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From scnakand...@apache.org
Subject [18/32] airavata-sandbox git commit: adding datacat system
Date Mon, 24 Aug 2015 19:28:56 GMT
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/inchi/InChIGenerator.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/inchi/InChIGenerator.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/inchi/InChIGenerator.java
new file mode 100644
index 0000000..145effe
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/inchi/InChIGenerator.java
@@ -0,0 +1,95 @@
+/*
+*
+* 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.inchi;
+
+import org.apache.airavata.datacat.parsers.gridchem.util.Constants;
+import org.apache.airavata.datacat.parsers.gridchem.util.GridChemProperties;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+public class InChIGenerator {
+
+    private String filePrefix;
+
+    public InChIGenerator(String filePrefix) {
+        this.filePrefix = filePrefix;
+    }
+
+    private BufferedReader runInChI(String molfile) throws IOException {
+        String[] command = {
+                "/bin/sh",
+                "-c",
+                "echo \"" + molfile + "\" | ./inchi-1 -STDIO -AuxNone -NoLabels -Key 2>/dev/null"
+        };
+        Process inchi = Runtime.getRuntime().exec(command);
+        try {
+            inchi.waitFor();
+        } catch (InterruptedException e) {
+            e.printStackTrace();
+        }
+        return new BufferedReader(new InputStreamReader(inchi.getInputStream()));
+    }
+
+    public InChI getInChI() throws IOException {
+        convertGaussian2Mol();
+        String molfile = readFile(GridChemProperties.getInstance().getProperty(
+                Constants.TMP_DIR,"") + "/" + filePrefix + ".mol");
+        BufferedReader input = runInChI(molfile);
+
+        String result = input.readLine();
+        String inchiStr = result == null ? "" : result;
+
+        result = input.readLine();
+        String inchiKey = result == null ? "" : result.substring(9);
+        InChI inChI = new InChI(inchiStr, inchiKey);
+        input.close();
+
+        return inChI;
+    }
+
+    private void convertGaussian2Mol() throws IOException {
+        Process inchi = Runtime.getRuntime().exec("babel -i g09 "
+                + GridChemProperties.getInstance().getProperty(Constants.TMP_DIR,"") + "/" + filePrefix + ".out -o mol "
+                + GridChemProperties.getInstance().getProperty(Constants.TMP_DIR,"") + "/" + filePrefix + ".mol\n");
+        try {
+            inchi.waitFor();
+        } catch (InterruptedException e) {
+            e.printStackTrace();
+        }
+    }
+
+    private String readFile(String filename) throws IOException {
+        BufferedReader in = new BufferedReader(new FileReader(filename));
+        String str = "";
+        String molfile = "";
+
+        while ((str = in.readLine()) != null) {
+            molfile = molfile + str + "\n";
+        }
+
+        in.close();
+
+        return molfile;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputLexer.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputLexer.java
new file mode 100644
index 0000000..0fbf3ff
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputLexer.java
@@ -0,0 +1,799 @@
+/*
+*
+* 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.input;/* The following code was generated by JFlex 1.4.3 on 9/11/14 6:37 PM */
+
+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 9/11/14 6:37 PM from the specification file
+ * <tt>input.flex</tt>
+ */
+public class InputLexer 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 INPUTF = 30;
+  public static final int ITER2 = 4;
+  public static final int INPUTE = 28;
+  public static final int INPUTD = 26;
+  public static final int INPUTC = 24;
+  public static final int INPUTB = 22;
+  public static final int INPUTA = 20;
+  public static final int INTVALUE = 8;
+  public static final int INPUT = 18;
+  public static final int IGNOREALL = 16;
+  public static final int ITER = 2;
+  public static final int YYINITIAL = 0;
+  public static final int FLOAT2 = 14;
+  public static final int FLOAT1 = 12;
+  public static final int FLOATVALUE = 10;
+  public static final int ITER3 = 6;
+
+  /**
+   * 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,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2, 
+     2,  2,  3,  3,  4,  4,  5,  5,  6,  6,  7,  7,  8,  8,  9, 9
+  };
+
+  /** 
+   * 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, 
+    11,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  2,  0, 31,  3,  0, 
+     1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  0,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0, 27, 25,  4,  0, 24, 29,  0,  0, 30,  0,  5, 28, 
+     0,  0,  0,  0, 23,  0,  0,  0, 20, 21, 22,  0,  0,  0,  0, 26, 
+     0,  0,  8,  0,  0,  9, 13,  0, 19, 17,  0,  0,  0,  7, 18, 12, 
+    16,  0, 10, 14, 15,  6,  0,  0,  0,  0,  0,  0,  2,  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 =
+    "\12\0\4\1\1\2\2\1\1\3\1\1\1\4\10\1"+
+    "\17\0\1\5\1\6\1\7\72\0\1\10\47\0\1\11"+
+    "\5\0\1\12\124\0\1\13\1\14";
+
+  private static int [] zzUnpackAction() {
+    int [] result = new int[237];
+    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\40\0\100\0\140\0\200\0\240\0\300\0\340"+
+    "\0\u0100\0\u0120\0\u0140\0\u0160\0\u0180\0\u01a0\0\u01c0\0\u01c0"+
+    "\0\u01e0\0\u0200\0\u0200\0\u0220\0\u0220\0\u0240\0\u0260\0\u0280"+
+    "\0\u02a0\0\u02c0\0\u02e0\0\u0300\0\u0320\0\u0340\0\u0360\0\u0380"+
+    "\0\u0240\0\u03a0\0\u0280\0\u03c0\0\u02c0\0\u03e0\0\u0400\0\u0420"+
+    "\0\u0440\0\u0460\0\u0480\0\u03a0\0\u03c0\0\u03e0\0\u04a0\0\u04c0"+
+    "\0\u04e0\0\u0500\0\u0520\0\u0540\0\u0560\0\u0580\0\u05a0\0\u05c0"+
+    "\0\u05e0\0\u0600\0\u0620\0\u0640\0\u0660\0\u0680\0\u06a0\0\u06c0"+
+    "\0\u06e0\0\u0700\0\u0720\0\u0740\0\u0760\0\u0780\0\u07a0\0\u07c0"+
+    "\0\u07e0\0\u0800\0\u0820\0\u0840\0\u0860\0\u0880\0\u08a0\0\u08c0"+
+    "\0\u08e0\0\u0900\0\u0920\0\u0940\0\u0960\0\u0980\0\u09a0\0\u09c0"+
+    "\0\u09e0\0\u0a00\0\u0a20\0\u0a40\0\u0a60\0\u0a80\0\u0aa0\0\u0ac0"+
+    "\0\u0ae0\0\u0b00\0\u0b20\0\u0b40\0\u0b60\0\u0b80\0\u0ba0\0\u0bc0"+
+    "\0\u0140\0\u0be0\0\u0c00\0\u0c20\0\u0c40\0\u0c60\0\u0c80\0\u0ca0"+
+    "\0\u0cc0\0\u0ce0\0\u0d00\0\u0d20\0\u0d40\0\u0d60\0\u0d80\0\u0da0"+
+    "\0\u0dc0\0\u0de0\0\u0e00\0\u0e20\0\u0e40\0\u0e60\0\u0e80\0\u0ea0"+
+    "\0\u0ec0\0\u0ee0\0\u0f00\0\u0f20\0\u0f40\0\u0f60\0\u0f80\0\u0fa0"+
+    "\0\u0fc0\0\u0fe0\0\u1000\0\u1020\0\u1040\0\u1060\0\u1080\0\u10a0"+
+    "\0\u0140\0\u10c0\0\u10e0\0\u1100\0\u1120\0\u1140\0\u0140\0\u1160"+
+    "\0\u1180\0\u11a0\0\u11c0\0\u11e0\0\u1200\0\u1220\0\u1240\0\u1260"+
+    "\0\u1280\0\u12a0\0\u12c0\0\u12e0\0\u1300\0\u1320\0\u1340\0\u1360"+
+    "\0\u1380\0\u13a0\0\u13c0\0\u13e0\0\u1400\0\u1420\0\u1440\0\u1460"+
+    "\0\u1480\0\u14a0\0\u14c0\0\u14e0\0\u1500\0\u1520\0\u1540\0\u1560"+
+    "\0\u1580\0\u15a0\0\u15c0\0\u15e0\0\u1600\0\u1620\0\u1640\0\u1660"+
+    "\0\u1680\0\u16a0\0\u16c0\0\u16e0\0\u1700\0\u1720\0\u1740\0\u1760"+
+    "\0\u1780\0\u17a0\0\u17c0\0\u17e0\0\u1800\0\u1820\0\u1840\0\u1860"+
+    "\0\u1880\0\u18a0\0\u18c0\0\u18e0\0\u1900\0\u1920\0\u1940\0\u1960"+
+    "\0\u1980\0\u19a0\0\u19c0\0\u19e0\0\u1a00\0\u1a20\0\u1a40\0\u1a60"+
+    "\0\u1a80\0\u1aa0\0\u1ac0\0\u1ae0\0\u1b00\0\u1b20\0\u1b40\0\u1b60"+
+    "\0\u1b80\0\u1ba0\0\u1bc0\0\u0140\0\u0140";
+
+  private static int [] zzUnpackRowMap() {
+    int [] result = new int[237];
+    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 =
+    "\5\13\1\14\56\13\1\15\2\13\1\16\51\13\1\17"+
+    "\1\20\34\13\1\21\1\13\1\22\1\23\34\13\1\23"+
+    "\1\13\1\24\1\25\34\13\1\25\1\13\1\26\1\27"+
+    "\34\13\1\27\1\13\1\30\1\31\34\13\1\31\1\13"+
+    "\1\32\1\33\34\13\1\33\37\13\1\34\46\0\1\35"+
+    "\44\0\1\36\54\0\1\37\10\0\1\17\37\0\1\17"+
+    "\35\0\1\40\1\0\1\22\37\0\1\24\37\0\1\41"+
+    "\1\0\1\42\35\0\1\41\37\0\1\43\1\0\1\44"+
+    "\35\0\1\43\37\0\1\45\1\0\1\46\35\0\1\45"+
+    "\75\0\1\47\7\0\1\50\43\0\1\51\55\0\1\52"+
+    "\45\0\1\53\1\0\1\54\37\0\1\55\37\0\1\56"+
+    "\75\0\1\57\10\0\1\60\42\0\1\61\56\0\1\62"+
+    "\44\0\1\63\37\0\1\64\11\0\1\65\41\0\1\66"+
+    "\55\0\1\67\45\0\1\70\37\0\1\71\12\0\1\72"+
+    "\40\0\1\73\31\0\1\74\71\0\1\75\37\0\1\76"+
+    "\13\0\1\77\37\0\1\100\57\0\1\101\43\0\1\102"+
+    "\37\0\1\103\14\0\1\104\36\0\1\105\56\0\1\106"+
+    "\44\0\1\107\37\0\1\110\15\0\1\111\35\0\1\112"+
+    "\60\0\1\113\42\0\1\114\37\0\1\115\13\0\1\116"+
+    "\37\0\1\117\30\0\1\120\72\0\1\121\37\0\1\122"+
+    "\16\0\1\123\34\0\1\124\56\0\1\125\44\0\1\126"+
+    "\37\0\1\127\17\0\1\130\33\0\1\131\30\0\1\132"+
+    "\72\0\1\133\37\0\1\134\11\0\1\135\53\0\1\136"+
+    "\47\0\1\137\41\0\1\140\37\0\1\141\20\0\1\142"+
+    "\32\0\1\143\62\0\1\144\40\0\1\145\37\0\1\146"+
+    "\16\0\1\147\34\0\1\150\55\0\1\151\45\0\1\152"+
+    "\37\0\1\153\13\0\1\154\37\0\1\155\63\0\1\156"+
+    "\37\0\1\157\21\0\1\160\31\0\1\161\63\0\1\162"+
+    "\37\0\1\163\22\0\1\164\30\0\1\165\63\0\1\166"+
+    "\37\0\1\167\13\0\1\170\37\0\1\171\63\0\1\172"+
+    "\37\0\1\173\17\0\1\174\33\0\1\175\63\0\1\176"+
+    "\37\0\1\177\23\0\1\200\27\0\1\201\63\0\1\202"+
+    "\37\0\1\203\21\0\1\204\31\0\1\205\63\0\1\206"+
+    "\37\0\1\207\16\0\1\210\34\0\1\211\63\0\1\212"+
+    "\37\0\1\213\13\0\1\214\37\0\1\215\63\0\1\216"+
+    "\37\0\1\217\12\0\1\220\53\0\1\221\50\0\1\222"+
+    "\37\0\1\223\6\0\1\224\70\0\1\225\37\0\1\226"+
+    "\22\0\1\227\54\0\1\230\37\0\1\231\37\0\1\232"+
+    "\37\0\1\233\37\0\1\234\37\0\1\235\37\0\1\236"+
+    "\37\0\1\237\37\0\1\240\37\0\1\241\37\0\1\242"+
+    "\37\0\1\243\37\0\1\244\37\0\1\245\37\0\1\246"+
+    "\37\0\1\247\37\0\1\250\37\0\1\251\37\0\1\252"+
+    "\37\0\1\253\37\0\1\254\37\0\1\255\37\0\1\256"+
+    "\37\0\1\257\37\0\1\260\37\0\1\261\37\0\1\262"+
+    "\37\0\1\263\37\0\1\264\37\0\1\265\37\0\1\266"+
+    "\37\0\1\267\37\0\1\270\37\0\1\271\37\0\1\272"+
+    "\37\0\1\273\37\0\1\274\37\0\1\275\37\0\1\276"+
+    "\37\0\1\277\37\0\1\300\37\0\1\301\37\0\1\302"+
+    "\37\0\1\303\37\0\1\304\37\0\1\305\37\0\1\306"+
+    "\37\0\1\307\37\0\1\310\37\0\1\311\37\0\1\312"+
+    "\37\0\1\313\37\0\1\314\37\0\1\315\37\0\1\316"+
+    "\37\0\1\317\37\0\1\320\37\0\1\321\37\0\1\322"+
+    "\37\0\1\323\37\0\1\324\37\0\1\325\37\0\1\326"+
+    "\37\0\1\327\37\0\1\330\37\0\1\331\37\0\1\332"+
+    "\37\0\1\333\37\0\1\334\37\0\1\335\37\0\1\336"+
+    "\37\0\1\337\37\0\1\340\37\0\1\341\37\0\1\342"+
+    "\37\0\1\343\37\0\1\344\37\0\1\345\37\0\1\346"+
+    "\37\0\1\347\37\0\1\350\37\0\1\351\37\0\1\352"+
+    "\37\0\1\353\37\0\1\354\37\0\1\355";
+
+  private static int [] zzUnpackTrans() {
+    int [] result = new int[7136];
+    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 =
+    "\12\0\1\11\21\1\17\0\3\1\72\0\1\11\47\0"+
+    "\1\11\5\0\1\11\124\0\2\11";
+
+  private static int [] zzUnpackAttribute() {
+    int [] result = new int[237];
+    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 InputLexer(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 InputLexer(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 6: 
+          { if  (Settings.DEBUG) System.out.println("InputFlex: Found y coord. in input");
+  yybegin (INPUTE);
+   return new Symbol(InputSym.INPUT6, new Float(yytext()));
+          }
+        case 13: break;
+        case 7: 
+          { if  (Settings.DEBUG) System.out.println("InputFlex: Found z coord. in input");
+  yybegin (INPUT);
+   return new Symbol(InputSym.INPUT7, new Float(yytext()));
+          }
+        case 14: break;
+        case 4: 
+          { if  (Settings.DEBUG) System.out.println("InputFlex: Found integer3 in input");
+  yybegin (INPUTC);
+   return new Symbol(InputSym.INPUT4, new Integer(yytext()));
+          }
+        case 15: break;
+        case 11: 
+          { if  (Settings.DEBUG) System.out.println("InputFlex: Found the second dash");
+  yybegin (ITER);
+   return new Symbol(InputSym.DASH2);
+          }
+        case 16: break;
+        case 5: 
+          { if  (Settings.DEBUG) System.out.println("InputFlex: Found x coord. in input");
+  yybegin (INPUTD);
+   return new Symbol(InputSym.INPUT5, new Float(yytext()));
+          }
+        case 17: break;
+        case 12: 
+          { if  (Settings.DEBUG) System.out.println("InputFlex: Found the first dash");
+  yybegin (INPUT);
+   return new Symbol(InputSym.DASH1);
+          }
+        case 18: break;
+        case 9: 
+          { if (Settings.DEBUG) System.out.println("InputFlex: Found Input Orientation");
+            yybegin(INPUTF);
+            return new Symbol(InputSym.INPUT1);
+          }
+        case 19: break;
+        case 8: 
+          { yybegin(IGNOREALL);
+      return new Symbol(InputSym.SCFDONE);
+          }
+        case 20: break;
+        case 3: 
+          { if  (Settings.DEBUG) System.out.println("InputFlex: Found integer2 in input");
+  yybegin (INPUTB);
+   return new Symbol(InputSym.INPUT3, new Integer(yytext()));
+          }
+        case 21: break;
+        case 10: 
+          { if (Settings.DEBUG) System.out.println("InputFlex: Found Number of steps");
+	   yybegin(ITER);
+	   return new Symbol(InputSym.FOUNDITER);
+          }
+        case 22: break;
+        case 1: 
+          { 
+          }
+        case 23: break;
+        case 2: 
+          { if  (Settings.DEBUG) System.out.println("InputFlex: Found integer1 in input");
+  yybegin (INPUTA);
+   return new Symbol(InputSym.INPUT2, new Integer(yytext()));
+          }
+        case 24: break;
+        default: 
+          if (zzInput == YYEOF && zzStartRead == zzCurrentPos) {
+            zzAtEOF = true;
+            zzDoEOF();
+              { return new java_cup.runtime.Symbol(InputSym.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 = InputSym.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 InputLexer <inputfile>");
+    }
+    else {
+      for (int i = 0; i < argv.length; i++) {
+        InputLexer scanner = null;
+        try {
+          scanner = new InputLexer( 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/input/InputParser.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputParser.java
new file mode 100644
index 0000000..97a583a
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputParser.java
@@ -0,0 +1,385 @@
+/*
+*
+* 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.input;
+
+
+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 InputParser extends java_cup.runtime.lr_parser implements GridChemQueueParser {
+
+  /** Default constructor. */
+  public InputParser() {super();}
+
+  /** Constructor which sets the default scanner. */
+  public InputParser(java_cup.runtime.Scanner s) {super(s);}
+
+    /**
+     * Constructor which uses a file reader.
+     */
+    public InputParser(final FileReader fileReader) {
+        super(new InputLexer(fileReader));
+    }
+
+
+    /** Production table. */
+  protected static final short _production_table[][] = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\015\000\002\003\005\000\002\002\004\000\002\004" +
+                    "\003\000\002\005\004\000\002\005\003\000\002\006\006" +
+                    "\000\002\016\004\000\002\016\003\000\002\017\010\000" +
+                    "\002\012\003\000\002\013\003\000\002\014\003\000\002" +
+                    "\015\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\031\000\004\005\005\001\002\000\004\004\010\001" +
+                    "\002\000\004\004\uffff\001\002\000\004\002\007\001\002" +
+                    "\000\004\002\000\001\002\000\004\007\015\001\002\000" +
+                    "\006\004\010\006\013\001\002\000\006\004\ufffd\006\ufffd" +
+                    "\001\002\000\004\002\001\001\002\000\006\004\ufffe\006" +
+                    "\ufffe\001\002\000\004\011\016\001\002\000\004\012\024" +
+                    "\001\002\000\006\010\ufffa\011\ufffa\001\002\000\006\010" +
+                    "\021\011\016\001\002\000\006\004\ufffc\006\ufffc\001\002" +
+                    "\000\006\010\ufffb\011\ufffb\001\002\000\004\013\025\001" +
+                    "\002\000\004\013\ufff8\001\002\000\004\016\026\001\002" +
+                    "\000\004\017\ufff7\001\002\000\004\017\030\001\002\000" +
+                    "\004\020\ufff6\001\002\000\004\020\032\001\002\000\006" +
+                    "\010\ufff5\011\ufff5\001\002\000\006\010\ufff9\011\ufff9\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\031\000\006\003\005\004\003\001\001\000\006\005" +
+                    "\010\006\011\001\001\000\002\001\001\000\002\001\001" +
+                    "\000\002\001\001\000\002\001\001\000\004\006\013\001" +
+                    "\001\000\002\001\001\000\002\001\001\000\002\001\001" +
+                    "\000\006\016\017\017\016\001\001\000\004\012\022\001" +
+                    "\001\000\002\001\001\000\004\017\021\001\001\000\002" +
+                    "\001\001\000\002\001\001\000\002\001\001\000\002\001" +
+                    "\001\000\004\013\026\001\001\000\002\001\001\000\004" +
+                    "\014\030\001\001\000\002\001\001\000\004\015\032\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
+    // z_coord, y_coord, x_coord and atomic number
+    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 zCount=0;
+        int xCount=0;
+        int yCount=0;
+        int atomCount=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("Z")){
+                    results.put("InputParser_z_coordinate_"+zCount,dataString);
+                    zCount++;
+                }else if(keyString.equalsIgnoreCase("Y")){
+                    results.put("InputParser_y_coordinate_"+yCount,dataString);
+                    yCount++;
+                }else if(keyString.equalsIgnoreCase("X")){
+                    results.put("InputParser_x_coordinate_"+xCount,dataString);
+                    xCount++;
+                }else if(keyString.equalsIgnoreCase("AtomicNumber")){
+                    results.put("InputParser_atomic_number_"+atomCount,dataString);
+                    atomCount++;
+                }
+            }
+
+        }
+        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 {
+
+ 
+  //__________________________________
+  public static boolean DEBUG = true;
+  private static JTable table;               
+  private static final String tableLabel = "SCF Intermediate Results:";
+// private static String cycle = "0";
+ 
+  
+  public static JTable getTable() {
+    return table;
+  }
+
+  public static String getTableLabel() {
+    return tableLabel;
+  }
+
+//   }
+
+  private final InputParser InputParser;
+
+  /** Constructor */
+  CUP$parser$actions(InputParser InputParser) {
+    this.InputParser = InputParser;
+  }
+
+  /** 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 12: // inp7 ::= INPUT7 
+            {
+              Object RESULT = null;
+		int in7left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int in7right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Float in7 = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+		 //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:Input:  z coordinate "+in7);
+   InputParser.addToResult("Z "+in7);
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(11/*inp7*/, ((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 11: // inp6 ::= INPUT6 
+            {
+              Object RESULT = null;
+		int in6left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int in6right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Float in6 = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+		 //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:Input:  y coordinate "+in6);
+   InputParser.addToResult("Y "+in6);
+
+              CUP$parser$result = new java_cup.runtime.Symbol(10/*inp6*/, ((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 10: // inp5 ::= INPUT5 
+            {
+              Object RESULT = null;
+		int in5left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int in5right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Float in5 = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+		 //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:Input:  x coordinate "+in5);
+   InputParser.addToResult("X "+in5);
+ 
+              CUP$parser$result = new java_cup.runtime.Symbol(9/*inp5*/, ((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 9: // inp3 ::= INPUT3 
+            {
+              Object RESULT = null;
+		int in3left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int in3right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Integer in3 = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+		 //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:Input:  atomic number "+in3);
+   InputParser.addToResult("AtomicNumber "+in3);
+              CUP$parser$result = new java_cup.runtime.Symbol(8/*inp3*/, ((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 8: // cycle2 ::= INPUT2 inp3 INPUT4 inp5 inp6 inp7 
+            {
+              Object RESULT = null;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(13/*cycle2*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-5)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+            }
+          return CUP$parser$result;
+
+          /*. . . . . . . . . . . . . . . . . . . .*/
+          case 7: // cycle1 ::= cycle2 
+            {
+              Object RESULT = null;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(12/*cycle1*/, ((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: // cycle1 ::= cycle1 cycle2 
+            {
+              Object RESULT = null;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(12/*cycle1*/, ((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 5: // scfcycle ::= INPUT1 DASH1 cycle1 DASH2 
+            {
+              Object RESULT = null;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(4/*scfcycle*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).left, ((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:Input: 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:Input:  found the start of 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;
+
+              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/input/InputSym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputSym.java
new file mode 100644
index 0000000..5d52fa3
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputSym.java
@@ -0,0 +1,46 @@
+/*
+*
+* 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.input;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Thu Sep 11 18:37:51 IST 2014
+//----------------------------------------------------
+
+/** CUP generated class containing symbol constants. */
+public class InputSym {
+  /* terminals */
+  public static final int ENERGY = 11;
+  public static final int EOF = 0;
+  public static final int ITERATION = 10;
+  public static final int INPUT7 = 14;
+  public static final int error = 1;
+  public static final int INPUT6 = 13;
+  public static final int INPUT5 = 12;
+  public static final int INPUT4 = 9;
+  public static final int SCFDONE = 4;
+  public static final int INPUT3 = 8;
+  public static final int FOUNDITER = 3;
+  public static final int INPUT2 = 7;
+  public static final int DASH2 = 6;
+  public static final int INPUT1 = 2;
+  public static final int DASH1 = 5;
+}
+

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodLexer.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodLexer.java
new file mode 100644
index 0000000..d9f9d08
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodLexer.java
@@ -0,0 +1,752 @@
+/*
+*
+* 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.method;/* The following code was generated by JFlex 1.4.3 on 9/11/14 11:51 PM */
+
+import java_cup.runtime.Symbol;
+import java_cup.sym;
+import org.apache.airavata.datacat.parsers.gridchem.Settings;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.PrintStream;
+
+
+/**
+ * This class is a scanner generated by 
+ * <a href="http://www.jflex.de/">JFlex</a> 1.4.3
+ * on 9/11/14 11:51 PM from the specification file
+ * <tt>method.flex</tt>
+ */
+public class MethodLexer 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 = 6;
+  public static final int ITER1 = 4;
+  public static final int YYINITIAL = 0;
+  public static final int ITER = 2;
+
+  /**
+   * 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,  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,  0,  0,  2,  0,  0, 
+     0,  7,  8,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0, 
+     0, 20, 10,  9, 21, 19,  0,  6,  0, 22,  0,  0,  0, 24, 15, 23, 
+    18, 12, 13, 11, 16, 14,  0,  0,  0, 17, 25,  0,  0,  0,  0,  0, 
+     0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  3, 
+     4,  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,  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\6\1\2\0\1\2\1\3\3\0\1\4\6\0"+
+    "\1\5\33\0\1\6\5\0\1\7\1\10\6\0\1\11";
+
+  private static int [] zzUnpackAction() {
+    int [] result = new int[66];
+    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\32\0\64\0\116\0\150\0\202\0\234\0\266"+
+    "\0\320\0\352\0\u0104\0\116\0\116\0\u011e\0\u0138\0\u0152"+
+    "\0\116\0\u016c\0\u0186\0\u01a0\0\u01ba\0\u01d4\0\u01ee\0\116"+
+    "\0\u0208\0\u0222\0\u023c\0\u0256\0\u0270\0\u028a\0\u02a4\0\u02be"+
+    "\0\u02d8\0\u02f2\0\u030c\0\u0326\0\u0340\0\u035a\0\u0374\0\u038e"+
+    "\0\u03a8\0\u03c2\0\u03dc\0\u03f6\0\u0410\0\u042a\0\u0444\0\u045e"+
+    "\0\u0478\0\u0492\0\u04ac\0\116\0\u04c6\0\u04e0\0\u04fa\0\u0514"+
+    "\0\u052e\0\116\0\116\0\u0548\0\u0562\0\u057c\0\u0596\0\u05b0"+
+    "\0\u05ca\0\116";
+
+  private static int [] zzUnpackRowMap() {
+    int [] result = new int[66];
+    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 =
+    "\2\4\1\5\32\4\1\6\2\4\1\7\2\4\1\10"+
+    "\3\4\1\11\46\4\34\0\1\12\33\0\1\13\34\0"+
+    "\1\14\1\15\33\0\1\16\35\0\1\17\15\0\1\20"+
+    "\34\0\1\21\37\0\1\22\35\0\1\23\14\0\1\24"+
+    "\31\0\1\25\47\0\1\26\13\0\1\27\43\0\1\30"+
+    "\36\0\1\31\12\0\1\32\51\0\1\33\11\0\1\34"+
+    "\30\0\1\35\32\0\1\36\35\0\1\37\14\0\1\40"+
+    "\3\0\1\41\4\0\1\42\44\0\1\43\33\0\1\44"+
+    "\34\0\1\45\11\0\1\46\53\0\1\47\30\0\1\50"+
+    "\26\0\1\51\13\0\1\52\54\0\1\53\21\0\1\54"+
+    "\42\0\1\55\5\0\1\56\55\0\1\57\11\0\1\60"+
+    "\53\0\1\61\3\0\1\62\52\0\1\63\27\0\1\64"+
+    "\36\0\1\65\5\0\1\66\46\0\1\67\43\0\1\70"+
+    "\2\0\1\71\47\0\1\72\34\0\1\73\10\0\1\74"+
+    "\31\0\1\75\31\0\1\76\31\0\1\77\31\0\1\100"+
+    "\31\0\1\101\31\0\1\102\27\0";
+
+  private static int [] zzUnpackTrans() {
+    int [] result = new int[1508];
+    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\5\1\2\0\2\11\3\0\1\11\6\0"+
+    "\1\11\33\0\1\11\5\0\2\11\6\0\1\11";
+
+  private static int [] zzUnpackAttribute() {
+    int [] result = new int[66];
+    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 MethodLexer(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 MethodLexer(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: 
+          { System.out.println("MethodFlex: Found opt ");
+   System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+
+     yybegin(IGNOREALL);
+     return new Symbol(MethodSym.RUNTYP);
+          }
+        case 10: break;
+        case 7: 
+          { if (Settings.DEBUG) System.out.println("MethodFlex: RUNTYP=GRADIENT");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print("gradient");
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(IGNOREALL);
+     return new Symbol(MethodSym.RUNTYP);
+          }
+        case 11: break;
+        case 8: 
+          { if (Settings.DEBUG) System.out.println("MethodFlex: RUNTYP=ENERGY");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print("optimize");
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(IGNOREALL);
+     return new Symbol(MethodSym.RUNTYP);
+          }
+        case 12: break;
+        case 9: 
+          { if (Settings.DEBUG) System.out.println("MethodFlex: Found Gaussian 98");
+           yybegin(ITER);
+	   return new Symbol(MethodSym.FOUNDITER);
+          }
+        case 13: break;
+        case 2: 
+          { if (Settings.DEBUG) System.out.println("MethodFlex: Found G1");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(IGNOREALL);
+     return new Symbol(MethodSym.RUNTYP);
+          }
+        case 14: break;
+        case 6: 
+          { if (Settings.DEBUG) System.out.println("MethodFlex: RUNTYP=ENERGY");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print("energy");
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(IGNOREALL);
+     return new Symbol(MethodSym.RUNTYP);
+          }
+        case 15: break;
+        case 3: 
+          { if (Settings.DEBUG) System.out.println("MethodFlex: Found G2");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(IGNOREALL);
+     return new Symbol(MethodSym.RUNTYP);
+          }
+        case 16: break;
+        case 1: 
+          { 
+          }
+        case 17: break;
+        case 5: 
+          { if (Settings.DEBUG) System.out.println("MethodFlex: Found CBS-Q");
+   if (Settings.DEBUG) System.out.println(yytext());
+ try{
+     PrintStream temp = new PrintStream(new FileOutputStream("runtype1"));
+     temp.print(yytext());
+     System.out.println(yytext());}
+   catch (IOException ie){ System.out.println("Error in Gaussian Lexer");}
+     yybegin(IGNOREALL);
+     return new Symbol(MethodSym.RUNTYP);
+          }
+        case 18: break;
+        default: 
+          if (zzInput == YYEOF && zzStartRead == zzCurrentPos) {
+            zzAtEOF = true;
+            zzDoEOF();
+              { return new java_cup.runtime.Symbol(sym.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 = sym.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 MethodLexer <inputfile>");
+    }
+    else {
+      for (int i = 0; i < argv.length; i++) {
+        MethodLexer scanner = null;
+        try {
+          scanner = new MethodLexer( 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/method/MethodParser.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodParser.java
new file mode 100644
index 0000000..4ff27bb
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodParser.java
@@ -0,0 +1,185 @@
+/*
+*
+* 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.method;
+
+
+import java_cup.runtime.lr_parser;
+import org.apache.airavata.datacat.parsers.gridchem.GridChemQueueParser;
+
+import java.io.FileReader;
+import java.util.HashMap;
+
+
+public class MethodParser extends java_cup.runtime.lr_parser implements GridChemQueueParser{
+
+  /** Default constructor. */
+  public MethodParser() {super();}
+
+  /** Constructor which sets the default scanner. */
+  public MethodParser(java_cup.runtime.Scanner s) {super(s);}
+
+    /**
+     * Constructor which uses a file reader.
+     */
+    public MethodParser(final FileReader fileReader) {
+        super(new MethodLexer(fileReader));
+    }
+
+
+    /** Production table. */
+  protected static final short _production_table[][] = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\003\000\002\003\003\000\002\002\004\000\002\004" +
+                    "\004"});
+
+  /** 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\006\000\004\004\005\001\002\000\004\002\001\001" +
+                    "\002\000\004\006\010\001\002\000\004\002\007\001\002" +
+                    "\000\004\002\000\001\002\000\004\002\uffff\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\006\000\006\003\005\004\003\001\001\000\002\001" +
+                    "\001\000\002\001\001\000\002\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;
+
+  /** 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;}
+
+    @Override
+    public HashMap<String, String> getParsedData() throws Exception {
+        return null;
+    }
+}
+
+/** Cup generated class to encapsulate user supplied action code.*/
+class CUP$parser$actions {
+
+ 
+  //__________________________________
+  public static boolean DEBUG = true;
+ 
+
+  private final MethodParser MethodParser;
+
+  /** Constructor */
+  CUP$parser$actions(MethodParser MethodParser) {
+    this.MethodParser = MethodParser;
+  }
+
+  /** 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 2: // scfintro ::= FOUNDITER RUNTYP 
+            {
+              Object RESULT = null;
+		 if (DEBUG) System.out.println("CUP:gaussian:  found FOUNDITER "); 
+              CUP$parser$result = new java_cup.runtime.Symbol(2/*scfintro*/, ((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 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 
+            {
+              Object RESULT = null;
+		 if (DEBUG) System.out.println("CUP:gaussian:  end of parse tree "); 
+	
+ 	     
+              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;
+
+          /* . . . . . .*/
+          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/method/MethodSym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodSym.java
new file mode 100644
index 0000000..b84f358
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodSym.java
@@ -0,0 +1,37 @@
+/*
+*
+* 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.method;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Thu Sep 11 23:51:20 IST 2014
+//----------------------------------------------------
+
+/** CUP generated class containing symbol constants. */
+public class MethodSym {
+  /* terminals */
+  public static final int RUNTYP = 4;
+  public static final int SCFDONE = 3;
+  public static final int error = 1;
+  public static final int FOUNDITER = 2;
+  public static final int RUNTYP1 = 5;
+  public static final int EOF = 0;
+}
+


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