/* * * (non-Javadoc) * @see java.lang.Object#toString() */ public String toString() { StringBuffer buf = new StringBuffer(); String nl = System.getProperty("line.separator"); buf.append( " # RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA "); buf.append(nl); for (int i = 0; i < groups.length; i++) { Group g = groups[i]; SecStrucState state = (SecStrucState) g.getProperty("secstruc"); // System.out.println("XX"+i+" "+g.getPDBCode() + " " + g.getPDBName() + // iter.getCurrentChain().getName() + " " + state); buf.append((i + 1) + "\t"); buf.append(g.getPDBName() + " "); buf.append(g.getPDBCode() + "\t"); boolean[] turns = state.getTurn(); for (int t = 0; t < 3; t++) { if (turns[t]) { buf.append('>'); } else { buf.append(' '); } } // tmp filler buf.append(" "); int p1 = state.getAccept1().getPartner(); if (p1 != 0) p1 -= i; double e1 = (state.getAccept1().getEnergy() / 1000.0); buf.append(String.format("%6d,%4.1f\t", p1, e1)); int p2 = state.getDonor1().getPartner(); if (p2 != 0) p2 -= i; double e2 = (state.getDonor1().getEnergy() / 1000.0); buf.append(String.format("%6d,%4.1f\t", p2, e2)); int p3 = state.getAccept1().getPartner(); if (p3 != 0) p3 -= i; double e3 = (state.getAccept2().getEnergy() / 1000.0); buf.append(String.format("%6d,%4.1f\t", p3, e3)); int p4 = state.getDonor2().getPartner(); if (p4 != 0) p4 -= i; double e4 = (state.getDonor2().getEnergy() / 1000.0); buf.append(String.format("%6d,%4.1f\t", p4, e4)); buf.append(nl); } return buf.toString(); }
/** detect helical turn patterns */ private void calculateTurns() { int l = groups.length; for (int i = 0; i < l; i++) { for (int turn = 3; turn <= 5; turn++) { if (i + turn >= l) continue; if (isBonded(i + turn, i)) { // System.out.println("is bondend " + (i+turn) + i ); for (int j = i; j < i + turn + 1; j++) { // System.out.println("turn at i:" + i + " j:" + j + " turn" + turn); SecStrucGroup group = groups[j]; SecStrucState state = (SecStrucState) group.getProperty("secstruc"); boolean[] turns = state.getTurn(); turns[turn - 3] = true; } } } } }