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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22 import jalview.datamodel.*;
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23 import jalview.schemes.ResidueProperties;
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29 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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37 public Sequence sequence;
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38 public boolean isVisible = false;
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40 public int pdbstart=0, pdbend=0, seqstart=0, seqend=0;
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42 //public DrawableSequence ds;
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44 public PDBChain(String id) {
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49 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 + " " + ((Bond)bonds.elementAt(i)).at1.resNumber +" " + offset+ "\n";
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56 public void makeCaBondList() {
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57 for (int i = 0; i < (residues.size() - 1) ; i++) {
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58 Residue tmpres = (Residue)residues.elementAt(i);
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59 Residue tmpres2 = (Residue)residues.elementAt(i+1);
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60 myAtom at1 = tmpres.findAtom("CA");
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61 myAtom at2 = tmpres2.findAtom("CA");
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62 if ((at1 != null) && (at2 != null)) {
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63 if (at1.chain.equals(at2.chain)) {
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70 public void makeBond(myAtom at1, myAtom at2) {
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71 float[] start = new float[3];
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72 float[] end = new float[3];
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82 bonds.addElement(new Bond(start, end, at1,at2));
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85 public void makeResidueList() {
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88 for (int i = 0; i < atoms.size(); i++) {
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90 myAtom tmp = (myAtom)atoms.elementAt(i);
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91 String resName = tmp.resName;
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92 int resNumber = tmp.resNumber;
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93 int res = resNumber;
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98 Vector resAtoms = new Vector();
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100 resAtoms.addElement((myAtom)atoms.elementAt(i));
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102 resNumber = ((myAtom)atoms.elementAt(i)).resNumber;
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104 //Add atoms to a vector while the residue number
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106 while ((resNumber == res) && (i < atoms.size())) {
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108 resAtoms.addElement((myAtom)atoms.elementAt(i));
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110 if (i < atoms.size()) {
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111 resNumber = ((myAtom)atoms.elementAt(i)).resNumber;
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117 //We need this to keep in step with the outer for i = loop
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120 //Make a new Residue object with the new atoms vector
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121 residues.addElement(new Residue(resAtoms, resNumber - 1,count));
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123 Residue tmpres = (Residue)residues.lastElement();
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124 myAtom tmpat = (myAtom)tmpres.atoms.elementAt(0);
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126 // Keep totting up the sequence
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127 if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {
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128 System.err.println("PDBReader:Null aa3Hash for " + tmpat.resName);
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131 ResidueProperties.aa[((Integer)ResidueProperties.getAA3Hash().get(tmpat.resName)).intValue()];
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132 seq = seq + tmpres2;
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134 // System.out.println(tmpat.resName + " " + tmpres2);
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136 sequence = new Sequence("PDB_seq",seq,1,seq.length());
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137 System.out.println("PDB Sequence is :\nSequence = " + seq);
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138 System.out.println("No of residues = " +residues.size());
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141 public void setChargeColours() {
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142 for (int i = 0; i < bonds.size(); i++) {
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144 Bond b = (Bond)bonds.elementAt(i);
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146 if (b.at1.resName.toUpperCase().equals("ASP") || b.at1.resName.toUpperCase().equals("GLU")) {
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147 b.startCol = Color.red;
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148 } else if (b.at1.resName.toUpperCase().equals("LYS") || b.at1.resName.toUpperCase().equals("ARG")) {
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149 b.startCol = Color.blue;
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150 } else if (b.at1.resName.toUpperCase().equals("CYS")) {
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151 b.startCol = Color.yellow;
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153 int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();
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154 b.startCol = Color.lightGray;
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156 if (b.at2.resName.toUpperCase().equals("ASP") || b.at2.resName.toUpperCase().equals("GLU")) {
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157 b.endCol = Color.red;
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158 } else if (b.at2.resName.toUpperCase().equals("LYS") || b.at2.resName.toUpperCase().equals("ARG")) {
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159 b.endCol = Color.blue;
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160 } else if (b.at2.resName.toUpperCase().equals("CYS")) {
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161 b.endCol = Color.yellow;
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163 int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
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164 b.endCol = Color.lightGray;
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166 } catch (Exception e) {
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167 Bond b = (Bond)bonds.elementAt(i);
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168 b.startCol = Color.gray;
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169 b.endCol = Color.gray;
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174 public void setHydrophobicityColours() {
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175 float hydmin = (float)ResidueProperties.getHydmin();
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176 float hydmax = (float)ResidueProperties.getHydmax();
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177 double[] hyd = ResidueProperties.getHyd();
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179 Hashtable AA3Hash = ResidueProperties.getAA3Hash();
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181 for (int i = 0; i < bonds.size(); i++) {
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183 Bond b = (Bond)bonds.elementAt(i);
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185 int atno = ((Integer)AA3Hash.get(b.at1.resName.toUpperCase())).intValue();
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186 float red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);
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188 if (red > (float)1.0) {
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191 if (red < (float)0.0) {
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195 b.startCol = new Color(red,(float)0.0,(float)1.0-red);
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196 atno = ((Integer)AA3Hash.get(b.at2.resName.toUpperCase())).intValue();
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198 red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);
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200 if (red > (float)1.0) {
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203 if (red < (float)0.0) {
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207 b.endCol = new Color(red,(float)0.2,(float)1.0-red);
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208 } catch (Exception e) {
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209 Bond b = (Bond)bonds.elementAt(i);
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210 b.startCol = Color.gray;
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211 b.endCol = Color.gray;
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217 public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {
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218 jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);
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221 for (int i = 0; i < bonds.size(); i++) {
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222 Bond tmp = (Bond)bonds.elementAt(i);
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225 if (tmp.at1.resNumber >= (offset + pdbstart - 1) && tmp.at1.resNumber <= (offset + pdbend - 1)) {
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227 int pos = seqstart + (tmp.at1.resNumber - pdbstart - offset) ;
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228 int index = seq.findIndex(pos);
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231 tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);
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234 tmp.startCol = Color.gray;
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237 if (tmp.at2.resNumber >= (offset + pdbstart -1) && tmp.at2.resNumber <= (pdbend+offset-1)) {
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239 int pos = seqstart + (tmp.at2.resNumber - pdbstart-offset);
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240 int index = seq.findIndex(pos);
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242 tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);
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245 tmp.endCol = Color.gray;
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247 } catch (Exception e) {
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248 tmp.startCol = Color.lightGray;
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249 tmp.endCol = Color.lightGray;
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254 public void setChainColours() {
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255 for (int i = 0; i < bonds.size(); i++) {
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256 Bond tmp = (Bond)bonds.elementAt(i);
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258 tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);
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259 tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);
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260 } catch (Exception e) {
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261 tmp.startCol = Color.lightGray;
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262 tmp.endCol = Color.lightGray;
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