[r12013]: cdk-qa / trunk / projects / 080813-00001 / extractZINCmol2AtomTypes.bsh Maximize Restore History

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extractZINCmol2AtomTypes.bsh    33 lines (31 with data), 820 Bytes

#!/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();
}