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