2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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21 import jalview.datamodel.*;
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23 import jalview.schemes.ResidueProperties;
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30 public class PDBChain {
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32 public Vector bonds = new Vector();
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33 public Vector atoms = new Vector();
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34 public Vector residues = new Vector();
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36 public Sequence sequence;
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37 public boolean isVisible = false;
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38 public int pdbstart = 0;
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39 public int pdbend = 0;
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40 public int seqstart = 0;
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41 public int seqend = 0;
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43 //public DrawableSequence ds;
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44 public PDBChain(String id) {
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48 public String print() {
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51 for (int i = 0; i < bonds.size(); i++) {
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52 tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " " +
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53 ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset +
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60 public void makeCaBondList() {
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61 for (int i = 0; i < (residues.size() - 1); i++) {
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62 Residue tmpres = (Residue) residues.elementAt(i);
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63 Residue tmpres2 = (Residue) residues.elementAt(i + 1);
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64 myAtom at1 = tmpres.findAtom("CA");
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65 myAtom at2 = tmpres2.findAtom("CA");
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67 if ((at1 != null) && (at2 != null)) {
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68 if (at1.chain.equals(at2.chain)) {
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75 public void makeBond(myAtom at1, myAtom at2) {
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76 float[] start = new float[3];
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77 float[] end = new float[3];
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87 bonds.addElement(new Bond(start, end, at1, at2));
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90 public void makeResidueList() {
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94 for (int i = 0; i < atoms.size(); i++) {
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95 myAtom tmp = (myAtom) atoms.elementAt(i);
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96 String resName = tmp.resName;
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97 int resNumber = tmp.resNumber;
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98 int res = resNumber;
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101 offset = resNumber;
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104 Vector resAtoms = new Vector();
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106 resAtoms.addElement((myAtom) atoms.elementAt(i));
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108 resNumber = ((myAtom) atoms.elementAt(i)).resNumber;
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110 //Add atoms to a vector while the residue number
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112 while ((resNumber == res) && (i < atoms.size())) {
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113 resAtoms.addElement((myAtom) atoms.elementAt(i));
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116 if (i < atoms.size()) {
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117 resNumber = ((myAtom) atoms.elementAt(i)).resNumber;
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123 //We need this to keep in step with the outer for i = loop
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126 //Make a new Residue object with the new atoms vector
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127 residues.addElement(new Residue(resAtoms, resNumber - 1, count));
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130 Residue tmpres = (Residue) residues.lastElement();
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131 myAtom tmpat = (myAtom) tmpres.atoms.elementAt(0);
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133 // Keep totting up the sequence
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134 if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {
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135 System.err.println("PDBReader:Null aa3Hash for " +
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138 String tmpres2 = ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()
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139 .get(tmpat.resName)).intValue()];
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140 seq = seq + tmpres2;
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143 // System.out.println(tmpat.resName + " " + tmpres2);
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146 sequence = new Sequence("PDB_seq", seq, 1, seq.length());
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147 System.out.println("PDB Sequence is :\nSequence = " + seq);
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148 System.out.println("No of residues = " + residues.size());
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151 public void setChargeColours() {
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152 for (int i = 0; i < bonds.size(); i++) {
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154 Bond b = (Bond) bonds.elementAt(i);
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156 if (b.at1.resName.toUpperCase().equals("ASP") ||
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157 b.at1.resName.toUpperCase().equals("GLU")) {
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158 b.startCol = Color.red;
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159 } else if (b.at1.resName.toUpperCase().equals("LYS") ||
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160 b.at1.resName.toUpperCase().equals("ARG")) {
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161 b.startCol = Color.blue;
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162 } else if (b.at1.resName.toUpperCase().equals("CYS")) {
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163 b.startCol = Color.yellow;
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165 int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();
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166 b.startCol = Color.lightGray;
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169 if (b.at2.resName.toUpperCase().equals("ASP") ||
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170 b.at2.resName.toUpperCase().equals("GLU")) {
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171 b.endCol = Color.red;
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172 } else if (b.at2.resName.toUpperCase().equals("LYS") ||
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173 b.at2.resName.toUpperCase().equals("ARG")) {
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174 b.endCol = Color.blue;
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175 } else if (b.at2.resName.toUpperCase().equals("CYS")) {
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176 b.endCol = Color.yellow;
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178 int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
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179 b.endCol = Color.lightGray;
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181 } catch (Exception e) {
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182 Bond b = (Bond) bonds.elementAt(i);
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183 b.startCol = Color.gray;
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184 b.endCol = Color.gray;
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189 public void setHydrophobicityColours() {
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190 float hydmin = (float) ResidueProperties.getHydmin();
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191 float hydmax = (float) ResidueProperties.getHydmax();
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192 double[] hyd = ResidueProperties.getHyd();
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194 Hashtable AA3Hash = ResidueProperties.getAA3Hash();
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196 for (int i = 0; i < bonds.size(); i++) {
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198 Bond b = (Bond) bonds.elementAt(i);
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200 int atno = ((Integer) AA3Hash.get(b.at1.resName.toUpperCase())).intValue();
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201 float red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);
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203 if (red > (float) 1.0) {
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207 if (red < (float) 0.0) {
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211 b.startCol = new Color(red, (float) 0.0, (float) 1.0 - red);
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212 atno = ((Integer) AA3Hash.get(b.at2.resName.toUpperCase())).intValue();
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214 red = ((float) hyd[atno] - hydmin) / (hydmax - hydmin);
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216 if (red > (float) 1.0) {
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220 if (red < (float) 0.0) {
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224 b.endCol = new Color(red, (float) 0.2, (float) 1.0 - red);
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225 } catch (Exception e) {
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226 Bond b = (Bond) bonds.elementAt(i);
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227 b.startCol = Color.gray;
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228 b.endCol = Color.gray;
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233 public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {
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234 jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);
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236 for (int i = 0; i < bonds.size(); i++) {
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237 Bond tmp = (Bond) bonds.elementAt(i);
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240 if ((tmp.at1.resNumber >= ((offset + pdbstart) - 1)) &&
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241 (tmp.at1.resNumber <= ((offset + pdbend) - 1))) {
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242 int pos = seqstart +
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243 (tmp.at1.resNumber - pdbstart - offset);
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244 int index = seq.findIndex(pos);
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246 tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(),
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249 tmp.startCol = Color.gray;
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252 if ((tmp.at2.resNumber >= ((offset + pdbstart) - 1)) &&
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253 (tmp.at2.resNumber <= ((pdbend + offset) - 1))) {
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254 int pos = seqstart +
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255 (tmp.at2.resNumber - pdbstart - offset);
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256 int index = seq.findIndex(pos);
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258 tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(),
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261 tmp.endCol = Color.gray;
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263 } catch (Exception e) {
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264 tmp.startCol = Color.lightGray;
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265 tmp.endCol = Color.lightGray;
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270 public void setChainColours() {
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271 for (int i = 0; i < bonds.size(); i++) {
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272 Bond tmp = (Bond) bonds.elementAt(i);
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275 tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);
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276 tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);
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277 } catch (Exception e) {
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278 tmp.startCol = Color.lightGray;
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279 tmp.endCol = Color.lightGray;
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