ReadMolfile.groovy

import org.openscience.cdk.ChemFile
import org.openscience.cdk.interfaces.IAtomContainer
import org.openscience.cdk.io.ISimpleChemObjectReader
import org.openscience.cdk.io.MDLV2000Reader
import org.openscience.cdk.io.MDLV3000Reader
import org.openscience.cdk.tools.manipulator.ChemFileManipulator

String v2000 = '''
  Mrv0541 02231512112D

  3  2  0  0  0  0            999 V2000
   -4.1987    0.0884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4842    0.5009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9008   -0.0825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
M  END
'''

String v3000 = '''
  Mrv0541 01191615492D

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 3 2 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C 2.31 -1.3337 0 0
M  V30 2 C 3.6437 -2.1037 0 0
M  V30 3 O 4.9774 -1.3337 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 2 3
M  V30 END BOND
M  V30 END CTAB
M  END
'''


// V2000
ISimpleChemObjectReader vreader = new MDLV2000Reader(new ByteArrayInputStream(v2000.getBytes()))
ChemFile chemFile = vreader.read(new ChemFile())
List<IAtomContainer> containersList = ChemFileManipulator.getAllAtomContainers(chemFile)
assert containersList != null
assert containersList.size() == 1
println "V2000 OK"

// V3000
reader = new MDLV3000Reader(new ByteArrayInputStream(v3000.getBytes()))
chemFile = reader.read(new ChemFile())
containersList = ChemFileManipulator.getAllAtomContainers(chemFile) // throws NPE. Why?
assert containersList != null
assert containersList.size() == 1
println "V3000 OK"