Use PDB column format

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index e38d7aa..0815dc0 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -37,35 +37,19 @@ public class Atom {
 \r
     public boolean isSelected = false;\r
 \r
-    public Atom(StringTokenizer str)\r
+    public Atom(String str)\r
     {\r
-        str.nextToken(); // Number, not used in MCview\r
-        this.name = str.nextToken(); // Name, not used in MCview\r
+        name =  str.substring(12,16);\r
 \r
-        this.resName = str.nextToken();\r
+        resName = str.substring(17,20);\r
 \r
-        String token1 = str.nextToken();\r
+        chain = str.substring(21,22);\r
 \r
-        String token2 = str.nextToken();\r
-\r
-        try{\r
-\r
-          this.chain = token1;\r
-          resNumber = Integer.parseInt(token2);\r
-\r
-          this.x = (float) (new Float(str.nextToken()).floatValue());\r
-          this.y = (float) (new Float(str.nextToken()).floatValue());\r
-          this.z = (float) (new Float(str.nextToken()).floatValue());\r
-\r
-        }catch(NumberFormatException ex)\r
-        {\r
-          chain = "A";\r
-          resNumber = Integer.parseInt(token1);\r
-          this.x = (float) (new Float(token2).floatValue());\r
-          this.y = (float) (new Float(str.nextToken()).floatValue());\r
-          this.z = (float) (new Float(str.nextToken()).floatValue());\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
     public void setColor(Color col) {\r

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 9c1d0e0..43c8e9d 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -139,10 +139,12 @@ public class PDBChain {
                                                                                   .get(tmpat.resName)).intValue()];\r
                 seq = seq + tmpres2;\r
             }\r
-\r
         }\r
 \r
-        sequence = new Sequence("PDB_seq", seq, 1, seq.length());\r
+        if(id.length()<1 || id.equals(" "))\r
+           id = "_";\r
+\r
+        sequence = new Sequence(id, seq, 1, seq.length());\r
      //   System.out.println("PDB Sequence is :\nSequence = " + seq);\r
      //   System.out.println("No of residues = " + residues.size());\r
     }\r

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index d1e4d65..2b22b24 100755 (executable)
--- 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 {\r
     public Vector chains = new Vector();\r
     Vector lineArray = new Vector();\r
+    String id;\r
 \r
     public PDBfile(String[] lines) {\r
         for (int i = 0; i < lines.length; i++)\r
@@ -68,22 +69,29 @@ public class PDBfile extends jalview.io.FileParse {
         parse();\r
     }\r
 \r
-    public void parse() {\r
-        for (int i = 0; i < lineArray.size(); i++) {\r
-            StringTokenizer str = new StringTokenizer(lineArray.elementAt(i)\r
-                                                               .toString());\r
+    public void parse()\r
+    {\r
+        String line;\r
+        for (int i = 0; i < lineArray.size(); i++)\r
+        {\r
 \r
-            if (str.hasMoreTokens()) {\r
-                String inStr = str.nextToken();\r
+           line = lineArray.elementAt(i).toString();\r
 \r
-                if (inStr.indexOf("ATOM") != -1) {\r
+           if (line.indexOf("HEADER") == 0)\r
+           {\r
+             id = line.substring(62, 67).trim();\r
+             continue;\r
+           }\r
+\r
+                if (line.indexOf("ATOM") == 0) {\r
                     try {\r
-                        Atom tmpatom = new Atom(str);\r
+                        Atom tmpatom = new Atom(line);\r
 \r
-                        if (findChain(tmpatom.chain) != null) {\r
-                            //   System.out.println("Adding to chain " + tmpatom.chain);\r
+                        if (findChain(tmpatom.chain) != null)\r
+                        {\r
                             findChain(tmpatom.chain).atoms.addElement(tmpatom);\r
-                        } else {\r
+                        } else\r
+                        {\r
                             PDBChain tmpchain = new PDBChain(tmpatom.chain);\r
                             chains.addElement(tmpchain);\r
                             tmpchain.atoms.addElement(tmpatom);\r
@@ -94,7 +102,6 @@ public class PDBfile extends jalview.io.FileParse {
                             lineArray.elementAt(i).toString());\r
                     }\r
                 }\r
-            }\r
         }\r
 \r
         makeResidueList();\r