From 4060c4dbd774eb4937c90e5fe866b3408fb330e8 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 18 Nov 2005 11:36:07 +0000
Subject: [PATCH] Use PDB column format

---
 src/MCview/Atom.java     |   32 ++++++++------------------------
 src/MCview/PDBChain.java |    6 ++++--
 src/MCview/PDBfile.java  |   31 +++++++++++++++++++------------
 3 files changed, 31 insertions(+), 38 deletions(-)

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index e38d7aa..0815dc0 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -37,35 +37,19 @@ public class Atom {
 
     public boolean isSelected = false;
 
-    public Atom(StringTokenizer str)
+    public Atom(String str)
     {
-        str.nextToken(); // Number, not used in MCview
-        this.name = str.nextToken(); // Name, not used in MCview
+        name =  str.substring(12,16);
 
-        this.resName = str.nextToken();
+        resName = str.substring(17,20);
 
-        String token1 = str.nextToken();
+        chain = str.substring(21,22);
 
-        String token2 = str.nextToken();
-
-        try{
-
-          this.chain = token1;
-          resNumber = Integer.parseInt(token2);
-
-          this.x = (float) (new Float(str.nextToken()).floatValue());
-          this.y = (float) (new Float(str.nextToken()).floatValue());
-          this.z = (float) (new Float(str.nextToken()).floatValue());
-
-        }catch(NumberFormatException ex)
-        {
-          chain = "A";
-          resNumber = Integer.parseInt(token1);
-          this.x = (float) (new Float(token2).floatValue());
-          this.y = (float) (new Float(str.nextToken()).floatValue());
-          this.z = (float) (new Float(str.nextToken()).floatValue());
-        }
+        resNumber = Integer.parseInt(str.substring(22,26).trim());
 
+        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());
     }
 
     public void setColor(Color col) {
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 9c1d0e0..43c8e9d 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -139,10 +139,12 @@ public class PDBChain {
                                                                                   .get(tmpat.resName)).intValue()];
                 seq = seq + tmpres2;
             }
-
         }
 
-        sequence = new Sequence("PDB_seq", seq, 1, seq.length());
+        if(id.length()<1 || id.equals(" "))
+           id = "_";
+
+        sequence = new Sequence(id, seq, 1, seq.length());
      //   System.out.println("PDB Sequence is :\nSequence = " + seq);
      //   System.out.println("No of residues = " + residues.size());
     }
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index d1e4d65..2b22b24 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -29,6 +29,7 @@ import java.awt.Color;
 public class PDBfile extends jalview.io.FileParse {
     public Vector chains = new Vector();
     Vector lineArray = new Vector();
+    String id;
 
     public PDBfile(String[] lines) {
         for (int i = 0; i < lines.length; i++)
@@ -68,22 +69,29 @@ public class PDBfile extends jalview.io.FileParse {
         parse();
     }
 
-    public void parse() {
-        for (int i = 0; i < lineArray.size(); i++) {
-            StringTokenizer str = new StringTokenizer(lineArray.elementAt(i)
-                                                               .toString());
+    public void parse()
+    {
+        String line;
+        for (int i = 0; i < lineArray.size(); i++)
+        {
 
-            if (str.hasMoreTokens()) {
-                String inStr = str.nextToken();
+           line = lineArray.elementAt(i).toString();
 
-                if (inStr.indexOf("ATOM") != -1) {
+           if (line.indexOf("HEADER") == 0)
+           {
+             id = line.substring(62, 67).trim();
+             continue;
+           }
+
+                if (line.indexOf("ATOM") == 0) {
                     try {
-                        Atom tmpatom = new Atom(str);
+                        Atom tmpatom = new Atom(line);
 
-                        if (findChain(tmpatom.chain) != null) {
-                            //   System.out.println("Adding to chain " + tmpatom.chain);
+                        if (findChain(tmpatom.chain) != null)
+                        {
                             findChain(tmpatom.chain).atoms.addElement(tmpatom);
-                        } else {
+                        } else
+                        {
                             PDBChain tmpchain = new PDBChain(tmpatom.chain);
                             chains.addElement(tmpchain);
                             tmpchain.atoms.addElement(tmpatom);
@@ -94,7 +102,6 @@ public class PDBfile extends jalview.io.FileParse {
                             lineArray.elementAt(i).toString());
                     }
                 }
-            }
         }
 
         makeResidueList();
-- 
1.7.10.2