X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=5176b1545203dcbac50cb5fbac4338666a906f54;hb=37b210ecad3c132b87c525f84e3b754a4edf12a6;hp=61ad26a2cbdc32e8281792039d3ee46d3aceeb0d;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 61ad26a..5176b15 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
- * 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.
+ * 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.
  * 
- * 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 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/>.
  */
 package MCview;
 
@@ -48,6 +47,8 @@ public class PDBChain
 
   public Sequence sequence;
 
+  public boolean isNa = false;
+
   public boolean isVisible = true;
 
   public int pdbstart = 0;
@@ -66,6 +67,21 @@ public class PDBChain
     this.id = id;
   }
 
+  /**
+   * character used to write newlines
+   */
+  protected String newline = System.getProperty("line.separator");
+
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+  }
+
+  public String getNewlineString()
+  {
+    return newline;
+  }
+
   public String print()
   {
     String tmp = "";
@@ -74,12 +90,19 @@ public class PDBChain
     {
       tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
               + ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
-              + "\n";
+              + newline;
     }
 
     return tmp;
   }
 
+  /**
+   * Annotate the residues with their corresponding positions in s1 using the
+   * alignment in as
+   * 
+   * @param as
+   * @param s1
+   */
   public void makeExactMapping(AlignSeq as, SequenceI s1)
   {
     int pdbpos = as.getSeq2Start() - 2;
@@ -116,7 +139,7 @@ public class PDBChain
    * 
    * @param seq
    * @param status
-   *                The Status of the transferred annotation
+   *          The Status of the transferred annotation
    * @return the features added to sq (or its dataset)
    */
   public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
@@ -134,8 +157,8 @@ public class PDBChain
     /**
      * Remove any existing features for this chain if they exist ?
      * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
-     * totfeat=seqsfeatures.length; // Remove any features for this exact chain ?
-     * for (int i=0; i<seqsfeatures.length; i++) { }
+     * totfeat=seqsfeatures.length; // Remove any features for this exact chain
+     * ? for (int i=0; i<seqsfeatures.length; i++) { }
      */
     if (status == null)
     {
@@ -151,10 +174,9 @@ public class PDBChain
                 - offset)).atoms.elementAt(0)).alignmentMapping);
         tx.setEnd(1 + ((Atom) ((Residue) residues.elementAt(tx.getEnd()
                 - offset)).atoms.elementAt(0)).alignmentMapping);
-        tx
-                .setStatus(status
-                        + ((tx.getStatus() == null || tx.getStatus()
-                                .length() == 0) ? "" : ":" + tx.getStatus()));
+        tx.setStatus(status
+                + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
+                        : ":" + tx.getStatus()));
         if (tx.begin != 0 && tx.end != 0)
           sq.addSequenceFeature(tx);
       }
@@ -164,17 +186,29 @@ public class PDBChain
 
   public void makeCaBondList()
   {
+    boolean na = false;
+    int numNa = 0;
     for (int i = 0; i < (residues.size() - 1); i++)
     {
       Residue tmpres = (Residue) residues.elementAt(i);
       Residue tmpres2 = (Residue) residues.elementAt(i + 1);
       Atom at1 = tmpres.findAtom("CA");
       Atom at2 = tmpres2.findAtom("CA");
-
+      na = false;
+      if ((at1 == null) && (at2 == null))
+      {
+        na = true;
+        at1 = tmpres.findAtom("P");
+        at2 = tmpres2.findAtom("P");
+      }
       if ((at1 != null) && (at2 != null))
       {
         if (at1.chain.equals(at2.chain))
         {
+          if (na)
+          {
+            numNa++;
+          }
           makeBond(at1, at2);
         }
       }
@@ -183,6 +217,10 @@ public class PDBChain
         System.out.println("not found " + i);
       }
     }
+    if (numNa > 0 && ((numNa / residues.size()) > 0.99))
+    {
+      isNa = true;
+    }
   }
 
   public void makeBond(Atom at1, Atom at2)
@@ -204,6 +242,8 @@ public class PDBChain
   public void makeResidueList()
   {
     int count = 0;
+    Object symbol;
+    boolean nucleotide = false;
     StringBuffer seq = new StringBuffer();
     Vector resFeatures = new Vector();
     Vector resAnnotation = new Vector();
@@ -254,17 +294,31 @@ public class PDBChain
       resFeatures.addElement(sf);
       resAnnotation.addElement(new Annotation(tmpat.tfactor));
       // Keep totting up the sequence
-      if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
+      if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
       {
-        seq.append("X");
-        // System.err.println("PDBReader:Null aa3Hash for " +
-        // tmpat.resName);
+        String nucname = tmpat.resName.trim();
+        if (tmpat.name.equalsIgnoreCase("CA")
+                || ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
+        {
+          seq.append("X");
+          // System.err.println("PDBReader:Null aa3Hash for " +
+          // tmpat.resName);
+        }
+        else
+        {
+          // nucleotide flag
+          nucleotide = true;
+          seq.append(nucname.charAt(0));
+        }
       }
       else
       {
-
-        seq.append(ResidueProperties.aa[((Integer) ResidueProperties
-                .getAA3Hash().get(tmpat.resName)).intValue()]);
+        if (nucleotide)
+        {
+          System.err
+                  .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+        }
+        seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
       }
       count++;
     }
@@ -273,15 +327,14 @@ public class PDBChain
     {
       id = " ";
     }
-
+    isNa = nucleotide;
     sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
-                                                                        // resNumber-offset
-                                                                        // ~=
-                                                                        // seq.size()
+    // resNumber-offset
+    // ~=
+    // seq.size()
     // Add normalised feature scores to RESNUM indicating start/end of sequence
-    //      sf.setScore(offset+count);
-                                                                           
-                                                                       
+    // sf.setScore(offset+count);
+
     // System.out.println("PDB Sequence is :\nSequence = " + seq);
     // System.out.println("No of residues = " + residues.size());
     for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
@@ -300,7 +353,7 @@ public class PDBChain
       resAnnotation.setElementAt(null, i);
     }
     AlignmentAnnotation tfactorann = new AlignmentAnnotation(
-            "PDB.CATempFactor", "CA Temperature Factor for "
+            "PDB.TempFactor", "Temperature Factor for "
                     + sequence.getName(), annots, 0, max,
             AlignmentAnnotation.LINE_GRAPH);
     tfactorann.setSequenceRef(sequence);
@@ -446,11 +499,9 @@ public class PDBChain
           }
         }
       }
-      sq
-              .addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
-                      "PDB Residue Numbering for " + this.pdbid + ":"
-                              + this.id, an, (float) min, (float) max,
-                      AlignmentAnnotation.LINE_GRAPH));
+      sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+              "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
+              an, (float) min, (float) max, AlignmentAnnotation.LINE_GRAPH));
     }
   }
 }