/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
+ * 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 java.awt.*;
+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 int type;
- Color color = Color.lightGray;
- public String chain;
- int alignmentMapping=-1;
+public class Atom
+{
+ public float x;
- public boolean isSelected = false;
+ public float y;
- public Atom(String str)
- {
- name = str.substring(12,15).trim();
+ 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;
- resName = str.substring(17,20);
+ public int atomIndex;
- chain = str.substring(21,22);
+ public float occupancy = 0;
- resNumber = Integer.parseInt(str.substring(22,26).trim());
+ public float tfactor = 0;
- this.x = (float) (new Float(str.substring(30,38).trim()).floatValue());
- this.y = (float) (new Float(str.substring(38,46).trim()).floatValue());
- this.z = (float) (new Float(str.substring(47,55).trim()).floatValue());
+ // 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);
+ 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();
}
- public Atom(float x,float y, float z) {
- this.x = x;
- this.y = y;
- this.z = z;
+ else
+ {
+ occupancy = 1f; // default occupancy
+ // see note above: occset=false;
}
- // public void setColor(Color col) {
- // this.color = col;
- // }
+ tm = str.substring(60, 66).trim();
+ if (tm.length() > 0)
+ {
+ tfactor = (new Float(tm).floatValue());
+ }
+ else
+ {
+ tfactor = 1f;
+ // see note above: tfacset=false;
+ }
+ }
+
+ public Atom(float x, float y, float z)
+ {
+ this.x = x;
+ this.y = y;
+ this.z = z;
+ }
}