2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
29 Color startCol = Color.lightGray;
31 Color endCol = Color.lightGray;
37 public Bond(float[] start, float[] end, Atom at1, Atom at2)
41 this.startCol = at1.color;
42 this.endCol = at2.color;
48 * public Bond(Bond bond) { this.start = new float[3];
50 * this.start[0] = bond.start[0]; this.start[1] = bond.start[1]; this.start[2] =
53 * this.end = new float[3];
55 * this.end[0] = bond.end[0]; this.end[1] = bond.end[1]; this.end[2] =
58 * this.startCol = bond.startCol; this.endCol = bond.endCol; }
60 * public float length() { float len = ((end[0] - start[0]) * (end[0] -
61 * start[0])) + ((end[1] - start[1]) * (end[1] - start[1])) + ((end[2] -
62 * start[2]) * (end[2] - start[2]));
64 * len = (float) (Math.sqrt(len));
69 public void translate(float x, float y, float z)
71 start[0] = (start[0] + x);
72 end[0] = (end[0] + x);
74 start[1] = (start[1] + y);
75 end[1] = (end[1] + y);
77 start[2] = (start[2] + z);
78 end[2] = (end[2] + z);