4 import java.awt.event.*;
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7 import javax.swing.*;
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9 public class rotCanvas extends JPanel implements KeyListener,
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11 MouseMotionListener {
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12 MCMatrix idmat = new MCMatrix(3,3);
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13 MCMatrix objmat = new MCMatrix(3,3);
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15 boolean redrawneeded =true;
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31 float centre[] = new float[3];
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32 float width[] = new float[3];
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40 boolean depthcue = true;
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41 boolean wire = false;
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42 boolean bymolecule = false;
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43 boolean zbuffer = true;
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54 Font font = new Font("Helvetica",Font.PLAIN,10);
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56 public rotCanvas(PDBfile pdb) throws IOException {
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59 this.prefsize = new Dimension( getWidth(), getHeight());
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61 //Initialize the matrices to identity
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63 for (int i = 0; i < 3; i++) {
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64 for (int j = 0; j < 3 ; j++) {
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66 idmat.addElement(i,j,0);
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67 objmat.addElement(i,j,0);
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69 idmat.addElement(i,j,1);
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70 objmat.addElement(i,j,1);
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75 addMouseMotionListener(this);
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76 addMouseListener(this);
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77 addKeyListener(this);
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80 ToolTipManager.sharedInstance().registerComponent(this);
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84 public void addPDBfile() {
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88 scale = findScale();
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90 System.out.println("Scale factor = " + scale);
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93 public void deleteBonds() {
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105 for (int i=0; i < pdb.chains.size(); i++) {
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106 ((PDBChain)pdb.chains.elementAt(i)).bonds = null;
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110 public void findWidth() {
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111 float max[] = new float[3];
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112 float min[] = new float[3];
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114 max[0] = (float)-1e30;
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115 max[1] = (float)-1e30;
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116 max[2] = (float)-1e30;
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118 min[0] = (float)1e30;
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119 min[1] = (float)1e30;
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120 min[2] = (float)1e30;
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122 for (int ii=0; ii < pdb.chains.size(); ii++) {
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123 if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {
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125 Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
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127 for (int i = 0; i < bonds.size(); i++) {
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128 Bond tmp = (Bond)bonds.elementAt(i);
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130 if (tmp.start[0] >= max[0])
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131 max[0] = tmp.start[0];
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132 if (tmp.start[1] >= max[1])
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133 max[1] = tmp.start[1];
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134 if (tmp.start[2] >= max[2])
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135 max[2] = tmp.start[2];
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136 if (tmp.start[0] <= min[0])
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137 min[0] = tmp.start[0];
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138 if (tmp.start[1] <= min[1])
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139 min[1] = tmp.start[1];
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140 if (tmp.start[2] <= min[2])
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141 min[2] = tmp.start[2];
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143 if (tmp.end[0] >= max[0])
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144 max[0] = tmp.end[0];
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145 if (tmp.end[1] >= max[1])
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146 max[1] = tmp.end[1];
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147 if (tmp.end[2] >= max[2])
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148 max[2] = tmp.end[2];
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149 if (tmp.end[0] <= min[0])
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150 min[0] = tmp.end[0];
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151 if (tmp.end[1] <= min[1])
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152 min[1] = tmp.end[1];
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153 if (tmp.end[2] <= min[2])
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154 min[2] = tmp.end[2];
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159 System.out.println("xmax " + max[0] + " min " + min[0]);
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160 System.out.println("ymax " + max[1] + " min " + min[1]);
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161 System.out.println("zmax " + max[2] + " min " + min[2]);
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163 width[0] = (float)Math.abs(max[0] - min[0]);
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164 width[1] = (float)Math.abs(max[1] - min[1]);
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165 width[2] = (float)Math.abs(max[2] - min[2]);
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167 maxwidth = width[0];
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169 if (width[1] > width[0])
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170 maxwidth = width[1];
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171 if (width[2] > width[1])
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172 maxwidth = width[2];
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174 System.out.println("Maxwidth = " + maxwidth);
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177 public float findScale() {
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178 int dim, width, height;
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180 if ( getWidth() != 0) {
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181 width = getWidth();
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182 height = getHeight();
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185 width = prefsize.width;
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186 height = prefsize.height;
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189 if (width < height) {
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195 return (float)(dim/(1.5d*maxwidth));
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200 public void findCentre() {
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206 //Find centre coordinate
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208 for (int ii = 0; ii < pdb.chains.size() ; ii++) {
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209 if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {
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211 Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
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213 bsize += bonds.size();
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215 for (int i = 0; i < bonds.size(); i++) {
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217 xtot = xtot + ((Bond)bonds.elementAt(i)).start[0] +
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218 ((Bond)bonds.elementAt(i)).end[0];
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220 ytot = ytot + ((Bond)bonds.elementAt(i)).start[1] +
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221 ((Bond)bonds.elementAt(i)).end[1];
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223 ztot = ztot + ((Bond)bonds.elementAt(i)).start[2] +
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224 ((Bond)bonds.elementAt(i)).end[2];
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229 centre[0] = xtot / (2 * (float)bsize);
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230 centre[1] = ytot / (2 * (float)bsize);
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231 centre[2] = ztot / (2 * (float)bsize);
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234 public void paintComponent(Graphics g) {
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235 //Only create the image at the beginning -
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236 //this saves much memory usage
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237 if ((img == null) || (prefsize.width != getWidth()) || (prefsize.height != getHeight())) {
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238 prefsize.width = getWidth();
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239 prefsize.height = getHeight();
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241 scale = findScale();
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242 img = createImage(prefsize.width,prefsize.height);
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243 ig = img.getGraphics();
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245 redrawneeded = true;
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248 if (redrawneeded == true) {
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249 drawBackground(ig,Color.black);
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251 redrawneeded = false;
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253 ig = img.getGraphics();
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256 g.drawImage(img,0,0,this);
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259 public void drawBackground(Graphics g, Color col) {
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261 g.fillRect(0,0,prefsize.width,prefsize.height);
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265 public void drawScene(Graphics g) {
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266 // Sort the bonds by z coord
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268 Vector bonds = new Vector();
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271 for (int ii = 0; ii < pdb.chains.size() ; ii++) {
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272 if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {
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274 Vector tmp = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
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276 for (int i=0; i < tmp.size(); i++) {
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277 bonds.addElement(tmp.elementAt(i));
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283 Zsort.Zsort(bonds);
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286 for (int i = 0; i < bonds.size(); i++) {
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287 Bond tmpBond = (Bond)bonds.elementAt(i);
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289 xstart = (int)((tmpBond.start[0] - centre[0])*scale + getWidth()/2);
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290 ystart = (int)((tmpBond.start[1] - centre[1])*scale + getHeight()/2);
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292 xend = (int)((tmpBond.end[0] - centre[0])*scale + getWidth()/2);
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293 yend = (int)((tmpBond.end[1] - centre[1])*scale + getHeight()/2);
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295 xmid = (xend+xstart)/2;
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296 ymid = (yend+ystart)/2;
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299 if (depthcue && !bymolecule) {
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301 if (tmpBond.start[2] < (centre[2] - maxwidth/6)) {
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302 g.setColor(tmpBond.startCol.darker().darker());
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303 drawLine(g,xstart,ystart,xmid,ymid);
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305 g.setColor(tmpBond.endCol.darker().darker());
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306 drawLine(g,xmid,ymid,xend,yend);
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307 } else if (tmpBond.start[2] < (centre[2]+maxwidth/6)) {
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308 g.setColor(tmpBond.startCol.darker());
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309 drawLine(g,xstart,ystart,xmid,ymid);
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311 g.setColor(tmpBond.endCol.darker());
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312 drawLine(g,xmid,ymid,xend,yend);
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314 g.setColor(tmpBond.startCol);
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315 drawLine(g,xstart,ystart,xmid,ymid);
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317 g.setColor(tmpBond.endCol);
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318 drawLine(g,xmid,ymid,xend,yend);
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320 } else if (depthcue && bymolecule) {
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321 if (tmpBond.start[2] < (centre[2] - maxwidth/6)) {
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322 g.setColor(Color.green.darker().darker());
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323 drawLine(g,xstart,ystart,xend,yend);
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325 } else if (tmpBond.start[2] < (centre[2]+maxwidth/6)) {
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326 g.setColor(Color.green.darker());
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327 drawLine(g,xstart,ystart,xend,yend);
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330 g.setColor(Color.green);
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331 drawLine(g,xstart,ystart,xend,yend);
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334 } else if (!depthcue && !bymolecule) {
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335 g.setColor(tmpBond.startCol);
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336 drawLine(g,xstart,ystart,xmid,ymid);
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337 g.setColor(tmpBond.endCol);
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338 drawLine(g,xmid,ymid,xend,yend);
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341 drawLine(g,xstart,ystart,xend,yend);
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346 public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {
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349 if (((float)Math.abs(y2-y1)/(float)Math.abs(x2-x1)) < 0.5) {
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351 g.drawLine(x1,y1,x2,y2);
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352 g.drawLine(x1+1,y1+1,x2+1,y2+1);
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353 g.drawLine(x1,y1-1,x2,y2-1);
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355 g.setColor(g.getColor().brighter());
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356 g.drawLine(x1,y1,x2,y2);
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357 g.drawLine(x1+1,y1,x2+1,y2);
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358 g.drawLine(x1-1,y1,x2-1,y2);
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362 g.drawLine(x1,y1,x2,y2);
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366 public Dimension minimumsize() {
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369 public Dimension preferredsize() {
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373 public void keyTyped(KeyEvent evt) { }
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374 public void keyReleased(KeyEvent evt) { }
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375 public void keyPressed(KeyEvent evt) {
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376 int key = evt.getKeyChar();
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378 if (evt.getKeyCode() == KeyEvent.VK_UP) {
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379 scale = (float)(scale * 1.1);
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380 redrawneeded = true;
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383 } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {
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384 scale = (float)(scale * 0.9);
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385 redrawneeded = true;
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388 } else if (key == 'w') {
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391 System.out.println("wireframe " + wire);
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392 redrawneeded = true;
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395 } else if (key == 'd') {
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396 depthcue = !depthcue;
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397 System.out.println("Depth cueing is " + depthcue);
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398 redrawneeded = true;
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401 } else if (key == 'm') {
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402 bymolecule = !bymolecule;
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403 System.out.println("Bymolecule is " + bymolecule);
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404 redrawneeded = true;
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407 } else if (key == 'z') {
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408 zbuffer = !zbuffer;
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409 System.out.println("Z buffering is " + zbuffer);
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410 redrawneeded = true;
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413 } else if (key == 'c') {
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414 bymolecule = false;
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415 pdb.setChainColours();
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416 System.out.println("Colouring by chain");
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417 redrawneeded = true;
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420 } else if (key == 'h') {
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421 bymolecule = false;
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422 pdb.setHydrophobicityColours();
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423 System.out.println("Colouring by hydrophobicity");
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424 redrawneeded = true;
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427 } else if (key == 'q') {
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428 bymolecule = false;
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429 pdb.setChargeColours();
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430 System.out.println("Colouring charges and cysteines");
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431 redrawneeded = true;
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438 public void mousePressed(MouseEvent e)
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448 public void mouseMoved(MouseEvent e)
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450 myAtom fatom = null;
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451 for (int ii = 0; ii < pdb.chains.size(); ii++)
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454 PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
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455 if (chain.isVisible)
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457 Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
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458 for (int i = 0; i < bonds.size(); i++)
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460 Bond tmpBond = (Bond) bonds.elementAt(i);
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461 int truex = (int) ( (tmpBond.start[0] - centre[0]) * scale +
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463 if (Math.abs(truex - e.getX()) <= 2)
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465 int truey = (int) ( (tmpBond.start[1] - centre[1]) * scale +
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467 if (Math.abs(truey - e.getY()) <= 2)
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468 fatom = tmpBond.at1;
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475 this.setToolTipText(fatom.resName);
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476 System.out.println(fatom.resName);
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479 this.setToolTipText(null);
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482 public void mouseClicked(MouseEvent e) { }
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483 public void mouseEntered(MouseEvent e) { }
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484 public void mouseExited(MouseEvent e) { }
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486 public void mouseDragged(MouseEvent evt) {
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487 int x = evt.getX();
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488 int y = evt.getY();
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492 MCMatrix objmat = new MCMatrix(3,3);
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493 objmat.setIdentity();
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495 if ((evt.getModifiers() & Event.META_MASK) != 0) {
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496 objmat.rotatez((float)((mx-omx)));
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498 objmat.rotatex((float)((my-omy)));
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499 objmat.rotatey((float)((omx-mx)));
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503 for (int ii = 0; ii < pdb.chains.size() ; ii++) {
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504 Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
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506 for (int i = 0; i < bonds.size(); i++) {
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508 Bond tmpBond = (Bond)bonds.elementAt(i);
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510 //Translate the bond so the centre is 0,0,0
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511 tmpBond.translate(-centre[0],-centre[1],-centre[2]);
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513 //Now apply the rotation matrix
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514 tmpBond.start = objmat.vectorMultiply(tmpBond.start);
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515 tmpBond.end = objmat.vectorMultiply(tmpBond.end);
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517 //Now translate back again
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518 tmpBond.translate(centre[0],centre[1],centre[2]);
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527 redrawneeded = true;
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529 paint(this.getGraphics());
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535 public void mouseReleased(MouseEvent evt) {
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536 int x = evt.getX();
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537 int y = evt.getY();
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540 myAtom tmp = findAtom(x,y);
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546 public void drawLabels() {
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547 redrawneeded = true;
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548 paint(this.getGraphics());
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550 for (int ii = 0; ii < pdb.chains.size() ; ii++) {
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552 PDBChain chain = (PDBChain)pdb.chains.elementAt(ii);
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554 if (chain.isVisible) {
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556 Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
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558 for (int i = 0; i < bonds.size(); i++) {
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559 Bond tmpBond = (Bond)bonds.elementAt(i);
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561 if (tmpBond.at1.isSelected) {
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562 labelAtom(img.getGraphics(),tmpBond,1);
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565 if (tmpBond.at2.isSelected) {
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566 labelAtom(img.getGraphics(),tmpBond,2);
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573 this.getGraphics().drawImage(img,0,0,this);
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579 public void labelAtom(Graphics g,Bond b, int n) {
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585 int xstart = (int)((b.start[0] - centre[0])*scale + getWidth()/2);
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586 int ystart = (int)((b.start[1] - centre[1])*scale + getHeight()/2);
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588 g.setColor(Color.red);
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589 g.drawString(b.at1.resName + "-" + b.at1.resNumber,xstart,ystart);
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594 int xstart = (int)((b.end[0] - centre[0])*scale + getWidth()/2);
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595 int ystart = (int)((b.end[1] - centre[1])*scale + getHeight()/2);
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597 g.setColor(Color.red);
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598 g.drawString(b.at2.resName + "-" + b.at2.resNumber,xstart,ystart);
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603 public myAtom findAtom(int x, int y) {
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604 myAtom fatom = null;
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606 int foundchain = -1;
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608 for (int ii = 0; ii < pdb.chains.size() ; ii++) {
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610 PDBChain chain = (PDBChain)pdb.chains.elementAt(ii);
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612 if (chain.isVisible) {
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614 Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
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616 for (int i = 0; i < bonds.size(); i++) {
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617 Bond tmpBond = (Bond)bonds.elementAt(i);
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619 int truex = (int)((tmpBond.start[0] - centre[0])*scale + getWidth()/2);
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621 if (Math.abs(truex - x) <= 2) {
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623 int truey = (int)((tmpBond.start[1] - centre[1])*scale + getHeight()/2);
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625 if (Math.abs(truey - y) <= 2) {
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627 System.out.println("Found match");
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628 System.out.println(x + " " + y);
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629 System.out.println(truex + " " + truey);
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630 System.out.println(tmpBond.start[0] + " " + tmpBond.start[1]);
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631 System.out.println("Atom 1 = " + tmpBond.at1.resName + " " +
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632 tmpBond.at1.resNumber + " " + tmpBond.at1.chain);
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633 fatom = tmpBond.at1;
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634 fatom.isSelected = !fatom.isSelected;
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641 if (fatom != null) //)&& chain.ds != null)
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643 chain = (PDBChain)pdb.chains.elementAt(foundchain);
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645 // int tmp = chain.ds.seqstart + fatom.resNumber - chain.offset;
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646 // int pos = chain.ds.findIndex(tmp);
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647 // System.out.println("Found seq " + chain.ds.name + " " + tmp + " " + pos);
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654 public void update(Graphics g) {
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