import charite.christo.strap.*; import java.io.File; import static java.lang.System.*; /* java DemoProtein_residueSets a1_SaccharomycesCerevisiae.pdb This demo shows how to convert an expression residue positions into a boolean array. Example: 1-3,5-6 ==> XXX.XXX.... If the number is followed by a colon, then the PDB-residue positions is used. Example 4:A is the residue of chain A with the PDB-number 4 */ public class DemoResidueSubset2 { public static void main(String argv[]) { /* Make a protein instance. */ final int OFFSET=1; final StrapProtein p= StrapProtein.newInstance(new File(argv[0])); { final String s="2-3,4,5,9"; out.println(s+" ==> "+toString(p.residueSubsetAsBooleanArray(s,OFFSET))); } { /* You can also refere to the pdb residue number and chain. */ final String s="2:A-3:A,4:A,5:A,9:A"; out.println(s+" ==> "+toString(p.residueSubsetAsBooleanArray(s,OFFSET))); } exit(0); } private static StringBuffer toString(boolean bb[]) { final StringBuffer sb=new StringBuffer(bb.length); for(boolean b:bb) sb.append(b ? 'X' : '.'); return sb; } }