2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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/>.
34 public String resName;
38 public char insCode = ' ';
40 public String resNumIns = null;
44 Color color = Color.lightGray;
48 public int alignmentMapping = -1;
52 public float occupancy = 0;
54 public float tfactor = 0;
55 // need these if we ever want to export Atom data
56 // public boolean tfacset=true,occset=true;
57 public boolean isSelected = false;
59 public Atom(String str)
61 atomIndex = Integer.parseInt(str.substring(6, 11).trim());
63 name = str.substring(12, 15).trim();
65 resName = str.substring(17, 20);
67 chain = str.substring(21, 22);
69 resNumber = Integer.parseInt(str.substring(22, 26).trim());
70 resNumIns = str.substring(22, 27);
71 insCode = str.substring(26, 27).charAt(0);
72 this.x = (float) (new Float(str.substring(30, 38).trim()).floatValue());
73 this.y = (float) (new Float(str.substring(38, 46).trim()).floatValue());
74 this.z = (float) (new Float(str.substring(47, 55).trim()).floatValue());
75 // optional entries - see JAL-730
76 String tm = str.substring(54, 60).trim();
78 occupancy = (float) (new Float(tm)).floatValue();
80 occupancy = 1f; // default occupancy
81 // see note above: occset=false;
83 tm = str.substring(60, 66).trim();
86 tfactor = (float) (new Float(tm).floatValue());
89 //see note above: tfacset=false;
93 public Atom(float x, float y, float z)
99 // public void setColor(Color col) {