2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
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);