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From scnakand...@apache.org
Subject [16/32] airavata-sandbox git commit: adding datacat system
Date Mon, 24 Aug 2015 19:28:54 GMT
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaParser.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaParser.java
new file mode 100644
index 0000000..4fffdcb
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaParser.java
@@ -0,0 +1,388 @@
+/*
+*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements.  See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership.  The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License.  You may obtain a copy of the License at
+*
+*   http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied.  See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*
+*/
+package org.apache.airavata.datacat.parsers.gridchem.mopta;
+
+
+import java_cup.runtime.lr_parser;
+import org.apache.airavata.datacat.parsers.gridchem.GridChemQueueParser;
+
+import javax.swing.*;
+import java.io.FileReader;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+
+public class MOptaParser extends java_cup.runtime.lr_parser implements GridChemQueueParser {
+
+    /**
+     * Constructor which uses a file reader.
+     */
+    public MOptaParser(final FileReader fileReader) {
+        super(new MOptaLexer(fileReader));
+    }
+
+
+    /**
+     * Production table.
+     */
+    protected static final short _production_table[][] =
+            lr_parser.unpackFromStrings(new String[]{
+                    "\000\010\000\002\003\005\000\002\002\004\000\002\004" +
+                            "\003\000\002\005\004\000\002\005\003\000\002\010\002" +
+                            "\000\002\006\015\000\002\007\003"});
+    /**
+     * Parse-action table.
+     */
+    protected static final short[][] _action_table =
+            lr_parser.unpackFromStrings(new String[]{
+                    "\000\025\000\004\004\005\001\002\000\004\011\012\001" +
+                            "\002\000\004\011\uffff\001\002\000\004\002\007\001\002" +
+                            "\000\004\002\000\001\002\000\006\005\026\011\012\001" +
+                            "\002\000\006\005\ufffd\011\ufffd\001\002\000\004\016\ufffc" +
+                            "\001\002\000\004\016\015\001\002\000\004\013\016\001" +
+                            "\002\000\004\013\ufffa\001\002\000\004\014\017\001\002" +
+                            "\000\004\015\020\001\002\000\004\017\021\001\002\000" +
+                            "\004\020\022\001\002\000\004\021\023\001\002\000\004" +
+                            "\022\024\001\002\000\004\023\025\001\002\000\006\005" +
+                            "\ufffb\011\ufffb\001\002\000\004\002\001\001\002\000\006" +
+                            "\005\ufffe\011\ufffe\001\002"});
+    /**
+     * <code>reduce_goto</code> table.
+     */
+    protected static final short[][] _reduce_table =
+            lr_parser.unpackFromStrings(new String[]{
+                    "\000\025\000\006\003\005\004\003\001\001\000\006\005" +
+                            "\007\006\010\001\001\000\002\001\001\000\002\001\001" +
+                            "\000\002\001\001\000\004\006\026\001\001\000\002\001" +
+                            "\001\000\004\010\012\001\001\000\004\007\013\001\001" +
+                            "\000\002\001\001\000\002\001\001\000\002\001\001\000" +
+                            "\002\001\001\000\002\001\001\000\002\001\001\000\002" +
+                            "\001\001\000\002\001\001\000\002\001\001\000\002\001" +
+                            "\001\000\002\001\001\000\002\001\001"});
+    /**
+     * Instance of action encapsulation class.
+     */
+    protected CUP$parser$actions action_obj;
+    //Each string is of the format
+    //energy and iteraction
+    private ArrayList<String> result = new ArrayList<String>();
+    private String tempStr = "";
+
+    /**
+     * Default constructor.
+     */
+    public MOptaParser() {
+        super();
+    }
+
+    /**
+     * Constructor which sets the default scanner.
+     */
+    public MOptaParser(java_cup.runtime.Scanner s) {
+        super(s);
+    }
+
+    /**
+     * Access to production table.
+     */
+    public short[][] production_table() {
+        return _production_table;
+    }
+
+    /**
+     * Access to parse-action table.
+     */
+    public short[][] action_table() {
+        return _action_table;
+    }
+
+    /**
+     * Access to <code>reduce_goto</code> table.
+     */
+    public short[][] reduce_table() {
+        return _reduce_table;
+    }
+
+    public void addToResult(String value) {
+        result.add(value);
+    }
+
+
+    public ArrayList<String> getResult() {
+        return result;
+    }
+
+    public String getTempStr() {
+        return tempStr;
+    }
+
+    public void setTempStr(String s) {
+        this.tempStr = s;
+    }
+
+
+    /*Adding the parsed data to the hash map */
+    @Override
+    public HashMap<String, String> getParsedData() throws Exception {
+        parse();
+        HashMap<String,String> results= new HashMap<String,String>();
+        int energyCount=0;
+        int iterationCount=0;
+        for(int i=0;i<result.size();i++){
+            String singleString = result.get(i);
+            String[] temp= singleString.split(" ");
+            if(temp.length>1){
+                String keyString= temp[0];
+                String dataString=temp[1];
+                if(keyString.equalsIgnoreCase("ENERGY")){
+                    results.put("MoptaParser_ENERGY_"+energyCount,dataString);
+                    energyCount++;
+                }else if(keyString.equalsIgnoreCase("ITERATION")){
+                    results.put("MoptaParser_ITERATION_"+iterationCount,dataString);
+                    iterationCount++;
+                }
+
+            }
+
+        }
+        return results;
+    }
+
+    /**
+     * Action encapsulation object initializer.
+     */
+    protected void init_actions() {
+        action_obj = new CUP$parser$actions(this);
+    }
+
+    /**
+     * Invoke a user supplied parse action.
+     */
+    public java_cup.runtime.Symbol do_action(
+            int act_num,
+            java_cup.runtime.lr_parser parser,
+            java.util.Stack stack,
+            int top)
+            throws java.lang.Exception {
+    /* call code in generated class */
+        return action_obj.CUP$parser$do_action(act_num, parser, stack, top);
+    }
+
+    /**
+     * Indicates start state.
+     */
+    public int start_state() {
+        return 0;
+    }
+
+    /**
+     * Indicates start production.
+     */
+    public int start_production() {
+        return 1;
+    }
+
+    /**
+     * <code>EOF</code> Symbol index.
+     */
+    public int EOF_sym() {
+        return 0;
+    }
+
+    /**
+     * <code>error</code> Symbol index.
+     */
+    public int error_sym() {
+        return 1;
+    }
+
+
+}
+
+/**
+ * Cup generated class to encapsulate user supplied action code.
+ */
+class CUP$parser$actions {
+
+
+    private static final String tableLabel = "SCF Intermediate Results:";
+    //__________________________________
+    public static boolean DEBUG = true;
+    private static JTable table;
+// private static String cycle = "0";
+    private final MOptaParser MOptaParser;
+
+    /**
+     * Constructor
+     */
+    CUP$parser$actions(MOptaParser MOptaParser) {
+        this.MOptaParser = MOptaParser;
+    }
+
+/*  public static void main(String[] args) throws IOException {
+     File temp = new File("temporary");
+     boolean append = true;
+     try{ 
+     FileWriter temp1 = new FileWriter(temp, append);
+     PrintWriter temp2 = new PrintWriter(temp1);}
+
+     catch (FileNotFoundException e)  {
+          System.out.println("no file, dude!");
+       }  */
+//   }
+
+    public static JTable getTable() {
+        return table;
+    }
+
+    public static String getTableLabel() {
+        return tableLabel;
+    }
+
+    /**
+     * Method with the actual generated action code.
+     */
+    public final java_cup.runtime.Symbol CUP$parser$do_action(
+            int CUP$parser$act_num,
+            java_cup.runtime.lr_parser CUP$parser$parser,
+            java.util.Stack CUP$parser$stack,
+            int CUP$parser$top)
+            throws java.lang.Exception {
+      /* Symbol object for return from actions */
+        java_cup.runtime.Symbol CUP$parser$result;
+
+      /* select the action based on the action number */
+        switch (CUP$parser$act_num) {
+          /*. . . . . . . . . . . . . . . . . . . .*/
+            case 7: // en ::= ENERGY
+            {
+                Object RESULT = null;
+                int eleft = ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).left;
+                int eright = ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right;
+                Float e = (Float) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).value;
+                //___________________________________________________________________
+                if (DEBUG) System.out.println("CUP:gscfa:scfcycle:  ENERGY " + e);
+                MOptaParser.addToResult("ENERGY "+e);
+//   temp2.println(e);
+//  parseSCF.putField("iteration "+cycle, "energy", e);
+
+                CUP$parser$result = new java_cup.runtime.Symbol(5/*en*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).left, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+            }
+            return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+            case 6: // scfcycle ::= INTCycle NT$0 en FLOAT1 FLOAT2 FLOAT3 FLOAT4 FLOAT5 FLOAT6 FLOAT7 FLOAT8
+            {
+                Object RESULT = null;
+                // propagate RESULT from NT$0
+                if (((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 9)).value != null)
+                    RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 9)).value;
+                int cleft = ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 10)).left;
+                int cright = ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 10)).right;
+                Integer c = (Integer) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 10)).value;
+
+                CUP$parser$result = new java_cup.runtime.Symbol(4/*scfcycle*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 10)).left, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+            }
+            return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+            case 5: // NT$0 ::=
+            {
+                Object RESULT = null;
+                int cleft = ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).left;
+                int cright = ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right;
+                Integer c = (Integer) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).value;
+                //___________________________________________________________________
+                if (DEBUG) System.out.println("CUP:gscfa:scfcycle:  ITERATION " + c);
+                MOptaParser.addToResult("ITERATION "+c);
+//  temp2.print(c);
+//   temp2.print(" "); 
+//  cycle = c;
+
+//  parseSCF.putField("iteration "+cycle, cycle);
+
+                CUP$parser$result = new java_cup.runtime.Symbol(6/*NT$0*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+            }
+            return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+            case 4: // scfpat ::= scfcycle
+            {
+                Object RESULT = null;
+
+                CUP$parser$result = new java_cup.runtime.Symbol(3/*scfpat*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).left, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+            }
+            return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+            case 3: // scfpat ::= scfpat scfcycle
+            {
+                Object RESULT = null;
+                if (DEBUG) System.out.println("CUP:gscfa: in scfpat");
+                CUP$parser$result = new java_cup.runtime.Symbol(3/*scfpat*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 1)).left, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+            }
+            return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+            case 2: // scfintro ::= FOUNDITER
+            {
+                Object RESULT = null;
+                if (DEBUG) System.out.println("CUP:gscfa:  found start of SCF Iteration");
+                CUP$parser$result = new java_cup.runtime.Symbol(2/*scfintro*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).left, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+            }
+            return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+            case 1: // $START ::= startpt EOF
+            {
+                Object RESULT = null;
+                int start_valleft = ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 1)).left;
+                int start_valright = ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 1)).right;
+                Object start_val = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 1)).value;
+                RESULT = start_val;
+                CUP$parser$result = new java_cup.runtime.Symbol(0/*$START*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 1)).left, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+            }
+          /* ACCEPT */
+            CUP$parser$parser.done_parsing();
+            return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+            case 0: // startpt ::= scfintro scfpat SCFDONE
+            {
+                Object RESULT = null;
+                if (DEBUG) System.out.println("CUP:gscfa:  end of parse tree ");
+                table = new JTable();
+
+//       table = parseSCF.getTable();
+
+                CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 2)).left, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+            }
+            return CUP$parser$result;
+
+          /* . . . . . .*/
+            default:
+                throw new Exception(
+                        "Invalid action number found in internal parse table");
+
+        }
+    }
+}
+

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaSym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaSym.java
new file mode 100644
index 0000000..664d448
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaSym.java
@@ -0,0 +1,51 @@
+/*
+*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements.  See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership.  The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License.  You may obtain a copy of the License at
+*
+*   http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied.  See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*
+*/
+package org.apache.airavata.datacat.parsers.gridchem.mopta;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Fri Sep 12 00:11:41 IST 2014
+//----------------------------------------------------
+
+/**
+ * CUP generated class containing symbol constants.
+ */
+public class MOptaSym {
+    /* terminals */
+    public static final int FLOAT5 = 14;
+    public static final int FLOAT4 = 13;
+    public static final int FLOAT3 = 11;
+    public static final int FLOAT2 = 10;
+    public static final int FLOAT1 = 9;
+    public static final int INTCycle = 7;
+    public static final int INT3 = 6;
+    public static final int FLOAT = 8;
+    public static final int INT2 = 5;
+    public static final int INT1 = 4;
+    public static final int EOF = 0;
+    public static final int FOUNDITER = 2;
+    public static final int error = 1;
+    public static final int SCFDONE = 3;
+    public static final int ENERGY = 12;
+    public static final int FLOAT8 = 17;
+    public static final int FLOAT7 = 16;
+    public static final int FLOAT6 = 15;
+}
+

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aLexer.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aLexer.java
new file mode 100644
index 0000000..54c0221
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aLexer.java
@@ -0,0 +1,681 @@
+/*
+*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements.  See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership.  The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License.  You may obtain a copy of the License at
+*
+*   http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied.  See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*
+*/
+package org.apache.airavata.datacat.parsers.gridchem.mp2to5a;/* The following code was generated by JFlex 1.4.3 on 9/14/14 11:25 AM */
+
+/* MP2 to MP5 Keywords
+   Last Update: 12/31/2000 
+   http://www.gaussian.com/00000456.htm
+*/
+
+import java_cup.runtime.Symbol;
+import org.apache.airavata.datacat.parsers.gridchem.Settings;
+
+
+/**
+ * This class is a scanner generated by 
+ * <a href="http://www.jflex.de/">JFlex</a> 1.4.3
+ * on 9/14/14 11:25 AM from the specification file
+ * <tt>mp2to5a.flex</tt>
+ */
+public class MP2to5aLexer implements java_cup.runtime.Scanner {
+
+  /** This character denotes the end of file */
+  public static final int YYEOF = -1;
+
+  /** initial size of the lookahead buffer */
+  private static final int ZZ_BUFFERSIZE = 16384;
+
+  /** lexical states */
+  public static final int IGNOREALL = 4;
+  public static final int FLOATVAL = 2;
+  public static final int YYINITIAL = 0;
+
+  /**
+   * ZZ_LEXSTATE[l] is the state in the DFA for the lexical state l
+   * ZZ_LEXSTATE[l+1] is the state in the DFA for the lexical state l
+   *                  at the beginning of a line
+   * l is of the form l = 2*k, k a non negative integer
+   */
+  private static final int ZZ_LEXSTATE[] = { 
+     0,  0,  1,  1,  2, 2
+  };
+
+  /** 
+   * Translates characters to character classes
+   */
+  private static final char [] ZZ_CMAP = {
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  6,  7,  0,  2,  0,  2,  3,  0, 
+     1,  1,  1,  1, 10, 15,  1,  1,  1,  1,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0, 11,  4,  0,  0,  0,  0,  0,  0,  0,  8,  0,  0, 
+     9, 12,  0, 13, 14, 16,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  4,  4,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  5,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0
+  };
+
+  /** 
+   * Translates DFA states to action switch labels.
+   */
+  private static final int [] ZZ_ACTION = zzUnpackAction();
+
+  private static final String ZZ_ACTION_PACKED_0 =
+    "\3\0\5\1\3\0\1\2\1\0\1\3\3\0\1\4"+
+    "\1\2\5\0\1\5\2\0\1\6\1\0\1\7";
+
+  private static int [] zzUnpackAction() {
+    int [] result = new int[30];
+    int offset = 0;
+    offset = zzUnpackAction(ZZ_ACTION_PACKED_0, offset, result);
+    return result;
+  }
+
+  private static int zzUnpackAction(String packed, int offset, int [] result) {
+    int i = 0;       /* index in packed string  */
+    int j = offset;  /* index in unpacked array */
+    int l = packed.length();
+    while (i < l) {
+      int count = packed.charAt(i++);
+      int value = packed.charAt(i++);
+      do result[j++] = value; while (--count > 0);
+    }
+    return j;
+  }
+
+
+  /** 
+   * Translates a state to a row index in the transition table
+   */
+  private static final int [] ZZ_ROWMAP = zzUnpackRowMap();
+
+  private static final String ZZ_ROWMAP_PACKED_0 =
+    "\0\0\0\21\0\42\0\63\0\104\0\125\0\146\0\167"+
+    "\0\210\0\231\0\146\0\252\0\273\0\63\0\314\0\335"+
+    "\0\356\0\63\0\377\0\377\0\u0110\0\u0121\0\u0132\0\u0143"+
+    "\0\63\0\u0154\0\u0165\0\63\0\u0176\0\63";
+
+  private static int [] zzUnpackRowMap() {
+    int [] result = new int[30];
+    int offset = 0;
+    offset = zzUnpackRowMap(ZZ_ROWMAP_PACKED_0, offset, result);
+    return result;
+  }
+
+  private static int zzUnpackRowMap(String packed, int offset, int [] result) {
+    int i = 0;  /* index in packed string  */
+    int j = offset;  /* index in unpacked array */
+    int l = packed.length();
+    while (i < l) {
+      int high = packed.charAt(i++) << 16;
+      result[j++] = high | packed.charAt(i++);
+    }
+    return j;
+  }
+
+  /** 
+   * The transition table of the DFA
+   */
+  private static final int [] ZZ_TRANS = zzUnpackTrans();
+
+  private static final String ZZ_TRANS_PACKED_0 =
+    "\10\4\1\5\7\4\1\6\1\4\1\7\1\10\2\4"+
+    "\1\10\4\4\1\7\4\4\1\7\22\4\32\0\1\11"+
+    "\17\0\1\12\11\0\1\13\1\0\1\14\6\0\1\13"+
+    "\4\0\1\13\2\0\1\13\10\0\1\13\4\0\1\13"+
+    "\13\0\1\15\4\0\1\16\12\0\1\17\10\0\1\14"+
+    "\2\0\2\20\4\0\1\14\1\20\3\0\1\14\7\0"+
+    "\1\21\31\0\1\22\2\0\1\23\1\24\2\0\1\24"+
+    "\4\0\1\23\4\0\1\23\14\0\1\25\1\0\1\26"+
+    "\4\0\1\23\10\0\1\23\4\0\1\23\15\0\1\27"+
+    "\17\0\1\30\14\0\1\31\25\0\1\32\1\0\1\33"+
+    "\11\0\1\34\25\0\1\35\13\0\1\36\11\0";
+
+  private static int [] zzUnpackTrans() {
+    int [] result = new int[391];
+    int offset = 0;
+    offset = zzUnpackTrans(ZZ_TRANS_PACKED_0, offset, result);
+    return result;
+  }
+
+  private static int zzUnpackTrans(String packed, int offset, int [] result) {
+    int i = 0;       /* index in packed string  */
+    int j = offset;  /* index in unpacked array */
+    int l = packed.length();
+    while (i < l) {
+      int count = packed.charAt(i++);
+      int value = packed.charAt(i++);
+      value--;
+      do result[j++] = value; while (--count > 0);
+    }
+    return j;
+  }
+
+
+  /* error codes */
+  private static final int ZZ_UNKNOWN_ERROR = 0;
+  private static final int ZZ_NO_MATCH = 1;
+  private static final int ZZ_PUSHBACK_2BIG = 2;
+
+  /* error messages for the codes above */
+  private static final String ZZ_ERROR_MSG[] = {
+    "Unkown internal scanner error",
+    "Error: could not match input",
+    "Error: pushback value was too large"
+  };
+
+  /**
+   * ZZ_ATTRIBUTE[aState] contains the attributes of state <code>aState</code>
+   */
+  private static final int [] ZZ_ATTRIBUTE = zzUnpackAttribute();
+
+  private static final String ZZ_ATTRIBUTE_PACKED_0 =
+    "\3\0\1\11\4\1\3\0\1\1\1\0\1\11\3\0"+
+    "\1\11\1\1\5\0\1\11\2\0\1\11\1\0\1\11";
+
+  private static int [] zzUnpackAttribute() {
+    int [] result = new int[30];
+    int offset = 0;
+    offset = zzUnpackAttribute(ZZ_ATTRIBUTE_PACKED_0, offset, result);
+    return result;
+  }
+
+  private static int zzUnpackAttribute(String packed, int offset, int [] result) {
+    int i = 0;       /* index in packed string  */
+    int j = offset;  /* index in unpacked array */
+    int l = packed.length();
+    while (i < l) {
+      int count = packed.charAt(i++);
+      int value = packed.charAt(i++);
+      do result[j++] = value; while (--count > 0);
+    }
+    return j;
+  }
+
+  /** the input device */
+  private java.io.Reader zzReader;
+
+  /** the current state of the DFA */
+  private int zzState;
+
+  /** the current lexical state */
+  private int zzLexicalState = YYINITIAL;
+
+  /** this buffer contains the current text to be matched and is
+      the source of the yytext() string */
+  private char zzBuffer[] = new char[ZZ_BUFFERSIZE];
+
+  /** the textposition at the last accepting state */
+  private int zzMarkedPos;
+
+  /** the current text position in the buffer */
+  private int zzCurrentPos;
+
+  /** startRead marks the beginning of the yytext() string in the buffer */
+  private int zzStartRead;
+
+  /** endRead marks the last character in the buffer, that has been read
+      from input */
+  private int zzEndRead;
+
+  /** number of newlines encountered up to the start of the matched text */
+  private int yyline;
+
+  /** the number of characters up to the start of the matched text */
+  private int yychar;
+
+  /**
+   * the number of characters from the last newline up to the start of the 
+   * matched text
+   */
+  private int yycolumn;
+
+  /** 
+   * zzAtBOL == true <=> the scanner is currently at the beginning of a line
+   */
+  private boolean zzAtBOL = true;
+
+  /** zzAtEOF == true <=> the scanner is at the EOF */
+  private boolean zzAtEOF;
+
+  /** denotes if the user-EOF-code has already been executed */
+  private boolean zzEOFDone;
+
+  /* user code: */
+  public static boolean DEBUG = false;
+
+
+  /**
+   * Creates a new scanner
+   * There is also a java.io.InputStream version of this constructor.
+   *
+   * @param   in  the java.io.Reader to read input from.
+   */
+  public MP2to5aLexer(java.io.Reader in) {
+    this.zzReader = in;
+  }
+
+  /**
+   * Creates a new scanner.
+   * There is also java.io.Reader version of this constructor.
+   *
+   * @param   in  the java.io.Inputstream to read input from.
+   */
+  public MP2to5aLexer(java.io.InputStream in) {
+    this(new java.io.InputStreamReader(in));
+  }
+
+
+  /**
+   * Refills the input buffer.
+   *
+   * @return      <code>false</code>, iff there was new input.
+   * 
+   * @exception   java.io.IOException  if any I/O-Error occurs
+   */
+  private boolean zzRefill() throws java.io.IOException {
+
+    /* first: make room (if you can) */
+    if (zzStartRead > 0) {
+      System.arraycopy(zzBuffer, zzStartRead,
+                       zzBuffer, 0,
+                       zzEndRead-zzStartRead);
+
+      /* translate stored positions */
+      zzEndRead-= zzStartRead;
+      zzCurrentPos-= zzStartRead;
+      zzMarkedPos-= zzStartRead;
+      zzStartRead = 0;
+    }
+
+    /* is the buffer big enough? */
+    if (zzCurrentPos >= zzBuffer.length) {
+      /* if not: blow it up */
+      char newBuffer[] = new char[zzCurrentPos*2];
+      System.arraycopy(zzBuffer, 0, newBuffer, 0, zzBuffer.length);
+      zzBuffer = newBuffer;
+    }
+
+    /* finally: fill the buffer with new input */
+    int numRead = zzReader.read(zzBuffer, zzEndRead,
+                                            zzBuffer.length-zzEndRead);
+
+    if (numRead > 0) {
+      zzEndRead+= numRead;
+      return false;
+    }
+    // unlikely but not impossible: read 0 characters, but not at end of stream    
+    if (numRead == 0) {
+      int c = zzReader.read();
+      if (c == -1) {
+        return true;
+      } else {
+        zzBuffer[zzEndRead++] = (char) c;
+        return false;
+      }     
+    }
+
+	// numRead < 0
+    return true;
+  }
+
+    
+  /**
+   * Closes the input stream.
+   */
+  public final void yyclose() throws java.io.IOException {
+    zzAtEOF = true;            /* indicate end of file */
+    zzEndRead = zzStartRead;  /* invalidate buffer    */
+
+    if (zzReader != null)
+      zzReader.close();
+  }
+
+
+  /**
+   * Resets the scanner to read from a new input stream.
+   * Does not close the old reader.
+   *
+   * All internal variables are reset, the old input stream 
+   * <b>cannot</b> be reused (internal buffer is discarded and lost).
+   * Lexical state is set to <tt>ZZ_INITIAL</tt>.
+   *
+   * @param reader   the new input stream 
+   */
+  public final void yyreset(java.io.Reader reader) {
+    zzReader = reader;
+    zzAtBOL  = true;
+    zzAtEOF  = false;
+    zzEOFDone = false;
+    zzEndRead = zzStartRead = 0;
+    zzCurrentPos = zzMarkedPos = 0;
+    yyline = yychar = yycolumn = 0;
+    zzLexicalState = YYINITIAL;
+  }
+
+
+  /**
+   * Returns the current lexical state.
+   */
+  public final int yystate() {
+    return zzLexicalState;
+  }
+
+
+  /**
+   * Enters a new lexical state
+   *
+   * @param newState the new lexical state
+   */
+  public final void yybegin(int newState) {
+    zzLexicalState = newState;
+  }
+
+
+  /**
+   * Returns the text matched by the current regular expression.
+   */
+  public final String yytext() {
+    return new String( zzBuffer, zzStartRead, zzMarkedPos-zzStartRead );
+  }
+
+
+  /**
+   * Returns the character at position <tt>pos</tt> from the 
+   * matched text. 
+   * 
+   * It is equivalent to yytext().charAt(pos), but faster
+   *
+   * @param pos the position of the character to fetch. 
+   *            A value from 0 to yylength()-1.
+   *
+   * @return the character at position pos
+   */
+  public final char yycharat(int pos) {
+    return zzBuffer[zzStartRead+pos];
+  }
+
+
+  /**
+   * Returns the length of the matched text region.
+   */
+  public final int yylength() {
+    return zzMarkedPos-zzStartRead;
+  }
+
+
+  /**
+   * Reports an error that occured while scanning.
+   *
+   * In a wellformed scanner (no or only correct usage of 
+   * yypushback(int) and a match-all fallback rule) this method 
+   * will only be called with things that "Can't Possibly Happen".
+   * If this method is called, something is seriously wrong
+   * (e.g. a JFlex bug producing a faulty scanner etc.).
+   *
+   * Usual syntax/scanner level error handling should be done
+   * in error fallback rules.
+   *
+   * @param   errorCode  the code of the errormessage to display
+   */
+  private void zzScanError(int errorCode) {
+    String message;
+    try {
+      message = ZZ_ERROR_MSG[errorCode];
+    }
+    catch (ArrayIndexOutOfBoundsException e) {
+      message = ZZ_ERROR_MSG[ZZ_UNKNOWN_ERROR];
+    }
+
+    throw new Error(message);
+  } 
+
+
+  /**
+   * Pushes the specified amount of characters back into the input stream.
+   *
+   * They will be read again by then next call of the scanning method
+   *
+   * @param number  the number of characters to be read again.
+   *                This number must not be greater than yylength()!
+   */
+  public void yypushback(int number)  {
+    if ( number > yylength() )
+      zzScanError(ZZ_PUSHBACK_2BIG);
+
+    zzMarkedPos -= number;
+  }
+
+
+  /**
+   * Contains user EOF-code, which will be executed exactly once,
+   * when the end of file is reached
+   */
+  private void zzDoEOF() throws java.io.IOException {
+    if (!zzEOFDone) {
+      zzEOFDone = true;
+      yyclose();
+    }
+  }
+
+
+  /**
+   * Resumes scanning until the next regular expression is matched,
+   * the end of input is encountered or an I/O-Error occurs.
+   *
+   * @return      the next token
+   * @exception   java.io.IOException  if any I/O-Error occurs
+   */
+  public java_cup.runtime.Symbol next_token() throws java.io.IOException {
+    int zzInput;
+    int zzAction;
+
+    // cached fields:
+    int zzCurrentPosL;
+    int zzMarkedPosL;
+    int zzEndReadL = zzEndRead;
+    char [] zzBufferL = zzBuffer;
+    char [] zzCMapL = ZZ_CMAP;
+
+    int [] zzTransL = ZZ_TRANS;
+    int [] zzRowMapL = ZZ_ROWMAP;
+    int [] zzAttrL = ZZ_ATTRIBUTE;
+
+    while (true) {
+      zzMarkedPosL = zzMarkedPos;
+
+      zzAction = -1;
+
+      zzCurrentPosL = zzCurrentPos = zzStartRead = zzMarkedPosL;
+  
+      zzState = ZZ_LEXSTATE[zzLexicalState];
+
+
+      zzForAction: {
+        while (true) {
+    
+          if (zzCurrentPosL < zzEndReadL)
+            zzInput = zzBufferL[zzCurrentPosL++];
+          else if (zzAtEOF) {
+            zzInput = YYEOF;
+            break zzForAction;
+          }
+          else {
+            // store back cached positions
+            zzCurrentPos  = zzCurrentPosL;
+            zzMarkedPos   = zzMarkedPosL;
+            boolean eof = zzRefill();
+            // get translated positions and possibly new buffer
+            zzCurrentPosL  = zzCurrentPos;
+            zzMarkedPosL   = zzMarkedPos;
+            zzBufferL      = zzBuffer;
+            zzEndReadL     = zzEndRead;
+            if (eof) {
+              zzInput = YYEOF;
+              break zzForAction;
+            }
+            else {
+              zzInput = zzBufferL[zzCurrentPosL++];
+            }
+          }
+          int zzNext = zzTransL[ zzRowMapL[zzState] + zzCMapL[zzInput] ];
+          if (zzNext == -1) break zzForAction;
+          zzState = zzNext;
+
+          int zzAttributes = zzAttrL[zzState];
+          if ( (zzAttributes & 1) == 1 ) {
+            zzAction = zzState;
+            zzMarkedPosL = zzCurrentPosL;
+            if ( (zzAttributes & 8) == 8 ) break zzForAction;
+          }
+
+        }
+      }
+
+      // store back cached position
+      zzMarkedPos = zzMarkedPosL;
+
+      switch (zzAction < 0 ? zzAction : ZZ_ACTION[zzAction]) {
+        case 4: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	  return new Symbol(MP2to5aSym.LIM, yytext());
+          }
+        case 8: break;
+        case 7: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	       return new Symbol(MP2to5aSym.VAR, yytext());
+          }
+        case 9: break;
+        case 2: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	   yybegin(YYINITIAL);
+	   return new Symbol(MP2to5aSym.FLOAT, yytext());
+          }
+        case 10: break;
+        case 3: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	 return new Symbol(MP2to5aSym.LIM, yytext());
+          }
+        case 11: break;
+        case 5: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	     return new Symbol(MP2to5aSym.VAR, yytext());
+          }
+        case 12: break;
+        case 6: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	      return new Symbol(MP2to5aSym.VAR, yytext());
+          }
+        case 13: break;
+        case 1: 
+          { 
+          }
+        case 14: break;
+        default: 
+          if (zzInput == YYEOF && zzStartRead == zzCurrentPos) {
+            zzAtEOF = true;
+            zzDoEOF();
+              { return new java_cup.runtime.Symbol(MP2to5aSym.EOF); }
+          } 
+          else {
+            zzScanError(ZZ_NO_MATCH);
+          }
+      }
+    }
+  }
+
+  /**
+   * Converts an int token code into the name of the
+   * token by reflection on the cup symbol class/interface sym
+   *
+   * This code was contributed by Karl Meissner <meissnersd@yahoo.com>
+   */
+  private String getTokenName(int token) {
+    try {
+      java.lang.reflect.Field [] classFields = MP2to5aSym.class.getFields();
+      for (int i = 0; i < classFields.length; i++) {
+        if (classFields[i].getInt(null) == token) {
+          return classFields[i].getName();
+        }
+      }
+    } catch (Exception e) {
+      e.printStackTrace(System.err);
+    }
+
+    return "UNKNOWN TOKEN";
+  }
+
+  /**
+   * Same as next_token but also prints the token to standard out
+   * for debugging.
+   *
+   * This code was contributed by Karl Meissner <meissnersd@yahoo.com>
+   */
+  public java_cup.runtime.Symbol debug_next_token() throws java.io.IOException {
+    java_cup.runtime.Symbol s = next_token();
+    System.out.println( " --"+ yytext() + "--" + getTokenName(s.sym) + "--");
+    return s;
+  }
+
+  /**
+   * Runs the scanner on input files.
+   *
+   * This is a standalone scanner, it will print any unmatched
+   * text to System.out unchanged.
+   *
+   * @param argv   the command line, contains the filenames to run
+   *               the scanner on.
+   */
+  public static void main(String argv[]) {
+    if (argv.length == 0) {
+      System.out.println("Usage : java MP2to5aLexer <inputfile>");
+    }
+    else {
+      for (int i = 0; i < argv.length; i++) {
+        MP2to5aLexer scanner = null;
+        try {
+          scanner = new MP2to5aLexer( new java.io.FileReader(argv[i]) );
+          while ( !scanner.zzAtEOF ) scanner.next_token();
+        }
+        catch (java.io.FileNotFoundException e) {
+          System.out.println("File not found : \""+argv[i]+"\"");
+        }
+        catch (java.io.IOException e) {
+          System.out.println("IO error scanning file \""+argv[i]+"\"");
+          System.out.println(e);
+        }
+        catch (Exception e) {
+          System.out.println("Unexpected exception:");
+          e.printStackTrace();
+        }
+      }
+    }
+  }
+
+
+}

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aParser.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aParser.java
new file mode 100644
index 0000000..1ae4db3
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aParser.java
@@ -0,0 +1,261 @@
+/*
+*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements.  See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership.  The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License.  You may obtain a copy of the License at
+*
+*   http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied.  See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*
+*/
+package org.apache.airavata.datacat.parsers.gridchem.mp2to5a;
+
+
+import java_cup.runtime.lr_parser;
+import org.apache.airavata.datacat.parsers.gridchem.GridChemQueueParser;
+import org.apache.airavata.datacat.parsers.gridchem.Settings;
+
+import java.io.FileReader;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+public class MP2to5aParser extends java_cup.runtime.lr_parser implements GridChemQueueParser {
+
+  /** Default constructor. */
+  public MP2to5aParser() {super();}
+
+  /** Constructor which sets the default scanner. */
+  public MP2to5aParser(java_cup.runtime.Scanner s) {super(s);}
+
+    /**
+     * Constructor which uses a file reader.
+     */
+    public MP2to5aParser(final FileReader fileReader) {
+        super(new MP2to5aLexer(fileReader));
+    }
+
+  /** Production table. */
+  protected static final short _production_table[][] = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\005\000\002\003\004\000\002\002\004\000\002\003" +
+                    "\003\000\002\004\003\000\002\004\003"});
+
+  /** Access to production table. */
+  public short[][] production_table() {return _production_table;}
+
+  /** Parse-action table. */
+  protected static final short[][] _action_table = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\007\000\006\023\004\024\006\001\002\000\010\002" +
+                    "\ufffe\023\ufffe\024\ufffe\001\002\000\010\002\uffff\023\uffff" +
+                    "\024\uffff\001\002\000\010\002\ufffd\023\ufffd\024\ufffd\001" +
+                    "\002\000\010\002\011\023\004\024\006\001\002\000\010" +
+                    "\002\001\023\001\024\001\001\002\000\004\002\000\001" +
+                    "\002"});
+
+  /** Access to parse-action table. */
+  public short[][] action_table() {return _action_table;}
+
+  /** <code>reduce_goto</code> table. */
+  protected static final short[][] _reduce_table = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\007\000\006\003\006\004\004\001\001\000\002\001" +
+                    "\001\000\002\001\001\000\002\001\001\000\004\004\007" +
+                    "\001\001\000\002\001\001\000\002\001\001"});
+
+  /** Access to <code>reduce_goto</code> table. */
+  public short[][] reduce_table() {return _reduce_table;}
+
+  /** Instance of action encapsulation class. */
+  protected CUP$parser$actions action_obj;
+
+
+    //Each string is of the format
+    //mp2SpecificOption
+    private ArrayList<String> result = new ArrayList<String>();
+    private String tempStr = "";
+
+
+    public ArrayList<String> getResult() {
+        return result;
+    }
+
+    public void addToResult(String value) {
+        result.add(value);
+    }
+
+
+    public String getTempStr() {
+        return tempStr;
+    }
+
+    public void setTempStr(String s) {
+        this.tempStr = s;
+    }
+
+    /*Adding the parsed data to the hash map */
+    @Override
+    public HashMap<String, String> getParsedData() throws Exception {
+       parse();
+       HashMap<String,String> results=new HashMap<String,String>();
+        int count=0;
+        for(int i=0;i<result.size();i++){
+            String singleString= result.get(i);
+            String[] temp= singleString.split(" ");
+            if(temp.length>1){
+                String keyString=temp[0];
+                String dataString=temp[1];
+                if(keyString.equalsIgnoreCase("SpecificOption")){
+                    results.put("MP2to5aParser_MP2_Specific_Option_"+count,dataString);
+                    count++;
+                }
+            }
+
+        }
+        return results;
+    }
+
+
+        /** Action encapsulation object initializer. */
+  protected void init_actions()
+    {
+      action_obj = new CUP$parser$actions(this);
+    }
+
+  /** Invoke a user supplied parse action. */
+  public java_cup.runtime.Symbol do_action(
+    int                        act_num,
+    java_cup.runtime.lr_parser parser,
+    java.util.Stack            stack,
+    int                        top)
+    throws java.lang.Exception
+  {
+    /* call code in generated class */
+    return action_obj.CUP$parser$do_action(act_num, parser, stack, top);
+  }
+
+  /** Indicates start state. */
+  public int start_state() {return 0;}
+  /** Indicates start production. */
+  public int start_production() {return 1;}
+
+  /** <code>EOF</code> Symbol index. */
+  public int EOF_sym() {return 0;}
+
+  /** <code>error</code> Symbol index. */
+  public int error_sym() {return 1;}
+
+
+  /** User initialization code. */
+  public void user_init() throws java.lang.Exception
+    {
+ if(Settings.DEBUG) System.out.println("CUP:mp2to5a:  entry");
+    }
+
+
+
+    ///public static boolean DEBUG = false;
+}
+
+/** Cup generated class to encapsulate user supplied action code.*/
+class CUP$parser$actions {
+  private final MP2to5aParser MP2to5aParser;
+
+  /** Constructor */
+  CUP$parser$actions(MP2to5aParser MP2to5aParser) {
+    this.MP2to5aParser = MP2to5aParser;
+  }
+
+  /** Method with the actual generated action code. */
+  public final java_cup.runtime.Symbol CUP$parser$do_action(
+    int                        CUP$parser$act_num,
+    java_cup.runtime.lr_parser CUP$parser$parser,
+    java.util.Stack            CUP$parser$stack,
+    int                        CUP$parser$top)
+    throws java.lang.Exception
+    {
+      /* Symbol object for return from actions */
+      java_cup.runtime.Symbol CUP$parser$result;
+
+      /* select the action based on the action number */
+      switch (CUP$parser$act_num)
+        {
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 4: // element ::= LIM 
+            {
+              Object RESULT = null;
+		int sleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int sright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		String s = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+		 if(Settings.DEBUG) System.out.println("CUP:mp2to5a:  MP2-Specific Option: "+s);
+         MP2to5aParser.addToResult("SpecificOption "+s);
+	  // ParseMP2to5.put("Limitations to MP5: ", s);
+              CUP$parser$result = new java_cup.runtime.Symbol(2/*element*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 3: // element ::= VAR 
+            {
+              Object RESULT = null;
+		int sleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int sright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		String s = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+		 if(Settings.DEBUG) System.out.println("CUP:mp2to5a:  MP2-Specific Option: "+s);
+                MP2to5aParser.addToResult("SpecificOption "+s);
+	   //ParseMP2to5.put("Variations of MP4: ", s);
+              CUP$parser$result = new java_cup.runtime.Symbol(2/*element*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 2: // startpt ::= element 
+            {
+              Object RESULT = null;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 1: // $START ::= startpt EOF 
+            {
+              Object RESULT = null;
+		int start_valleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left;
+		int start_valright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).right;
+		Object start_val = (Object)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value;
+		RESULT = start_val;
+              CUP$parser$result = new java_cup.runtime.Symbol(0/*$START*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          /* ACCEPT */
+          CUP$parser$parser.done_parsing();
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 0: // startpt ::= startpt element 
+            {
+              Object RESULT = null;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /* . . . . . .*/
+          default:
+            throw new Exception(
+               "Invalid action number found in internal parse table");
+
+        }
+    }
+}
+

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aSym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aSym.java
new file mode 100644
index 0000000..709154a
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aSym.java
@@ -0,0 +1,51 @@
+/*
+*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements.  See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership.  The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License.  You may obtain a copy of the License at
+*
+*   http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied.  See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*
+*/
+package org.apache.airavata.datacat.parsers.gridchem.mp2to5a;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Sun Sep 14 11:25:52 IST 2014
+//----------------------------------------------------
+
+/** CUP generated class containing symbol constants. */
+public class MP2to5aSym {
+  /* terminals */
+  public static final int E4_SDTQ = 8;
+  public static final int MP2OPT = 16;
+  public static final int LIM = 18;
+  public static final int UMP4_SDQ = 11;
+  public static final int UMP4_SDTQ = 12;
+  public static final int E4_DQ = 6;
+  public static final int FCOPT = 13;
+  public static final int UMP4_DQ = 10;
+  public static final int E4_SDQ = 7;
+  public static final int E3 = 5;
+  public static final int E2 = 2;
+  public static final int FLOAT = 19;
+  public static final int EOF = 0;
+  public static final int error = 1;
+  public static final int MP4_T = 4;
+  public static final int FCOPT2 = 14;
+  public static final int ALGOPT = 15;
+  public static final int VAR = 17;
+  public static final int EUMP3 = 9;
+  public static final int EUMP2 = 3;
+}
+

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bLexer.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bLexer.java
new file mode 100644
index 0000000..fa065ff
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bLexer.java
@@ -0,0 +1,687 @@
+package org.apache.airavata.datacat.parsers.gridchem.mp2to5b;/* The following code was generated by JFlex 1.4.3 on 9/14/14 11:52 AM */
+
+/* MP2 to MP5 Keywords
+   Last Update: 12/31/2000 
+   http://www.gaussian.com/00000456.htm
+*/
+
+import java_cup.runtime.Symbol;
+import org.apache.airavata.datacat.parsers.gridchem.Settings;
+
+
+/**
+ * This class is a scanner generated by 
+ * <a href="http://www.jflex.de/">JFlex</a> 1.4.3
+ * on 9/14/14 11:52 AM from the specification file
+ * <tt>mp2to5b.flex</tt>
+ */
+public class MP2to5bLexer implements java_cup.runtime.Scanner {
+
+  /** This character denotes the end of file */
+  public static final int YYEOF = -1;
+
+  /** initial size of the lookahead buffer */
+  private static final int ZZ_BUFFERSIZE = 16384;
+
+  /** lexical states */
+  public static final int IGNOREALL = 4;
+  public static final int FLOATVAL = 2;
+  public static final int YYINITIAL = 0;
+
+  /**
+   * ZZ_LEXSTATE[l] is the state in the DFA for the lexical state l
+   * ZZ_LEXSTATE[l+1] is the state in the DFA for the lexical state l
+   *                  at the beginning of a line
+   * l is of the form l = 2*k, k a non negative integer
+   */
+  private static final int ZZ_LEXSTATE[] = { 
+     0,  0,  1,  1,  2, 2
+  };
+
+  /** 
+   * Translates characters to character classes
+   */
+  private static final char [] ZZ_CMAP = {
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  3,  7, 15,  4,  0, 
+     1,  2, 18,  2, 16, 14, 17,  2,  2,  2,  0,  0,  0, 26,  0,  0, 
+     0, 27,  0,  9,  5,  5,  8,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0, 12, 28,  0,  0,  0, 13,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0, 20,  0,  0, 21, 19,  0,  0,  0, 22,  0,  0, 11,  0, 23, 24, 
+     0,  0,  0,  0,  0, 10,  0, 25,  0,  0,  0,  0,  6,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0
+  };
+
+  /** 
+   * Translates DFA states to action switch labels.
+   */
+  private static final int [] ZZ_ACTION = zzUnpackAction();
+
+  private static final String ZZ_ACTION_PACKED_0 =
+    "\3\0\13\1\1\0\1\2\5\0\1\3\2\0\1\4"+
+    "\1\5\7\0\1\6\3\0\1\7\1\4\4\0\1\10"+
+    "\3\0\1\11\2\0\1\12";
+
+  private static int [] zzUnpackAction() {
+    int [] result = new int[51];
+    int offset = 0;
+    offset = zzUnpackAction(ZZ_ACTION_PACKED_0, offset, result);
+    return result;
+  }
+
+  private static int zzUnpackAction(String packed, int offset, int [] result) {
+    int i = 0;       /* index in packed string  */
+    int j = offset;  /* index in unpacked array */
+    int l = packed.length();
+    while (i < l) {
+      int count = packed.charAt(i++);
+      int value = packed.charAt(i++);
+      do result[j++] = value; while (--count > 0);
+    }
+    return j;
+  }
+
+
+  /** 
+   * Translates a state to a row index in the transition table
+   */
+  private static final int [] ZZ_ROWMAP = zzUnpackRowMap();
+
+  private static final String ZZ_ROWMAP_PACKED_0 =
+    "\0\0\0\35\0\72\0\127\0\164\0\221\0\256\0\313"+
+    "\0\350\0\u0105\0\u0122\0\u013f\0\u015c\0\u0179\0\u0196\0\127"+
+    "\0\u01b3\0\u01d0\0\u01ed\0\u020a\0\u0227\0\127\0\u0244\0\u015c"+
+    "\0\u0261\0\127\0\u027e\0\u029b\0\u02b8\0\u02d5\0\u02f2\0\u030f"+
+    "\0\u032c\0\127\0\u0349\0\u0366\0\u0383\0\127\0\u03a0\0\u03a0"+
+    "\0\u03bd\0\u03da\0\u03f7\0\127\0\u0414\0\u0431\0\u044e\0\127"+
+    "\0\u046b\0\u0488\0\127";
+
+  private static int [] zzUnpackRowMap() {
+    int [] result = new int[51];
+    int offset = 0;
+    offset = zzUnpackRowMap(ZZ_ROWMAP_PACKED_0, offset, result);
+    return result;
+  }
+
+  private static int zzUnpackRowMap(String packed, int offset, int [] result) {
+    int i = 0;  /* index in packed string  */
+    int j = offset;  /* index in unpacked array */
+    int l = packed.length();
+    while (i < l) {
+      int high = packed.charAt(i++) << 16;
+      result[j++] = high | packed.charAt(i++);
+    }
+    return j;
+  }
+
+  /** 
+   * The transition table of the DFA
+   */
+  private static final int [] ZZ_TRANS = zzUnpackTrans();
+
+  private static final String ZZ_TRANS_PACKED_0 =
+    "\1\4\1\5\6\4\1\6\1\7\2\4\1\10\1\11"+
+    "\1\12\1\13\1\4\1\14\14\4\2\15\1\16\2\4"+
+    "\1\16\7\4\1\15\1\16\3\15\47\4\44\0\1\17"+
+    "\36\0\1\20\1\21\55\0\1\22\16\0\1\20\5\0"+
+    "\1\23\37\0\1\24\15\0\1\25\46\0\1\26\22\0"+
+    "\1\27\26\0\2\30\1\0\1\31\11\0\1\30\1\0"+
+    "\3\30\13\0\2\30\13\0\1\30\1\0\3\30\13\0"+
+    "\1\32\46\0\1\33\55\0\1\34\24\0\1\35\37\0"+
+    "\1\36\6\0\1\32\15\0\1\37\37\0\1\40\13\0"+
+    "\2\31\2\0\2\41\7\0\1\31\1\0\3\31\1\41"+
+    "\1\0\1\41\22\0\1\42\55\0\1\43\25\0\1\44"+
+    "\34\0\1\45\27\0\1\46\36\0\1\46\13\0\2\47"+
+    "\1\50\2\0\1\50\7\0\1\47\1\50\3\47\23\0"+
+    "\1\51\40\0\1\52\47\0\1\53\5\0\2\47\13\0"+
+    "\1\47\1\0\3\47\22\0\1\54\52\0\1\55\37\0"+
+    "\1\56\32\0\1\57\37\0\1\60\27\0\1\61\37\0"+
+    "\1\62\35\0\1\63\3\0";
+
+  private static int [] zzUnpackTrans() {
+    int [] result = new int[1189];
+    int offset = 0;
+    offset = zzUnpackTrans(ZZ_TRANS_PACKED_0, offset, result);
+    return result;
+  }
+
+  private static int zzUnpackTrans(String packed, int offset, int [] result) {
+    int i = 0;       /* index in packed string  */
+    int j = offset;  /* index in unpacked array */
+    int l = packed.length();
+    while (i < l) {
+      int count = packed.charAt(i++);
+      int value = packed.charAt(i++);
+      value--;
+      do result[j++] = value; while (--count > 0);
+    }
+    return j;
+  }
+
+
+  /* error codes */
+  private static final int ZZ_UNKNOWN_ERROR = 0;
+  private static final int ZZ_NO_MATCH = 1;
+  private static final int ZZ_PUSHBACK_2BIG = 2;
+
+  /* error messages for the codes above */
+  private static final String ZZ_ERROR_MSG[] = {
+    "Unkown internal scanner error",
+    "Error: could not match input",
+    "Error: pushback value was too large"
+  };
+
+  /**
+   * ZZ_ATTRIBUTE[aState] contains the attributes of state <code>aState</code>
+   */
+  private static final int [] ZZ_ATTRIBUTE = zzUnpackAttribute();
+
+  private static final String ZZ_ATTRIBUTE_PACKED_0 =
+    "\3\0\1\11\12\1\1\0\1\11\5\0\1\11\2\0"+
+    "\1\1\1\11\7\0\1\11\3\0\1\11\1\1\4\0"+
+    "\1\11\3\0\1\11\2\0\1\11";
+
+  private static int [] zzUnpackAttribute() {
+    int [] result = new int[51];
+    int offset = 0;
+    offset = zzUnpackAttribute(ZZ_ATTRIBUTE_PACKED_0, offset, result);
+    return result;
+  }
+
+  private static int zzUnpackAttribute(String packed, int offset, int [] result) {
+    int i = 0;       /* index in packed string  */
+    int j = offset;  /* index in unpacked array */
+    int l = packed.length();
+    while (i < l) {
+      int count = packed.charAt(i++);
+      int value = packed.charAt(i++);
+      do result[j++] = value; while (--count > 0);
+    }
+    return j;
+  }
+
+  /** the input device */
+  private java.io.Reader zzReader;
+
+  /** the current state of the DFA */
+  private int zzState;
+
+  /** the current lexical state */
+  private int zzLexicalState = YYINITIAL;
+
+  /** this buffer contains the current text to be matched and is
+      the source of the yytext() string */
+  private char zzBuffer[] = new char[ZZ_BUFFERSIZE];
+
+  /** the textposition at the last accepting state */
+  private int zzMarkedPos;
+
+  /** the current text position in the buffer */
+  private int zzCurrentPos;
+
+  /** startRead marks the beginning of the yytext() string in the buffer */
+  private int zzStartRead;
+
+  /** endRead marks the last character in the buffer, that has been read
+      from input */
+  private int zzEndRead;
+
+  /** number of newlines encountered up to the start of the matched text */
+  private int yyline;
+
+  /** the number of characters up to the start of the matched text */
+  private int yychar;
+
+  /**
+   * the number of characters from the last newline up to the start of the 
+   * matched text
+   */
+  private int yycolumn;
+
+  /** 
+   * zzAtBOL == true <=> the scanner is currently at the beginning of a line
+   */
+  private boolean zzAtBOL = true;
+
+  /** zzAtEOF == true <=> the scanner is at the EOF */
+  private boolean zzAtEOF;
+
+  /** denotes if the user-EOF-code has already been executed */
+  private boolean zzEOFDone;
+
+  /* user code: */
+  public static boolean DEBUG = false;
+
+
+  /**
+   * Creates a new scanner
+   * There is also a java.io.InputStream version of this constructor.
+   *
+   * @param   in  the java.io.Reader to read input from.
+   */
+  public MP2to5bLexer(java.io.Reader in) {
+    this.zzReader = in;
+  }
+
+  /**
+   * Creates a new scanner.
+   * There is also java.io.Reader version of this constructor.
+   *
+   * @param   in  the java.io.Inputstream to read input from.
+   */
+  public MP2to5bLexer(java.io.InputStream in) {
+    this(new java.io.InputStreamReader(in));
+  }
+
+
+  /**
+   * Refills the input buffer.
+   *
+   * @return      <code>false</code>, iff there was new input.
+   * 
+   * @exception   java.io.IOException  if any I/O-Error occurs
+   */
+  private boolean zzRefill() throws java.io.IOException {
+
+    /* first: make room (if you can) */
+    if (zzStartRead > 0) {
+      System.arraycopy(zzBuffer, zzStartRead,
+                       zzBuffer, 0,
+                       zzEndRead-zzStartRead);
+
+      /* translate stored positions */
+      zzEndRead-= zzStartRead;
+      zzCurrentPos-= zzStartRead;
+      zzMarkedPos-= zzStartRead;
+      zzStartRead = 0;
+    }
+
+    /* is the buffer big enough? */
+    if (zzCurrentPos >= zzBuffer.length) {
+      /* if not: blow it up */
+      char newBuffer[] = new char[zzCurrentPos*2];
+      System.arraycopy(zzBuffer, 0, newBuffer, 0, zzBuffer.length);
+      zzBuffer = newBuffer;
+    }
+
+    /* finally: fill the buffer with new input */
+    int numRead = zzReader.read(zzBuffer, zzEndRead,
+                                            zzBuffer.length-zzEndRead);
+
+    if (numRead > 0) {
+      zzEndRead+= numRead;
+      return false;
+    }
+    // unlikely but not impossible: read 0 characters, but not at end of stream    
+    if (numRead == 0) {
+      int c = zzReader.read();
+      if (c == -1) {
+        return true;
+      } else {
+        zzBuffer[zzEndRead++] = (char) c;
+        return false;
+      }     
+    }
+
+	// numRead < 0
+    return true;
+  }
+
+    
+  /**
+   * Closes the input stream.
+   */
+  public final void yyclose() throws java.io.IOException {
+    zzAtEOF = true;            /* indicate end of file */
+    zzEndRead = zzStartRead;  /* invalidate buffer    */
+
+    if (zzReader != null)
+      zzReader.close();
+  }
+
+
+  /**
+   * Resets the scanner to read from a new input stream.
+   * Does not close the old reader.
+   *
+   * All internal variables are reset, the old input stream 
+   * <b>cannot</b> be reused (internal buffer is discarded and lost).
+   * Lexical state is set to <tt>ZZ_INITIAL</tt>.
+   *
+   * @param reader   the new input stream 
+   */
+  public final void yyreset(java.io.Reader reader) {
+    zzReader = reader;
+    zzAtBOL  = true;
+    zzAtEOF  = false;
+    zzEOFDone = false;
+    zzEndRead = zzStartRead = 0;
+    zzCurrentPos = zzMarkedPos = 0;
+    yyline = yychar = yycolumn = 0;
+    zzLexicalState = YYINITIAL;
+  }
+
+
+  /**
+   * Returns the current lexical state.
+   */
+  public final int yystate() {
+    return zzLexicalState;
+  }
+
+
+  /**
+   * Enters a new lexical state
+   *
+   * @param newState the new lexical state
+   */
+  public final void yybegin(int newState) {
+    zzLexicalState = newState;
+  }
+
+
+  /**
+   * Returns the text matched by the current regular expression.
+   */
+  public final String yytext() {
+    return new String( zzBuffer, zzStartRead, zzMarkedPos-zzStartRead );
+  }
+
+
+  /**
+   * Returns the character at position <tt>pos</tt> from the 
+   * matched text. 
+   * 
+   * It is equivalent to yytext().charAt(pos), but faster
+   *
+   * @param pos the position of the character to fetch. 
+   *            A value from 0 to yylength()-1.
+   *
+   * @return the character at position pos
+   */
+  public final char yycharat(int pos) {
+    return zzBuffer[zzStartRead+pos];
+  }
+
+
+  /**
+   * Returns the length of the matched text region.
+   */
+  public final int yylength() {
+    return zzMarkedPos-zzStartRead;
+  }
+
+
+  /**
+   * Reports an error that occured while scanning.
+   *
+   * In a wellformed scanner (no or only correct usage of 
+   * yypushback(int) and a match-all fallback rule) this method 
+   * will only be called with things that "Can't Possibly Happen".
+   * If this method is called, something is seriously wrong
+   * (e.g. a JFlex bug producing a faulty scanner etc.).
+   *
+   * Usual syntax/scanner level error handling should be done
+   * in error fallback rules.
+   *
+   * @param   errorCode  the code of the errormessage to display
+   */
+  private void zzScanError(int errorCode) {
+    String message;
+    try {
+      message = ZZ_ERROR_MSG[errorCode];
+    }
+    catch (ArrayIndexOutOfBoundsException e) {
+      message = ZZ_ERROR_MSG[ZZ_UNKNOWN_ERROR];
+    }
+
+    throw new Error(message);
+  } 
+
+
+  /**
+   * Pushes the specified amount of characters back into the input stream.
+   *
+   * They will be read again by then next call of the scanning method
+   *
+   * @param number  the number of characters to be read again.
+   *                This number must not be greater than yylength()!
+   */
+  public void yypushback(int number)  {
+    if ( number > yylength() )
+      zzScanError(ZZ_PUSHBACK_2BIG);
+
+    zzMarkedPos -= number;
+  }
+
+
+  /**
+   * Contains user EOF-code, which will be executed exactly once,
+   * when the end of file is reached
+   */
+  private void zzDoEOF() throws java.io.IOException {
+    if (!zzEOFDone) {
+      zzEOFDone = true;
+      yyclose();
+    }
+  }
+
+
+  /**
+   * Resumes scanning until the next regular expression is matched,
+   * the end of input is encountered or an I/O-Error occurs.
+   *
+   * @return      the next token
+   * @exception   java.io.IOException  if any I/O-Error occurs
+   */
+  public java_cup.runtime.Symbol next_token() throws java.io.IOException {
+    int zzInput;
+    int zzAction;
+
+    // cached fields:
+    int zzCurrentPosL;
+    int zzMarkedPosL;
+    int zzEndReadL = zzEndRead;
+    char [] zzBufferL = zzBuffer;
+    char [] zzCMapL = ZZ_CMAP;
+
+    int [] zzTransL = ZZ_TRANS;
+    int [] zzRowMapL = ZZ_ROWMAP;
+    int [] zzAttrL = ZZ_ATTRIBUTE;
+
+    while (true) {
+      zzMarkedPosL = zzMarkedPos;
+
+      zzAction = -1;
+
+      zzCurrentPosL = zzCurrentPos = zzStartRead = zzMarkedPosL;
+  
+      zzState = ZZ_LEXSTATE[zzLexicalState];
+
+
+      zzForAction: {
+        while (true) {
+    
+          if (zzCurrentPosL < zzEndReadL)
+            zzInput = zzBufferL[zzCurrentPosL++];
+          else if (zzAtEOF) {
+            zzInput = YYEOF;
+            break zzForAction;
+          }
+          else {
+            // store back cached positions
+            zzCurrentPos  = zzCurrentPosL;
+            zzMarkedPos   = zzMarkedPosL;
+            boolean eof = zzRefill();
+            // get translated positions and possibly new buffer
+            zzCurrentPosL  = zzCurrentPos;
+            zzMarkedPosL   = zzMarkedPos;
+            zzBufferL      = zzBuffer;
+            zzEndReadL     = zzEndRead;
+            if (eof) {
+              zzInput = YYEOF;
+              break zzForAction;
+            }
+            else {
+              zzInput = zzBufferL[zzCurrentPosL++];
+            }
+          }
+          int zzNext = zzTransL[ zzRowMapL[zzState] + zzCMapL[zzInput] ];
+          if (zzNext == -1) break zzForAction;
+          zzState = zzNext;
+
+          int zzAttributes = zzAttrL[zzState];
+          if ( (zzAttributes & 1) == 1 ) {
+            zzAction = zzState;
+            zzMarkedPosL = zzCurrentPosL;
+            if ( (zzAttributes & 8) == 8 ) break zzForAction;
+          }
+
+        }
+      }
+
+      // store back cached position
+      zzMarkedPos = zzMarkedPosL;
+
+      switch (zzAction < 0 ? zzAction : ZZ_ACTION[zzAction]) {
+        case 4: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	   yybegin(YYINITIAL);
+	   return new Symbol(MP2to5bSym.FLOAT, yytext());
+          }
+        case 11: break;
+        case 8: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	    return new Symbol(MP2to5bSym.FCOPT, yytext());
+          }
+        case 12: break;
+        case 10: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+		return new Symbol(MP2to5bSym.FCOPT, yytext());
+          }
+        case 13: break;
+        case 9: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	     return new Symbol(MP2to5bSym.FCOPT, yytext());
+          }
+        case 14: break;
+        case 5: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	 return new Symbol(MP2to5bSym.FCOPT2, yytext());
+          }
+        case 15: break;
+        case 7: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	  return new Symbol(MP2to5bSym.FCOPT2, yytext());
+          }
+        case 16: break;
+        case 6: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	  return new Symbol(MP2to5bSym.FCOPT, yytext());
+          }
+        case 17: break;
+        case 3: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	return new Symbol(MP2to5bSym.FCOPT2, yytext());
+          }
+        case 18: break;
+        case 2: 
+          { if(Settings.DEBUG) System.out.println("JFlex:mp2to5:  "+yytext());
+	return new Symbol(MP2to5bSym.FCOPT, yytext());
+          }
+        case 19: break;
+        case 1: 
+          { 
+          }
+        case 20: break;
+        default: 
+          if (zzInput == YYEOF && zzStartRead == zzCurrentPos) {
+            zzAtEOF = true;
+            zzDoEOF();
+              { return new java_cup.runtime.Symbol(MP2to5bSym.EOF); }
+          } 
+          else {
+            zzScanError(ZZ_NO_MATCH);
+          }
+      }
+    }
+  }
+
+  /**
+   * Converts an int token code into the name of the
+   * token by reflection on the cup symbol class/interface sym
+   *
+   * This code was contributed by Karl Meissner <meissnersd@yahoo.com>
+   */
+  private String getTokenName(int token) {
+    try {
+      java.lang.reflect.Field [] classFields = MP2to5bSym.class.getFields();
+      for (int i = 0; i < classFields.length; i++) {
+        if (classFields[i].getInt(null) == token) {
+          return classFields[i].getName();
+        }
+      }
+    } catch (Exception e) {
+      e.printStackTrace(System.err);
+    }
+
+    return "UNKNOWN TOKEN";
+  }
+
+  /**
+   * Same as next_token but also prints the token to standard out
+   * for debugging.
+   *
+   * This code was contributed by Karl Meissner <meissnersd@yahoo.com>
+   */
+  public java_cup.runtime.Symbol debug_next_token() throws java.io.IOException {
+    java_cup.runtime.Symbol s = next_token();
+    System.out.println( " --"+ yytext() + "--" + getTokenName(s.sym) + "--");
+    return s;
+  }
+
+  /**
+   * Runs the scanner on input files.
+   *
+   * This is a standalone scanner, it will print any unmatched
+   * text to System.out unchanged.
+   *
+   * @param argv   the command line, contains the filenames to run
+   *               the scanner on.
+   */
+  public static void main(String argv[]) {
+    if (argv.length == 0) {
+      System.out.println("Usage : java MP2to5bLexer <inputfile>");
+    }
+    else {
+      for (int i = 0; i < argv.length; i++) {
+        MP2to5bLexer scanner = null;
+        try {
+          scanner = new MP2to5bLexer( new java.io.FileReader(argv[i]) );
+          while ( !scanner.zzAtEOF ) scanner.next_token();
+        }
+        catch (java.io.FileNotFoundException e) {
+          System.out.println("File not found : \""+argv[i]+"\"");
+        }
+        catch (java.io.IOException e) {
+          System.out.println("IO error scanning file \""+argv[i]+"\"");
+          System.out.println(e);
+        }
+        catch (Exception e) {
+          System.out.println("Unexpected exception:");
+          e.printStackTrace();
+        }
+      }
+    }
+  }
+
+
+}

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bParser.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bParser.java
new file mode 100644
index 0000000..ba61f5f
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bParser.java
@@ -0,0 +1,263 @@
+/*
+*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements.  See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership.  The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License.  You may obtain a copy of the License at
+*
+*   http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied.  See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*
+*/
+package org.apache.airavata.datacat.parsers.gridchem.mp2to5b;
+
+
+import java_cup.runtime.lr_parser;
+import org.apache.airavata.datacat.parsers.gridchem.GridChemQueueParser;
+import org.apache.airavata.datacat.parsers.gridchem.Settings;
+
+import java.io.FileReader;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+
+public class MP2to5bParser extends java_cup.runtime.lr_parser implements GridChemQueueParser{
+
+  /** Default constructor. */
+  public MP2to5bParser() {super();}
+
+  /** Constructor which sets the default scanner. */
+  public MP2to5bParser(java_cup.runtime.Scanner s) {super(s);}
+
+    /**
+     * Constructor which uses a file reader.
+     */
+    public MP2to5bParser(final FileReader fileReader) {
+        super(new MP2to5bLexer(fileReader));
+    }
+
+    /** Production table. */
+  protected static final short _production_table[][] = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\005\000\002\003\004\000\002\002\004\000\002\003" +
+                    "\003\000\002\004\003\000\002\004\003"});
+
+  /** Access to production table. */
+  public short[][] production_table() {return _production_table;}
+
+  /** Parse-action table. */
+  protected static final short[][] _action_table = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\007\000\006\017\004\020\005\001\002\000\010\002" +
+                    "\ufffe\017\ufffe\020\ufffe\001\002\000\010\002\ufffd\017\ufffd" +
+                    "\020\ufffd\001\002\000\010\002\uffff\017\uffff\020\uffff\001" +
+                    "\002\000\010\002\011\017\004\020\005\001\002\000\010" +
+                    "\002\001\017\001\020\001\001\002\000\004\002\000\001" +
+                    "\002"});
+
+  /** Access to parse-action table. */
+  public short[][] action_table() {return _action_table;}
+
+  /** <code>reduce_goto</code> table. */
+  protected static final short[][] _reduce_table = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\007\000\006\003\006\004\005\001\001\000\002\001" +
+                    "\001\000\002\001\001\000\002\001\001\000\004\004\007" +
+                    "\001\001\000\002\001\001\000\002\001\001"});
+
+  /** Access to <code>reduce_goto</code> table. */
+  public short[][] reduce_table() {return _reduce_table;}
+
+  /** Instance of action encapsulation class. */
+  protected CUP$parser$actions action_obj;
+
+    //Each string is of the format
+    //mp2SpecificOption
+    private ArrayList<String> result = new ArrayList<String>();
+    private String tempStr = "";
+
+
+    public ArrayList<String> getResult() {
+        return result;
+    }
+
+
+    public void addToResult(String value) {
+        result.add(value);
+    }
+
+    public String getTempStr() {
+        return tempStr;
+    }
+
+    public void setTempStr(String s) {
+        this.tempStr = s;
+    }
+
+    /*Adding the parsed data to the hash map */
+    @Override
+    public HashMap<String, String> getParsedData() throws Exception {
+        parse();
+        HashMap<String, String> results = new HashMap<String,String>();
+        int j=0;
+        for (int i=0; i<result.size();i++){
+            String resultString= result.get(i);
+            String[] temp=resultString.split(" ");
+            if(temp.length<3){
+                continue;
+            }
+            String element=temp[2]+" "+temp[3]+" "+temp[4];
+            if (element.equalsIgnoreCase("Frozen Core Option:")){
+                j++;
+                String tempString= "MP2to5b_Frozen Core Option_" + j;
+                results.put(tempString,temp[6]);
+            }else{
+                continue;
+            }
+        }
+        return results;
+    }
+
+  /** Action encapsulation object initializer. */
+  protected void init_actions()
+    {
+      action_obj = new CUP$parser$actions(this);
+    }
+
+  /** Invoke a user supplied parse action. */
+  public java_cup.runtime.Symbol do_action(
+    int                        act_num,
+    java_cup.runtime.lr_parser parser,
+    java.util.Stack            stack,
+    int                        top)
+    throws java.lang.Exception
+  {
+    /* call code in generated class */
+    return action_obj.CUP$parser$do_action(act_num, parser, stack, top);
+  }
+
+  /** Indicates start state. */
+  public int start_state() {return 0;}
+  /** Indicates start production. */
+  public int start_production() {return 1;}
+
+  /** <code>EOF</code> Symbol index. */
+  public int EOF_sym() {return 0;}
+
+  /** <code>error</code> Symbol index. */
+  public int error_sym() {return 1;}
+
+
+  /** User initialization code. */
+  public void user_init() throws java.lang.Exception
+    {
+ if(Settings.DEBUG) System.out.println("CUP:mp2to5b:  entry");
+    }
+
+
+
+    ///public static boolean DEBUG = false;
+}
+
+/** Cup generated class to encapsulate user supplied action code.*/
+class CUP$parser$actions {
+  private final MP2to5bParser MP2to5bParser;
+
+  /** Constructor */
+  CUP$parser$actions(MP2to5bParser MP2to5bParser) {
+    this.MP2to5bParser = MP2to5bParser;
+  }
+
+  /** Method with the actual generated action code. */
+  public final java_cup.runtime.Symbol CUP$parser$do_action(
+    int                        CUP$parser$act_num,
+    java_cup.runtime.lr_parser CUP$parser$parser,
+    java.util.Stack            CUP$parser$stack,
+    int                        CUP$parser$top)
+    throws java.lang.Exception
+    {
+      /* Symbol object for return from actions */
+      java_cup.runtime.Symbol CUP$parser$result;
+
+      /* select the action based on the action number */
+      switch (CUP$parser$act_num)
+        {
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 4: // element ::= FCOPT2 
+            {
+              Object RESULT = null;
+		int sleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int sright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		String s = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+		 if(Settings.DEBUG) System.out.println("CUP:mp2to5b:  Frozen Core Option:  "+s);
+         MP2to5bParser.addToResult("CUP:mp2to5b:  Frozen Core Option:  "+s);
+               	//   ParseMP2to5.put("Frozen Core Option?  (Check raw output)  ", s);
+              CUP$parser$result = new java_cup.runtime.Symbol(2/*element*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 3: // element ::= FCOPT 
+            {
+              Object RESULT = null;
+		int sleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int sright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		String s = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+		 if(Settings.DEBUG) System.out.println("CUP:mp2to5b:  Frozen Core Option:  "+s);
+         MP2to5bParser.addToResult("CUP:mp2to5b:  Frozen Core Option:  "+s);
+
+	//   ParseMP2to5.put("Frozen Core Option:  ", s);
+              CUP$parser$result = new java_cup.runtime.Symbol(2/*element*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 2: // startpt ::= element 
+            {
+              Object RESULT = null;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 1: // $START ::= startpt EOF 
+            {
+              Object RESULT = null;
+		int start_valleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left;
+		int start_valright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).right;
+		Object start_val = (Object)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value;
+		RESULT = start_val;
+              CUP$parser$result = new java_cup.runtime.Symbol(0/*$START*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          /* ACCEPT */
+          CUP$parser$parser.done_parsing();
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 0: // startpt ::= startpt element 
+            {
+              Object RESULT = null;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /* . . . . . .*/
+          default:
+            throw new Exception(
+               "Invalid action number found in internal parse table");
+
+        }
+    }
+}
+

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bSym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bSym.java
new file mode 100644
index 0000000..69f1e51
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bSym.java
@@ -0,0 +1,51 @@
+/*
+*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements.  See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership.  The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License.  You may obtain a copy of the License at
+*
+*   http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied.  See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*
+*/
+package org.apache.airavata.datacat.parsers.gridchem.mp2to5b;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Sun Sep 14 11:52:08 IST 2014
+//----------------------------------------------------
+
+/** CUP generated class containing symbol constants. */
+public class MP2to5bSym {
+  /* terminals */
+  public static final int E4_SDTQ = 8;
+  public static final int MP2OPT = 16;
+  public static final int LIM = 18;
+  public static final int UMP4_SDQ = 11;
+  public static final int UMP4_SDTQ = 12;
+  public static final int E4_DQ = 6;
+  public static final int FCOPT = 13;
+  public static final int UMP4_DQ = 10;
+  public static final int E4_SDQ = 7;
+  public static final int E3 = 5;
+  public static final int E2 = 2;
+  public static final int FLOAT = 19;
+  public static final int EOF = 0;
+  public static final int error = 1;
+  public static final int MP4_T = 4;
+  public static final int FCOPT2 = 14;
+  public static final int ALGOPT = 15;
+  public static final int VAR = 17;
+  public static final int EUMP3 = 9;
+  public static final int EUMP2 = 3;
+}
+


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