.3,-42.9},{-133.0,-42.9},{-109.5,-32.2},
       {-106.9,-21.4},{-44.3,-21.4},{-44.3,-71.1},{-180.,-71.1}}],
  Line[{{-156.5,-60.4},{-54.7,-60.4},{-54.7,-40.2},{-100.4,-40.2},
       {-123.9,-51.0},{-156.5,-51.0},{-156.5,-60.4}}],
  Line[{{-180.,-163.8},{-75.6,-163.8},{-46.9,-180.}}],
  Line[{{62.6,14.7},{62.6,96.7},{45.6,79.2},{45.6,26.8},{62.6,14.7}}]
        }] ;

  Show[Graphics[ Data,
    Ticks->{Range[-180.,180.,60.],Range[-180.,180.,60.]},
    AxesOrigin->{-180.,-180.},
    PlotRange->{{-180., +180.}, {-180., +180.}},
    AspectRatio->1,
    Frame->True,
    Axes->True,
    AxesLabel->{"phi","psi"},PlotLabel->"Ramachandran Plot" 
    ]];