1 /* Copyright (C) 1998 Michele Clamp
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3 * This program is free software; you can redistribute it and/or
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4 * modify it under the terms of the GNU General Public License
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5 * as published by the Free Software Foundation; either version 2
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6 * of the License, or (at your option) any later version.
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8 * This program is distributed in the hope that it will be useful,
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9 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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10 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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11 * GNU General Public License for more details.
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13 * You should have received a copy of the GNU General Public License
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14 * along with this program; if not, write to the Free Software
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15 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
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19 import jalview.datamodel.*;
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20 import jalview.schemes.ResidueProperties;
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26 public class PDBChain {
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29 public Vector bonds = new Vector();
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30 public Vector atoms = new Vector();
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31 public Vector residues = new Vector();
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34 public Sequence sequence;
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35 public boolean isVisible = false;
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37 public int pdbstart=0, pdbend=0, seqstart=0, seqend=0;
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39 //public DrawableSequence ds;
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41 public PDBChain(String id) {
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46 public String print() {
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48 for (int i=0; i < bonds.size() ;i++) {
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49 tmp = tmp + ((Bond)bonds.elementAt(i)).at1.resName + " " + ((Bond)bonds.elementAt(i)).at1.resNumber +" " + offset+ "\n";
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53 public void makeCaBondList() {
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54 for (int i = 0; i < (residues.size() - 1) ; i++) {
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55 Residue tmpres = (Residue)residues.elementAt(i);
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56 Residue tmpres2 = (Residue)residues.elementAt(i+1);
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57 myAtom at1 = tmpres.findAtom("CA");
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58 myAtom at2 = tmpres2.findAtom("CA");
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59 if ((at1 != null) && (at2 != null)) {
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60 if (at1.chain.equals(at2.chain)) {
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67 public void makeBond(myAtom at1, myAtom at2) {
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68 float[] start = new float[3];
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69 float[] end = new float[3];
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79 bonds.addElement(new Bond(start, end, at1,at2));
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82 public void makeResidueList() {
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85 for (int i = 0; i < atoms.size(); i++) {
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87 myAtom tmp = (myAtom)atoms.elementAt(i);
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88 String resName = tmp.resName;
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89 int resNumber = tmp.resNumber;
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90 int res = resNumber;
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95 Vector resAtoms = new Vector();
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97 resAtoms.addElement((myAtom)atoms.elementAt(i));
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99 resNumber = ((myAtom)atoms.elementAt(i)).resNumber;
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101 //Add atoms to a vector while the residue number
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103 while ((resNumber == res) && (i < atoms.size())) {
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105 resAtoms.addElement((myAtom)atoms.elementAt(i));
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107 if (i < atoms.size()) {
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108 resNumber = ((myAtom)atoms.elementAt(i)).resNumber;
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114 //We need this to keep in step with the outer for i = loop
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117 //Make a new Residue object with the new atoms vector
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118 residues.addElement(new Residue(resAtoms, resNumber - 1,count));
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120 Residue tmpres = (Residue)residues.lastElement();
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121 myAtom tmpat = (myAtom)tmpres.atoms.elementAt(0);
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123 // Keep totting up the sequence
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124 if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {
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125 System.err.println("PDBReader:Null aa3Hash for " + tmpat.resName);
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128 ResidueProperties.aa[((Integer)ResidueProperties.getAA3Hash().get(tmpat.resName)).intValue()];
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129 seq = seq + tmpres2;
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131 // System.out.println(tmpat.resName + " " + tmpres2);
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133 sequence = new Sequence("PDB_seq",seq,1,seq.length());
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134 System.out.println("PDB Sequence is :\nSequence = " + seq);
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135 System.out.println("No of residues = " +residues.size());
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138 public void setChargeColours() {
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139 for (int i = 0; i < bonds.size(); i++) {
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141 Bond b = (Bond)bonds.elementAt(i);
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143 if (b.at1.resName.toUpperCase().equals("ASP") || b.at1.resName.toUpperCase().equals("GLU")) {
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144 b.startCol = Color.red;
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145 } else if (b.at1.resName.toUpperCase().equals("LYS") || b.at1.resName.toUpperCase().equals("ARG")) {
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146 b.startCol = Color.blue;
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147 } else if (b.at1.resName.toUpperCase().equals("CYS")) {
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148 b.startCol = Color.yellow;
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150 int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();
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151 b.startCol = Color.lightGray;
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153 if (b.at2.resName.toUpperCase().equals("ASP") || b.at2.resName.toUpperCase().equals("GLU")) {
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154 b.endCol = Color.red;
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155 } else if (b.at2.resName.toUpperCase().equals("LYS") || b.at2.resName.toUpperCase().equals("ARG")) {
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156 b.endCol = Color.blue;
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157 } else if (b.at2.resName.toUpperCase().equals("CYS")) {
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158 b.endCol = Color.yellow;
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160 int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
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161 b.endCol = Color.lightGray;
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163 } catch (Exception e) {
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164 Bond b = (Bond)bonds.elementAt(i);
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165 b.startCol = Color.gray;
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166 b.endCol = Color.gray;
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171 public void setHydrophobicityColours() {
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172 float hydmin = (float)ResidueProperties.getHydmin();
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173 float hydmax = (float)ResidueProperties.getHydmax();
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174 double[] hyd = ResidueProperties.getHyd();
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176 Hashtable AA3Hash = ResidueProperties.getAA3Hash();
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178 for (int i = 0; i < bonds.size(); i++) {
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180 Bond b = (Bond)bonds.elementAt(i);
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182 int atno = ((Integer)AA3Hash.get(b.at1.resName.toUpperCase())).intValue();
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183 float red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);
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185 if (red > (float)1.0) {
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188 if (red < (float)0.0) {
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192 b.startCol = new Color(red,(float)0.0,(float)1.0-red);
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193 atno = ((Integer)AA3Hash.get(b.at2.resName.toUpperCase())).intValue();
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195 red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);
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197 if (red > (float)1.0) {
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200 if (red < (float)0.0) {
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204 b.endCol = new Color(red,(float)0.2,(float)1.0-red);
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205 } catch (Exception e) {
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206 Bond b = (Bond)bonds.elementAt(i);
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207 b.startCol = Color.gray;
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208 b.endCol = Color.gray;
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214 public void colourBySequence(jalview.gui.AlignViewport av, Sequence seq) {
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215 jalview.gui.SequenceRenderer sr = new jalview.gui.SequenceRenderer(av);
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218 for (int i = 0; i < bonds.size(); i++) {
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219 Bond tmp = (Bond)bonds.elementAt(i);
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222 if (tmp.at1.resNumber >= (offset + pdbstart - 1) && tmp.at1.resNumber <= (offset + pdbend - 1)) {
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224 int pos = seqstart + (tmp.at1.resNumber - pdbstart - offset) ;
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225 int index = seq.findIndex(pos);
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228 tmp.startCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);
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231 tmp.startCol = Color.gray;
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234 if (tmp.at2.resNumber >= (offset + pdbstart -1) && tmp.at2.resNumber <= (pdbend+offset-1)) {
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236 int pos = seqstart + (tmp.at2.resNumber - pdbstart-offset);
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237 int index = seq.findIndex(pos);
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239 tmp.endCol = sr.getResidueBoxColour(av.getGlobalColourScheme(), seq, index);
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242 tmp.endCol = Color.gray;
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244 } catch (Exception e) {
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245 tmp.startCol = Color.lightGray;
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246 tmp.endCol = Color.lightGray;
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251 public void setChainColours() {
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252 for (int i = 0; i < bonds.size(); i++) {
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253 Bond tmp = (Bond)bonds.elementAt(i);
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255 tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);
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256 tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);
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257 } catch (Exception e) {
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258 tmp.startCol = Color.lightGray;
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259 tmp.endCol = Color.lightGray;
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