The Chemistry Development Kit

--- a
+++ b/cdk-qa/trunk/projects/080813-00001/extractZINCmol2AtomTypes.bsh
@@ -0,0 +1,33 @@
+#!/usr/bin/bsh
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.BufferedReader;
+
+File file = new File("10_p0.1.mol2");
+BufferedReader reader = new BufferedReader(
+  new FileReader(file)
+);
+String line = reader.readLine();
+boolean inAtomBlock = false;
+int counter = 0;
+while (line != null && counter <= 1000) {
+  if (line.startsWith("ZINC")) {
+    print(line);
+  } else if (line.startsWith("@<TRIPOS>ATOM")) {
+    inAtomBlock = true;
+    line = reader.readLine();
+    counter++;
+  } else if (line.startsWith("@<TRIPOS>BOND")) {
+    inAtomBlock = false;
+  }
+  if (inAtomBlock) {
+    String atomtype = line.substring(47,53).trim();
+    if (atomtype.endsWith(".ar")) {
+      print(atomtype.substring(0,atomtype.indexOf(".ar"))+".2");
+    } else {
+      print(atomtype);
+    }
+  }
+  line = reader.readLine();
+}