import three; import cpkcolors; // A sample Protein Data Bank file for this example is available from // http://ndbserver.rutgers.edu/ftp/NDB/coordinates/na-biol/100d.pdb1 currentlight=White; //currentlight=nolight; defaultrender.merge=true; // Fast low-quality rendering //defaultrender.merge=false; // Slow high-quality rendering bool pixel=false; // Set to true to draw dots as pixels. real width=10*linewidth(currentpen); size(200); currentprojection=perspective(30,30,15); pen chainpen=green; pen hetpen=purple; string filename="100d.pdb1"; //string filename=getstring("filename"); string prefix=stripextension(filename); file data=input(filename); pen color(string e) { e=replace(e," ",""); int n=length(e); if(n < 1) return currentpen; if(n > 1) e=substr(e,0,1)+downcase(substr(e,1,n-1)); int index=find(Element == e); if(index < 0) return currentpen; return rgb(Hexcolor[index]); } // ATOM string[] name,altLoc,resName,chainID,iCode,element,charge; int[] serial,resSeq; real[][] occupancy,tempFactor; bool newchain=true; struct bond { int i,j; void operator init(int i, int j) { this.i=i; this.j=j; } } bond[] bonds; struct atom { string name; triple v; void operator init(string name, triple v) { this.name=name; this.v=v; } } struct chain { int[] serial; atom[] a; } int[] serials; chain[] chains; atom[] atoms; while(true) { string line=data; if(eof(data)) break; string record=replace(substr(line,0,6)," ",""); if(record == "TER") {newchain=true; continue;} bool ATOM=record == "ATOM"; bool HETATOM=record == "HETATM"; int serial; atom a; if(ATOM || HETATOM) { serial=(int) substr(line,6,5); a.name=substr(line,76,2); a.v=((real) substr(line,30,8), (real) substr(line,38,8), (real) substr(line,46,8)); } if(ATOM) { if(newchain) { chains.push(new chain); newchain=false; } chain c=chains[chains.length-1]; c.serial.push(serial); c.a.push(a); continue; } if(HETATOM) { serials.push(serial); atoms.push(a); } if(record == "CONECT") { int k=0; int i=(int) substr(line,6,5); while(true) { string s=replace(substr(line,11+k,5)," ",""); if(s == "") break; k += 5; int j=(int) s; if(j <= i) continue; bonds.push(bond(i,j)); } } } write("Number of atomic chains: ",chains.length); int natoms; begingroup3("chained"); for(chain c : chains) { for(int i=0; i < c.a.length-1; ++i) draw(c.a[i].v--c.a[i+1].v,chainpen,currentlight); for(atom a : c.a) if(pixel) pixel(a.v,color(a.name),width); else dot(a.v,color(a.name),currentlight); natoms += c.a.length; } endgroup3(); write("Number of chained atoms: ",natoms); write("Number of hetero atoms: ",atoms.length); begingroup3("hetero"); for(atom h : atoms) if(pixel) pixel(h.v,color(h.name),width); else dot(h.v,color(h.name),currentlight); endgroup3(); write("Number of hetero bonds: ",bonds.length); begingroup3("bonds"); for(bond b : bonds) { triple v(int i) {return atoms[find(serials == i)].v;} draw(v(b.i)--v(b.j),hetpen,currentlight); } endgroup3(); string options; string viewfilename=prefix+".views"; if(!error(input(viewfilename,check=false))) options="3Dviews="+viewfilename; shipout(prefix,options=options);