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[Jmol-commits] SF.net SVN: jmol: [7766] trunk/Jmol/src/org/jmol/shapebio
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From: <ha...@us...> - 2007-05-20 16:51:47
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Revision: 7766
http://svn.sourceforge.net/jmol/?rev=7766&view=rev
Author: hansonr
Date: 2007-05-20 09:51:42 -0700 (Sun, 20 May 2007)
Log Message:
-----------
working
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/shapebio/AlphaPolymer.java
trunk/Jmol/src/org/jmol/shapebio/AminoPolymer.java
trunk/Jmol/src/org/jmol/shapebio/BioPolymer.java
trunk/Jmol/src/org/jmol/shapebio/Helix.java
trunk/Jmol/src/org/jmol/shapebio/ProteinStructure.java
trunk/Jmol/src/org/jmol/shapebio/Turn.java
Added Paths:
-----------
trunk/Jmol/src/org/jmol/shapebio/AlphaMonomer.java
Removed Paths:
-------------
trunk/Jmol/src/org/jmol/shapebio/AlphaMonomer.java
Deleted: trunk/Jmol/src/org/jmol/shapebio/AlphaMonomer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/AlphaMonomer.java 2007-05-20 12:26:31 UTC (rev 7765)
+++ trunk/Jmol/src/org/jmol/shapebio/AlphaMonomer.java 2007-05-20 16:51:42 UTC (rev 7766)
@@ -1,142 +0,0 @@
-/* $RCSfile$
- * $Author: hansonr $
- * $Date: 2007-02-15 11:45:59 -0600 (Thu, 15 Feb 2007) $
- * $Revision: 6834 $
- *
- * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
- *
- * Contact: mi...@jm...
- *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
- * version 2.1 of the License, or (at your option) any later version.
- *
- * This library 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
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this library; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- */
-package org.jmol.shapebio;
-
-import javax.vecmath.Point3f;
-
-import org.jmol.modelset.Atom;
-import org.jmol.modelset.Chain;
-import org.jmol.viewer.JmolConstants;
-
-public class AlphaMonomer extends Monomer {
-
- final static byte[] alphaOffsets = { 0 };
-
- static Monomer
- validateAndAllocate(Chain chain, String group3, int seqcode,
- int firstIndex, int lastIndex,
- int[] specialAtomIndexes, Atom[] atoms) {
- if (firstIndex != lastIndex ||
- specialAtomIndexes[JmolConstants.ATOMID_ALPHA_CARBON] != firstIndex)
- return null;
- return new AlphaMonomer(chain, group3, seqcode,
- firstIndex, lastIndex, alphaOffsets);
- }
-
- ////////////////////////////////////////////////////////////////
-
- AlphaMonomer(Chain chain, String group3, int seqcode,
- int firstAtomIndex, int lastAtomIndex,
- byte[] offsets) {
- super(chain, group3, seqcode,
- firstAtomIndex, lastAtomIndex, offsets);
- }
-
- boolean isAlphaMonomer() { return true; }
-
- private ProteinStructure proteinStructure;
-
- ProteinStructure getProteinStructure() { return proteinStructure; }
-
- void setStructure(ProteinStructure proteinStructure) {
- this.proteinStructure = proteinStructure;
- }
-
- public byte getProteinStructureType() {
- return proteinStructure == null ? JmolConstants.PROTEIN_STRUCTURE_NONE
- : proteinStructure.type;
- }
-
- public int getProteinStructureID() {
- return proteinStructure != null ? proteinStructure.uniqueID : -1;
- }
-
- public boolean isHelix() {
- return proteinStructure != null &&
- proteinStructure.type == JmolConstants.PROTEIN_STRUCTURE_HELIX;
- }
-
- public boolean isSheet() {
- return proteinStructure != null &&
- proteinStructure.type == JmolConstants.PROTEIN_STRUCTURE_SHEET;
- }
-
- /**
- *
- * @param iType
- * @param monomerIndexCurrent a pointer to the current ProteinStructure
- * @return a pointer to this ProteinStructure
- */
- public int setProteinStructureType(byte iType, int monomerIndexCurrent) {
- if (monomerIndexCurrent < 0) {
- if (proteinStructure != null) {
- int nAbandoned = proteinStructure.removeMonomer(monomerIndex);
- if (nAbandoned > 0)
- getBioPolymer().removeProteinStructure(monomerIndex + 1, nAbandoned);
- }
- switch (iType) {
- case JmolConstants.PROTEIN_STRUCTURE_HELIX:
- setStructure(new Helix((AlphaPolymer) bioPolymer, monomerIndex, 1));
- break;
- case JmolConstants.PROTEIN_STRUCTURE_SHEET:
- setStructure(new Sheet((AminoPolymer) bioPolymer, monomerIndex, 1));
- break;
- case JmolConstants.PROTEIN_STRUCTURE_TURN:
- setStructure(new Turn((AlphaPolymer) bioPolymer, monomerIndex, 1));
- break;
- case JmolConstants.PROTEIN_STRUCTURE_NONE:
- setStructure(null);
- }
- } else {
- setStructure(getBioPolymer().getProteinStructure(monomerIndexCurrent));
- if (proteinStructure != null)
- proteinStructure.addMonomer(monomerIndex);
- }
- return monomerIndex;
- }
-
- final public Atom getAtom(byte specialAtomID) {
- return (specialAtomID == JmolConstants.ATOMID_ALPHA_CARBON
- ? getLeadAtom()
- : null);
- }
-
- final public Point3f getAtomPoint(byte specialAtomID) {
- return (specialAtomID == JmolConstants.ATOMID_ALPHA_CARBON
- ? getLeadAtomPoint()
- : null);
- }
-
- boolean isConnectedAfter(Monomer possiblyPreviousMonomer) {
- if (possiblyPreviousMonomer == null)
- return true;
- if (! (possiblyPreviousMonomer instanceof AlphaMonomer))
- return false;
- float distance =
- getLeadAtomPoint().distance(possiblyPreviousMonomer.getLeadAtomPoint());
- // jan reichert in email to miguel on 10 May 2004 said 4.2 looked good
- return distance <= 4.2f;
- }
-
-}
Added: trunk/Jmol/src/org/jmol/shapebio/AlphaMonomer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/AlphaMonomer.java (rev 0)
+++ trunk/Jmol/src/org/jmol/shapebio/AlphaMonomer.java 2007-05-20 16:51:42 UTC (rev 7766)
@@ -0,0 +1,142 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2007-02-15 11:45:59 -0600 (Thu, 15 Feb 2007) $
+ * $Revision: 6834 $
+ *
+ * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
+ *
+ * Contact: mi...@jm...
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library 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
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.jmol.shapebio;
+
+import javax.vecmath.Point3f;
+
+import org.jmol.modelset.Atom;
+import org.jmol.modelset.Chain;
+import org.jmol.viewer.JmolConstants;
+
+public class AlphaMonomer extends Monomer {
+
+ final static byte[] alphaOffsets = { 0 };
+
+ static Monomer
+ validateAndAllocate(Chain chain, String group3, int seqcode,
+ int firstIndex, int lastIndex,
+ int[] specialAtomIndexes, Atom[] atoms) {
+ if (firstIndex != lastIndex ||
+ specialAtomIndexes[JmolConstants.ATOMID_ALPHA_CARBON] != firstIndex)
+ return null;
+ return new AlphaMonomer(chain, group3, seqcode,
+ firstIndex, lastIndex, alphaOffsets);
+ }
+
+ ////////////////////////////////////////////////////////////////
+
+ AlphaMonomer(Chain chain, String group3, int seqcode,
+ int firstAtomIndex, int lastAtomIndex,
+ byte[] offsets) {
+ super(chain, group3, seqcode,
+ firstAtomIndex, lastAtomIndex, offsets);
+ }
+
+ boolean isAlphaMonomer() { return true; }
+
+ private ProteinStructure proteinStructure;
+
+ ProteinStructure getProteinStructure() { return proteinStructure; }
+
+ void setStructure(ProteinStructure proteinStructure) {
+ this.proteinStructure = proteinStructure;
+ }
+
+ public byte getProteinStructureType() {
+ return proteinStructure == null ? JmolConstants.PROTEIN_STRUCTURE_NONE
+ : proteinStructure.type;
+ }
+
+ public int getProteinStructureID() {
+ return proteinStructure != null ? proteinStructure.uniqueID : -1;
+ }
+
+ public boolean isHelix() {
+ return proteinStructure != null &&
+ proteinStructure.type == JmolConstants.PROTEIN_STRUCTURE_HELIX;
+ }
+
+ public boolean isSheet() {
+ return proteinStructure != null &&
+ proteinStructure.type == JmolConstants.PROTEIN_STRUCTURE_SHEET;
+ }
+
+ /**
+ *
+ * @param iType
+ * @param monomerIndexCurrent a pointer to the current ProteinStructure
+ * @return a pointer to this ProteinStructure
+ */
+ public int setProteinStructureType(byte iType, int monomerIndexCurrent) {
+ if (monomerIndexCurrent < 0) {
+ if (proteinStructure != null) {
+ int nAbandoned = proteinStructure.removeMonomer(monomerIndex);
+ if (nAbandoned > 0)
+ getBioPolymer().removeProteinStructure(monomerIndex + 1, nAbandoned);
+ }
+ switch (iType) {
+ case JmolConstants.PROTEIN_STRUCTURE_HELIX:
+ setStructure(new Helix((AlphaPolymer) bioPolymer, monomerIndex, 1));
+ break;
+ case JmolConstants.PROTEIN_STRUCTURE_SHEET:
+ setStructure(new Sheet((AminoPolymer) bioPolymer, monomerIndex, 1));
+ break;
+ case JmolConstants.PROTEIN_STRUCTURE_TURN:
+ setStructure(new Turn((AlphaPolymer) bioPolymer, monomerIndex, 1));
+ break;
+ case JmolConstants.PROTEIN_STRUCTURE_NONE:
+ setStructure(null);
+ }
+ } else {
+ setStructure(getBioPolymer().getProteinStructure(monomerIndexCurrent));
+ if (proteinStructure != null)
+ proteinStructure.addMonomer(monomerIndex);
+ }
+ return monomerIndex;
+ }
+
+ final public Atom getAtom(byte specialAtomID) {
+ return (specialAtomID == JmolConstants.ATOMID_ALPHA_CARBON
+ ? getLeadAtom()
+ : null);
+ }
+
+ final public Point3f getAtomPoint(byte specialAtomID) {
+ return (specialAtomID == JmolConstants.ATOMID_ALPHA_CARBON
+ ? getLeadAtomPoint()
+ : null);
+ }
+
+ boolean isConnectedAfter(Monomer possiblyPreviousMonomer) {
+ if (possiblyPreviousMonomer == null)
+ return true;
+ if (! (possiblyPreviousMonomer instanceof AlphaMonomer))
+ return false;
+ float distance =
+ getLeadAtomPoint().distance(possiblyPreviousMonomer.getLeadAtomPoint());
+ // jan reichert in email to miguel on 10 May 2004 said 4.2 looked good
+ return distance <= 4.2f;
+ }
+
+}
Modified: trunk/Jmol/src/org/jmol/shapebio/AlphaPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/AlphaPolymer.java 2007-05-20 12:26:31 UTC (rev 7765)
+++ trunk/Jmol/src/org/jmol/shapebio/AlphaPolymer.java 2007-05-20 16:51:42 UTC (rev 7766)
@@ -23,6 +23,13 @@
*/
package org.jmol.shapebio;
+import org.jmol.shapebio.AminoPolymer;
+import org.jmol.shapebio.BioPolymer;
+import org.jmol.shapebio.Helix;
+import org.jmol.shapebio.Monomer;
+import org.jmol.shapebio.ProteinStructure;
+import org.jmol.shapebio.Sheet;
+import org.jmol.shapebio.Turn;
import org.jmol.util.Logger;
import org.jmol.util.Measure;
import org.jmol.viewer.JmolConstants;
Modified: trunk/Jmol/src/org/jmol/shapebio/AminoPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/AminoPolymer.java 2007-05-20 12:26:31 UTC (rev 7765)
+++ trunk/Jmol/src/org/jmol/shapebio/AminoPolymer.java 2007-05-20 16:51:42 UTC (rev 7766)
@@ -24,6 +24,7 @@
package org.jmol.shapebio;
import org.jmol.modelset.Atom;
+import org.jmol.shapebio.AlphaPolymer;
import org.jmol.util.Logger;
import org.jmol.util.Measure;
import org.jmol.viewer.JmolConstants;
Modified: trunk/Jmol/src/org/jmol/shapebio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/BioPolymer.java 2007-05-20 12:26:31 UTC (rev 7765)
+++ trunk/Jmol/src/org/jmol/shapebio/BioPolymer.java 2007-05-20 16:51:42 UTC (rev 7766)
@@ -25,6 +25,7 @@
import org.jmol.modelset.Group;
import org.jmol.modelset.Polymer;
+import org.jmol.shapebio.AlphaPolymer;
import org.jmol.shape.Closest;
import org.jmol.util.BitSetUtil;
import org.jmol.util.Logger;
Modified: trunk/Jmol/src/org/jmol/shapebio/Helix.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/Helix.java 2007-05-20 12:26:31 UTC (rev 7765)
+++ trunk/Jmol/src/org/jmol/shapebio/Helix.java 2007-05-20 16:51:42 UTC (rev 7766)
@@ -27,6 +27,7 @@
import javax.vecmath.Vector3f;
import org.jmol.g3d.Graphics3D;
+import org.jmol.shapebio.AlphaPolymer;
import org.jmol.viewer.JmolConstants;
class Helix extends ProteinStructure {
Modified: trunk/Jmol/src/org/jmol/shapebio/ProteinStructure.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/ProteinStructure.java 2007-05-20 12:26:31 UTC (rev 7765)
+++ trunk/Jmol/src/org/jmol/shapebio/ProteinStructure.java 2007-05-20 16:51:42 UTC (rev 7766)
@@ -26,6 +26,7 @@
import javax.vecmath.Point3f;
import javax.vecmath.Vector3f;
+import org.jmol.shapebio.AlphaPolymer;
import org.jmol.util.Logger;
import org.jmol.viewer.JmolConstants;
Modified: trunk/Jmol/src/org/jmol/shapebio/Turn.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/Turn.java 2007-05-20 12:26:31 UTC (rev 7765)
+++ trunk/Jmol/src/org/jmol/shapebio/Turn.java 2007-05-20 16:51:42 UTC (rev 7766)
@@ -23,6 +23,7 @@
*/
package org.jmol.shapebio;
+import org.jmol.shapebio.AlphaPolymer;
import org.jmol.viewer.JmolConstants;
public class Turn extends ProteinStructure {
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