// DodecahedralGrid.java // // // Copyright 2004, Ethan Bolker and Bogdan Calota package edu.umb.cs.eb.folding; import java.util.*; /** * Model a grid of rhombic dodecahedra containing a polypeptide chain. * * In standard coordinate system, occupiable cells are those for which * the sum of the coordinates is even. * * 0-0-0 1-0-0 2-0-0 3-0-0 * 0-1-0 1-1-0 2-1-0 3-1-0 * 0-2-0 1-2-0 2-2-0 3-2-0 * * ... * 0-0-3 1-0-3 2-0-3 3-0-3 * 0-1-3 1-1-3 2-1-3 3-1-3 * 0-2-3 1-2-3 2-2-3 3-2-3 */ public class DodecahedralGrid extends ThreeDGrid { public DodecahedralGrid( Polypeptide pp ) { super(pp); allDirections = getAllDirections(); setNextDirectionsStraight(); setNextDirectionsBent(); setNextDirections(); // // this.pp = pp; // numAcids = pp.getLength(); // acids = pp.getAcidArray(); size = 4*numAcids + 1; cells = new AcidInChain[size][size][size]; points = new GridPoint[size][size][size]; for (int i = 0; i < size; i++) { for (int j = 0; j < size; j++) { for (int k = 0; k < size; k++) { cells[i][j][k] = null; points[i][j][k] = new GridPoint(i,j,k); } } } allDirections = getAllDirections(); setNextDirections(); // following should go in superclass constructor but fails there if (pp.isFolded()) { GridPoint currentP = getCenter(); set(0, currentP, Direction.none); Direction d = pp.getNextDirection(0); for (int i = 1; i < numAcids; i++ ) { currentP = nextCell( d, currentP ); set(i, currentP, d); d = pp.getNextDirection(i); } } } // tools for Directions public final Direction NW = Direction.NW; public final Direction NE = Direction.NE; public final Direction SW = Direction.SW; public final Direction SE = Direction.SE; public final Direction NU = Direction.NU; public final Direction ND = Direction.ND; public final Direction SU = Direction.SU; public final Direction SD = Direction.SD; public final Direction EU = Direction.EU; public final Direction ED = Direction.ED; public final Direction WU = Direction.WU; public final Direction WD = Direction.WD; protected Direction[] getAllDirections() { Direction[] all = {NE,NW,SE,SW,NU,ND,SU,SD,EU,ED,WU,WD}; return all; } protected Direction getFirstDirection() { return NE; } public Direction[] getThirdPlacement() { Direction[] directions = { NE, ND, NW, NU, EU, WU }; return directions; } public String toString() { StringBuffer buf = new StringBuffer(); for (int lyr = 0; lyr < size; lyr++) { for (int row = 0; row < size; row++) { for (int col = 0; col < size; col++) { buf.append( cells[row][col][lyr] == null ? "---" : cells[row][col][lyr].name ); buf.append(' '); } buf.append('\n'); } buf.append('\n'); } return buf.toString(); } protected Direction getDirection(GridPoint p1, GridPoint p2) { int x1 = p1.x; int y1 = p1.y; int z1 = p1.z; int x2 = p2.x; int y2 = p2.y; int z2 = p2.z; if (z1 == z2 ) { if (y1+1 == y2) { if (x1+1 == x2) return NE; return NW; } if (x1+1 == x2) return SE; return SW; } if (y1 == y2) { if (z1+1 == z2) { if (x1+1 == x2) return EU; return WU; } if (x1+1 == x2) return ED; return WD; } if (x1 == x2) { if (y1+1 == y2) { if (z1+1 == z2) return NU; return ND; } if (z1+1 == z2) return SU; return SD; } return Direction.none; } protected GridPoint nextCell(Direction direction, GridPoint p) { // System.out.println(p); int x = p.x; int y = p.y; int z = p.z; // EW NS UD if (direction == NE) return points[x+1][y+1][z]; if (direction == NW) return points[x-1][y+1][z]; if (direction == SE) return points[x+1][y-1][z]; if (direction == SW) return points[x-1][y-1][z]; if (direction == NU) return points[x][y+1][z+1]; if (direction == ND) return points[x][y+1][z-1]; if (direction == SU) return points[x][y-1][z+1]; if (direction == SD) return points[x][y-1][z-1]; if (direction == EU) return points[x+1][y][z+1]; if (direction == ED) return points[x+1][y][z-1]; if (direction == WU) return points[x-1][y][z+1]; if (direction == WD) return points[x-1][y][z-1]; if (direction == Direction.none) return p; return null; } // coming from some Direction, try to continue in the same // Direction. Make right handed coordinate turn if you must turn. protected Direction[] getDirectionRing3() { return null; } protected int getNumDirections() { return 12; } public void setNextDirectionsStraight() { straightMap = new HashMap(); Direction[] nextNE = {NE,NU,EU,ED,ND,NW,SE,SD,WD,WU,SU}; // 1 straightMap.put(NE, nextNE); Direction[] nextNU = {NU,EU,NE,NW,WU,SU,ND,WD,SW,SE,ED}; // 2 straightMap.put(NU, nextNU); Direction[] nextNW = {NW,ND,WD,WU,NU,NE,SW,SU,EU,ED,SD}; // 9 straightMap.put(NW, nextNW); Direction[] nextND = {ND,NE,ED,WD,NW,NU,SD,SW,WU,EU,SE}; // 10 straightMap.put(ND, nextND); Direction[] nextSE = {SE,EU,SU,SD,ED,NE,SW,WD,ND,NU,WU}; // 4 straightMap.put(SE, nextSE); Direction[] nextSU = {SU,WU,SW,SE,EU,NU,SD,ED,NE,NW,WD}; // 5 straightMap.put(SU, nextSU); Direction[] nextSW = {SW,SU,WU,WD,SD,SE,NW,ND,ED,EU,NU}; // 7 straightMap.put(SW, nextSW); Direction[] nextSD = {SD,SW,WD,ED,SE,SU,ND,NE,EU,WU,NW}; // 11 straightMap.put(SD, nextSD); Direction[] nextEU = {EU,NE,NU,SU,SE,ED,WU,SW,SD,ND,NW}; // 3 straightMap.put(EU, nextEU); Direction[] nextED = {ED,ND,NE,SE,SD,WD,EU,SU,SW,NW,NU}; // 12 straightMap.put(ED, nextED); Direction[] nextWU = {WU,SW,SU,NU,NW,WD,EU,NE,ND,SD,SE}; // 6 straightMap.put(WU, nextWU); Direction[] nextWD = {WD,NW,ND,SD,SW,WU,ED,SE,SU,NU,NE}; // 8 straightMap.put(WD, nextWD); } public static void main( String[] args ) { // System.out.println("on hex grid"); // Polypeptide pp = new Polypeptide( args ); // System.out.println(pp); // Grid g = new HexGrid(pp); // Folder f = new BruteForceFolder(pp, g); // Folder f = new IncrementalFolder(pp, g); // f.fold(); // System.out.println(f.report()); // System.out.println(g); // System.out.println("on Dodecahedral grid"); // Polypeptide pp; // = new Polypeptide( args ); // pp = PolypeptideFactory.getInstance().createPolypeptide // (args, // false, // true, // "", // "", // "virtual"); // System.out.println(pp); // Grid g = new DodecahedralGrid(pp); // Folder f = new BruteForceFolder(pp, g); // f.fold(); // System.out.println(f.report()); // System.out.println(g); } }