-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package MCview;\r
-\r
-import java.awt.*;\r
-\r
-\r
-public class Atom {\r
- float x;\r
- float y;\r
- float z;\r
- int number;\r
- String name;\r
- String resName;\r
- int resNumber;\r
- int type;\r
- Color color = Color.lightGray;\r
- String chain;\r
- int alignmentMapping=-1;\r
-\r
- public boolean isSelected = false;\r
-\r
- public Atom(String str)\r
- {\r
- name = str.substring(12,15).trim();\r
-\r
- resName = str.substring(17,20);\r
-\r
- chain = str.substring(21,22);\r
-\r
- resNumber = Integer.parseInt(str.substring(22,26).trim());\r
-\r
- this.x = (float) (new Float(str.substring(30,38).trim()).floatValue());\r
- this.y = (float) (new Float(str.substring(38,46).trim()).floatValue());\r
- this.z = (float) (new Float(str.substring(47,55).trim()).floatValue());\r
-\r
- }\r
-\r
- // public void setColor(Color col) {\r
- // this.color = col;\r
- // }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package MCview;
+
+import jalview.schemes.ResidueProperties;
+
+import java.awt.Color;
+
+public class Atom
+{
+ public float x;
+
+ public float y;
+
+ public float z;
+
+ public int number;
+
+ public String name;
+
+ public String resName;
+
+ public int resNumber;
+
+ public char insCode = ' ';
+
+ public String resNumIns = null;
+
+ public int type;
+
+ Color color = Color.lightGray;
+
+ public String chain;
+
+ /**
+ * this is a temporary value - designed to store the position in sequence that
+ * this atom corresponds to after aligning the chain to a SequenceI object. Do
+ * not rely on its value being correct when visualizing sequence colourings on
+ * the structure - use the StructureSelectionManager's mapping instead.
+ */
+ public int alignmentMapping = -1;
+
+ public int atomIndex;
+
+ public float occupancy = 0;
+
+ public float tfactor = 0;
+
+ // need these if we ever want to export Atom data
+ // public boolean tfacset=true,occset=true;
+ public boolean isSelected = false;
+
+ public Atom(String str)
+ {
+ atomIndex = Integer.parseInt(str.substring(6, 11).trim());
+
+ name = str.substring(12, 15).trim();
+
+ resName = str.substring(17, 20);
+ // JAL-1828 treat MSE Selenomethionine as MET (etc)
+ resName = ResidueProperties.getCanonicalAminoAcid(resName);
+
+ chain = str.substring(21, 22);
+
+ resNumber = Integer.parseInt(str.substring(22, 26).trim());
+ resNumIns = str.substring(22, 27).trim();
+ insCode = str.substring(26, 27).charAt(0);
+ this.x = (new Float(str.substring(30, 38).trim()).floatValue());
+ this.y = (new Float(str.substring(38, 46).trim()).floatValue());
+ this.z = (new Float(str.substring(47, 55).trim()).floatValue());
+ // optional entries - see JAL-730
+ String tm = str.substring(54, 60).trim();
+ if (tm.length() > 0)
+ {
+ occupancy = (new Float(tm)).floatValue();
+ }
+ else
+ {
+ occupancy = 1f; // default occupancy
+ // see note above: occset=false;
+ }
+ tm = str.substring(60, 66).trim();
+ if (tm.length() > 0)
+ {
+ tfactor = (new Float(tm).floatValue());
+ }
+ else
+ {
+ tfactor = 1f;
+ // see note above: tfacset=false;
+ }
+ }
+
+ @Override
+ public boolean equals(Object that)
+ {
+ if (this == that || that == null)
+ {
+ return true;
+ }
+ if (that instanceof Atom)
+ {
+ Atom other = (Atom) that;
+ return other.resName.equals(this.resName)
+ && other.resNumber == this.resNumber
+ && other.resNumIns.equals(this.resNumIns)
+ && other.chain.equals(this.chain);
+ }
+ return false;
+ }
+
+ public Atom(float x, float y, float z)
+ {
+ this.x = x;
+ this.y = y;
+ this.z = z;
+ }
+}