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.
35 public String resName;
39 public char insCode = ' ';
41 public String resNumIns = null;
45 Color color = Color.lightGray;
50 * this is a temporary value - designed to store the position in sequence that
51 * this atom corresponds to after aligning the chain to a SequenceI object. Do
52 * not rely on its value being correct when visualizing sequence colourings on
53 * the structure - use the StructureSelectionManager's mapping instead.
55 public int alignmentMapping = -1;
59 public float occupancy = 0;
61 public float tfactor = 0;
63 // need these if we ever want to export Atom data
64 // public boolean tfacset=true,occset=true;
65 public boolean isSelected = false;
67 public Atom(String str)
69 atomIndex = Integer.parseInt(str.substring(6, 11).trim());
71 name = str.substring(12, 15).trim();
73 resName = str.substring(17, 20);
75 chain = str.substring(21, 22);
77 resNumber = Integer.parseInt(str.substring(22, 26).trim());
78 resNumIns = str.substring(22, 27);
79 insCode = str.substring(26, 27).charAt(0);
80 this.x = (float) (new Float(str.substring(30, 38).trim()).floatValue());
81 this.y = (float) (new Float(str.substring(38, 46).trim()).floatValue());
82 this.z = (float) (new Float(str.substring(47, 55).trim()).floatValue());
83 // optional entries - see JAL-730
84 String tm = str.substring(54, 60).trim();
87 occupancy = (float) (new Float(tm)).floatValue();
91 occupancy = 1f; // default occupancy
92 // see note above: occset=false;
94 tm = str.substring(60, 66).trim();
97 tfactor = (float) (new Float(tm).floatValue());
102 // see note above: tfacset=false;
106 public Atom(float x, float y, float z)
112 // public void setColor(Color col) {