[Cdk-commits] SF.net SVN: cdk: [8984] trunk/cdk-qa/projects/070928-0001/AtomTypeQA.java

[<raj...@us...>]

Revision: 8984
          http://cdk.svn.sourceforge.net/cdk/?rev=8984&view=rev
Author:   rajarshi
Date:     2007-09-28 16:58:47 -0700 (Fri, 28 Sep 2007)

Log Message:
-----------
Added atom type qa code

Added Paths:
-----------
    trunk/cdk-qa/projects/070928-0001/AtomTypeQA.java

Added: trunk/cdk-qa/projects/070928-0001/AtomTypeQA.java
===================================================================
--- trunk/cdk-qa/projects/070928-0001/AtomTypeQA.java	                        (rev 0)
+++ trunk/cdk-qa/projects/070928-0001/AtomTypeQA.java	2007-09-28 23:58:47 UTC (rev 8984)
@@ -0,0 +1,82 @@
+
+
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.exception.InvalidSmilesException;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.smiles.InterruptableSmilesParser;
+
+import java.io.*;
+
+/**
+ * @author rguha
+ */
+public class AtomTypeQA {
+
+    public static void main(String[] args) throws IOException {
+        if (args.length != 1) {
+            System.out.println("Usage: AtomTypeQA SMILES_FILE");
+            System.exit(-1);
+        }
+
+        InterruptableSmilesParser sp = new InterruptableSmilesParser(DefaultChemObjectBuilder.getInstance());
+
+        String header = "cid\taAtNum\tAtSym\n";
+        BufferedWriter output = new BufferedWriter(new FileWriter("atype-report.txt"));
+        output.write(header);
+
+        BufferedWriter badsmiles = new BufferedWriter(new FileWriter("smiles-failure.txt"));
+
+        BufferedReader input = new BufferedReader(new FileReader(args[0]));
+        int nmol = 0;
+        int nbad = 0;
+        while (true) {
+            String line = input.readLine();
+            if (line == null) break;
+
+            // assuming that the only things we get are a smiles and a cid
+            String[] tokens = line.trim().split("\t");
+            String smiles = tokens[0];
+            String title = tokens[1];
+
+            IMolecule mol = null;
+            try {
+                mol = sp.parseSmiles(smiles, 5000);
+            } catch (InvalidSmilesException e) {
+                badsmiles.write(smiles+"\t"+title+"\n");
+                nbad++;
+                nmol++;
+                continue;
+            }
+
+            CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(mol.getBuilder());
+            int natom = mol.getAtomCount();
+            for (int i = 0; i < natom; i++) {
+                IAtom atom = mol.getAtom(i);
+                try {
+                    IAtomType type = matcher.findMatchingAtomType(mol, atom);
+                } catch (CDKException e) {
+                    String report = title + "\t" + i + "\t" + atom.getSymbol() + "\n";
+                    output.write(report);
+                }
+            }
+            nmol++;
+            if (nmol % 1000 == 0) {
+                System.out.print("\rProcessed " + nmol + " [Bad SMI = " + nbad + "]");
+                output.flush();
+                badsmiles.flush();
+                System.out.flush();
+            }
+        }
+
+        input.close();
+        output.close();
+        badsmiles.close();
+
+        System.out.println("\nDone");
+    }
+}


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