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 DrawableSequence ds;
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39 public PDBChain(String id) {
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44 public String print() {
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46 for (int i=0; i < bonds.size() ;i++) {
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47 tmp = tmp + ((Bond)bonds.elementAt(i)).at1.resName + " " + ((Bond)bonds.elementAt(i)).at1.resNumber +" " + offset+ "\n";
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51 public void makeCaBondList() {
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52 for (int i = 0; i < (residues.size() - 1) ; i++) {
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53 Residue tmpres = (Residue)residues.elementAt(i);
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54 Residue tmpres2 = (Residue)residues.elementAt(i+1);
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55 myAtom at1 = tmpres.findAtom("CA");
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56 myAtom at2 = tmpres2.findAtom("CA");
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57 if ((at1 != null) && (at2 != null)) {
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58 if (at1.chain.equals(at2.chain)) {
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65 public void makeBond(myAtom at1, myAtom at2) {
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66 float[] start = new float[3];
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67 float[] end = new float[3];
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77 bonds.addElement(new Bond(start, end, at1,at2));
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80 public void makeResidueList() {
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83 for (int i = 0; i < atoms.size(); i++) {
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85 myAtom tmp = (myAtom)atoms.elementAt(i);
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86 String resName = tmp.resName;
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87 int resNumber = tmp.resNumber;
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88 int res = resNumber;
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93 Vector resAtoms = new Vector();
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95 resAtoms.addElement((myAtom)atoms.elementAt(i));
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97 resNumber = ((myAtom)atoms.elementAt(i)).resNumber;
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99 //Add atoms to a vector while the residue number
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101 while ((resNumber == res) && (i < atoms.size())) {
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103 resAtoms.addElement((myAtom)atoms.elementAt(i));
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105 if (i < atoms.size()) {
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106 resNumber = ((myAtom)atoms.elementAt(i)).resNumber;
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112 //We need this to keep in step with the outer for i = loop
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115 //Make a new Residue object with the new atoms vector
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116 residues.addElement(new Residue(resAtoms, resNumber - 1,count));
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118 Residue tmpres = (Residue)residues.lastElement();
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119 myAtom tmpat = (myAtom)tmpres.atoms.elementAt(0);
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121 // Keep totting up the sequence
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122 if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {
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123 System.out.println("Null aa3Hash for " + tmpat.resName);
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126 ResidueProperties.aa[((Integer)ResidueProperties.getAA3Hash().get(tmpat.resName)).intValue()];
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127 seq = seq + tmpres2;
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129 // System.out.println(tmpat.resName + " " + tmpres2);
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131 sequence = new Sequence("PDB_seq",seq,1,seq.length());
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132 System.out.println("Sequence = " + seq);
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133 System.out.println("No of residues = " +residues.size());
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136 public void setChargeColours() {
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137 for (int i = 0; i < bonds.size(); i++) {
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139 Bond b = (Bond)bonds.elementAt(i);
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141 if (b.at1.resName.toUpperCase().equals("ASP") || b.at1.resName.toUpperCase().equals("GLU")) {
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142 b.startCol = Color.red;
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143 } else if (b.at1.resName.toUpperCase().equals("LYS") || b.at1.resName.toUpperCase().equals("ARG")) {
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144 b.startCol = Color.blue;
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145 } else if (b.at1.resName.toUpperCase().equals("CYS")) {
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146 b.startCol = Color.yellow;
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148 int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();
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149 b.startCol = Color.lightGray;
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151 if (b.at2.resName.toUpperCase().equals("ASP") || b.at2.resName.toUpperCase().equals("GLU")) {
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152 b.endCol = Color.red;
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153 } else if (b.at2.resName.toUpperCase().equals("LYS") || b.at2.resName.toUpperCase().equals("ARG")) {
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154 b.endCol = Color.blue;
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155 } else if (b.at2.resName.toUpperCase().equals("CYS")) {
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156 b.endCol = Color.yellow;
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158 int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();
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159 b.endCol = Color.lightGray;
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161 } catch (Exception e) {
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162 Bond b = (Bond)bonds.elementAt(i);
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163 b.startCol = Color.gray;
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164 b.endCol = Color.gray;
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169 public void setHydrophobicityColours() {
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170 float hydmin = (float)ResidueProperties.getHydmin();
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171 float hydmax = (float)ResidueProperties.getHydmax();
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172 double[] hyd = ResidueProperties.getHyd();
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174 Hashtable AA3Hash = ResidueProperties.getAA3Hash();
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176 for (int i = 0; i < bonds.size(); i++) {
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178 Bond b = (Bond)bonds.elementAt(i);
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180 int atno = ((Integer)AA3Hash.get(b.at1.resName.toUpperCase())).intValue();
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181 float red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);
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183 if (red > (float)1.0) {
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186 if (red < (float)0.0) {
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190 b.startCol = new Color(red,(float)0.0,(float)1.0-red);
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191 atno = ((Integer)AA3Hash.get(b.at2.resName.toUpperCase())).intValue();
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193 red = ((float)hyd[atno] - hydmin)/(hydmax - hydmin);
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195 if (red > (float)1.0) {
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198 if (red < (float)0.0) {
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202 b.endCol = new Color(red,(float)0.2,(float)1.0-red);
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203 } catch (Exception e) {
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204 Bond b = (Bond)bonds.elementAt(i);
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205 b.startCol = Color.gray;
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206 b.endCol = Color.gray;
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212 public void colourBySequence(Sequence seq) {
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214 // for (int i = 0; i < bonds.size(); i++) {
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215 // Bond tmp = (Bond)bonds.elementAt(i);
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218 // if (tmp.at1.resNumber >= (offset + seq.pdbstart - 1) && tmp.at1.resNumber <= (offset + seq.pdbend - 1)) {
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220 // int pos = seq.seqtart() + (tmp.at1.resNumber - seq.pdbstart - offset) ;
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221 // int index = seq.findIndex(pos);
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223 // tmp.startCol = (Color)seq.getResidueBoxColour(index);
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226 // tmp.startCol = Color.gray;
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229 // if (tmp.at2.resNumber >= (offset + seq.pdbstart -1) && tmp.at2.resNumber <= (seq.pdbend+offset-1)) {
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231 // int pos = seq.seqstart + (tmp.at2.resNumber - seq.pdbstart-offset);
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232 // int index = seq.findIndex(pos);
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234 // tmp.endCol = (Color)seq.getResidueBoxColour(index);
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237 // tmp.endCol = Color.gray;
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239 // } catch (Exception e) {
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240 // tmp.startCol = Color.lightGray;
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241 // tmp.endCol = Color.lightGray;
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246 public void setChainColours() {
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247 for (int i = 0; i < bonds.size(); i++) {
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248 Bond tmp = (Bond)bonds.elementAt(i);
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250 tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);
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251 tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);
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252 } catch (Exception e) {
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253 tmp.startCol = Color.lightGray;
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254 tmp.endCol = Color.lightGray;
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