X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=c4fe563123894da879ff4dc1bb45d7585ff0e898;hb=75d17bc3d8444203906499e651df6a69f6c2f518;hp=1aa5cac3e57e06e8907da3f44190a820dab349cb;hpb=485ceb23bbae52bb2b0fd1def01e1f6822ececcf;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 1aa5cac..c4fe563 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,144 +1,169 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 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
+*/
 package MCview;
 
-import jalview.datamodel.*;
 import java.io.*;
+
 import java.net.*;
+
 import java.util.*;
+import java.awt.Color;
 
 
 public class PDBfile extends jalview.io.FileParse {
+    public Vector chains = new Vector();
+    Vector lineArray = new Vector();
+    String id;
 
-  public Vector chains = new Vector();
+    public PDBfile(String[] lines) {
+        for (int i = 0; i < lines.length; i++)
+            lineArray.addElement(lines[i]);
 
-  Vector lineArray = new Vector();
-
-  public PDBfile(String [] lines)
-  {
-    for(int i=0; i<lines.length; i++)
-      lineArray.add(lines[i]);
+        noLines = lineArray.size();
+        parse();
+    }
 
-    noLines = lineArray.size();
-    parse();
-  }
+    public PDBfile(String inFile, String inType) throws IOException {
+        super(inFile, inType);
 
-  public PDBfile(String inFile, String inType) throws IOException {
+        String line;
+        this.lineArray = new Vector();
 
-    super(inFile,inType);
+        BufferedReader dataIn;
 
-    String line;
-    this.lineArray = new Vector();
-    BufferedReader dataIn;
+        if (inType.equals("File")) {
+            dataIn = new BufferedReader(new FileReader(inFile));
+        }
+        else if(inType.equals("Paste"))
+        {
+            dataIn = new BufferedReader(new StringReader(inFile));
+        }
+        else {
+            URL url = new URL(inFile);
+            this.fileSize = 0;
+            dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+        }
 
-    if (inType.equals("File"))
-      dataIn =  new BufferedReader(new FileReader( inFile ));
+        while ((line = dataIn.readLine()) != null) {
+            lineArray.addElement(line);
+        }
 
-    else
-    {
-      URL url = new URL(inFile);
-      this.fileSize = 0;
-      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    }
+        noLines = lineArray.size();
 
-    while ((line = dataIn.readLine()) != null) {
-      lineArray.addElement(line);
+        parse();
     }
-    noLines = lineArray.size();
 
-    parse();
-
-}
+    public void parse()
+    {
+        PDBChain tmpchain;
+        String line;
+        boolean modelFlag = false;
+        for (int i = 0; i < lineArray.size(); i++)
+        {
+
+           line = lineArray.elementAt(i).toString();
+
+           if (line.indexOf("HEADER") == 0)
+           {
+             id = line.substring(62, 67).trim();
+             continue;
+           }
+
+           if(line.indexOf("MODEL")==0)
+             modelFlag = true;
+
+           if(modelFlag && line.indexOf("ENDMDL")==0)
+             break;
+
+           if (line.indexOf("ATOM")==0 || line.indexOf("HETATM")==0 )
+            {
+                    try {
+                        Atom tmpatom = new Atom(line);
+
+                        //Jalview is only interested in CA bonds????
+                        if(!tmpatom.name.equals("CA"))
+                          continue;
+
+                        tmpchain = findChain(tmpatom.chain);
+                        if ( tmpchain != null)
+                        {
+                          tmpchain.atoms.addElement(tmpatom);
+                        }
+                        else
+                        {
+                            tmpchain = new PDBChain(tmpatom.chain);
+                            chains.addElement(tmpchain);
+                            tmpchain.atoms.addElement(tmpatom);
+                        }
+                    } catch (NumberFormatException e) {
+                        System.err.println("Caught" + e);
+                        System.err.println("Record not added to PDB model:" +
+                            lineArray.elementAt(i).toString());
+                    }
+                }
+        }
 
+        makeResidueList();
+        makeCaBondList();
+    }
 
-  public void parse() {
-
-    for (int i = 0; i < lineArray.size(); i++) {
-      StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());
-      if (str.hasMoreTokens()) {
-        String inStr = str.nextToken();
-
-        if (inStr.indexOf("ATOM") != -1) {
-          try {
-            myAtom tmpatom = new myAtom(str);
-            if (findChain(tmpatom.chain) != null) {
-           //   System.out.println("Adding to chain " + tmpatom.chain);
-              findChain(tmpatom.chain).atoms.addElement(tmpatom);
-            } else {
-            //  System.out.println("Making chain " + tmpatom.chain);
-              PDBChain tmpchain = new PDBChain(tmpatom.chain);
-              chains.addElement(tmpchain);
-              tmpchain.atoms.addElement(tmpatom);
-            }
-          } catch(NumberFormatException e) {
-            System.out.println("Caught" +  e);
-            System.out.println("Atom not added");
-          }
+    public void makeResidueList() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).makeResidueList();
         }
-      }
     }
-    makeResidueList();
-    makeCaBondList();
-    //    for (int i=0; i < chains.size() ; i++) {
-    //  String pog = ((PDBChain)chains.elementAt(i)).print();
-    //  System.out.println(pog);
-    // }
-  }
-
-  public void makeResidueList() {
-    for (int i=0; i < chains.size() ; i++) {
-      ((PDBChain)chains.elementAt(i)).makeResidueList();
-    }
-  }
-  public void makeCaBondList() {
-    for (int i=0; i < chains.size() ; i++) {
-      ((PDBChain)chains.elementAt(i)).makeCaBondList();
-    }
-  }
-
-  public PDBChain findChain(String id) {
-    for (int i=0; i < chains.size(); i++) {
-      // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
-      if (((PDBChain)chains.elementAt(i)).id.equals(id)) {
-        return (PDBChain)chains.elementAt(i);
-      }
+
+    public void makeCaBondList() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).makeCaBondList();
+        }
     }
-    return null;
-  }
 
+    public PDBChain findChain(String id) {
+        for (int i = 0; i < chains.size(); i++) {
+            if (((PDBChain) chains.elementAt(i)).id.equals(id)) {
+                return (PDBChain) chains.elementAt(i);
+            }
+        }
 
-  public void setChargeColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setChargeColours();
+        return null;
     }
-  }
 
-  public void setHydrophobicityColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setHydrophobicityColours();
+    public void setChargeColours() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).setChargeColours();
+        }
     }
-  }
-
-  public void colourBySequence(Sequence seq) {
-//SMJS TODO
-//    int max = seq.maxchain;
-//    if (seq.maxchain != -1) {
-//      ((PDBChain)chains.elementAt(max)).colourBySequence(seq);
-//    }
-  }
-
-  public void setChainColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setChainColours();
+
+    public void setHydrophobicityColours() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).setHydrophobicityColours();
+        }
     }
-  }
-  public static void main(String[] args) {
-    try {
-      PDBfile pdb = new PDBfile("enkp1.pdb","File");
-    } catch(IOException e) {
-      System.out.println(e);
-      System.exit(0);
+
+    public void setChainColours()
+    {
+       for (int i = 0; i < chains.size(); i++)
+       {
+            ((PDBChain) chains.elementAt(i)).setChainColours(
+                     Color.getHSBColor(1.0f / (float)i, .4f, 1.0f)
+                );
+        }
     }
-  }
 }
-
-
-