Index: src/Graph/unittests/AdjacencyListUnitTest.cpp
===================================================================
--- src/Graph/unittests/AdjacencyListUnitTest.cpp	(revision 0fad93db3291c128f999fcbf427d65f1824b785b)
+++ src/Graph/unittests/AdjacencyListUnitTest.cpp	(revision 0fad93db3291c128f999fcbf427d65f1824b785b)
@@ -0,0 +1,281 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
+ * 
+ *
+ *   This file is part of MoleCuilder.
+ *
+ *    MoleCuilder is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 2 of the License, or
+ *    (at your option) any later version.
+ *
+ *    MoleCuilder is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with MoleCuilder.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+/*
+ * AdjacencyListUnitTest.cpp
+ *
+ *  Created on: Oct 17, 2011
+ *      Author: heber
+ */
+
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "AdjacencyListUnitTest.hpp"
+
+#include <cppunit/CompilerOutputter.h>
+#include <cppunit/extensions/TestFactoryRegistry.h>
+#include <cppunit/ui/text/TestRunner.h>
+
+#include <boost/lambda/lambda.hpp>
+#include <iostream>
+#include <iterator>
+#include <iostream>
+#include <vector>
+
+#include "CodePatterns/Assert.hpp"
+#include "CodePatterns/Log.hpp"
+
+#include "Atom/atom.hpp"
+#include "Descriptors/AtomDescriptor.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
+#include "Graph/AdjacencyList.hpp"
+#include "molecule.hpp"
+#include "World.hpp"
+#include "WorldTime.hpp"
+
+#ifdef HAVE_TESTRUNNER
+#include "UnitTestMain.hpp"
+#endif /*HAVE_TESTRUNNER*/
+
+/********************************************** Test classes **************************************/
+// Registers the fixture into the 'registry'
+CPPUNIT_TEST_SUITE_REGISTRATION( AdjacencyListTest );
+
+static std::string adjacencyfile ="\
+1 2\n\
+2 1 3\n\
+3 2 4\n\
+4 3 5\n\
+5 4 6\n\
+6 5 7\n\
+7 6 8\n\
+8 7 9\n\
+9 8 10\n\
+10 9\n";
+
+static std::string wrongadjacencyfile1 ="\
+1 2\n\
+2 1\n\
+4 5\n\
+5 4 6\n\
+6 5 7\n\
+7 6 8\n\
+8 7 9\n\
+9 8 10\n\
+10 9\n";
+
+static std::string wrongadjacencyfile2 ="\
+1 2\n\
+2 1 3\n\
+3 2 4\n\
+4 3 5\n\
+5 4 6\n\
+6 5 7\n\
+7 6 8\n\
+8 7 9\n\
+9 8 10\n\
+10 9 11\n\
+11 10";
+
+static std::string wrongadjacencyfile3 ="\
+1 2\n\
+2 1 3\n\
+3 2 4\n\
+4 3 5\n\
+5 4 7\n\
+6\n\
+7 5 8\n\
+8 7 9\n\
+9 8 10\n\
+10 9 11\n\
+11 10";
+
+// set up and tear down
+void AdjacencyListTest::setUp()
+{
+  // failing asserts should be thrown
+  ASSERT_DO(Assert::Throw);
+
+  const element *hydrogen = World::getInstance().getPeriode()->FindElement(1);
+  CPPUNIT_ASSERT(hydrogen != NULL);
+
+  TestMolecule = World::getInstance().createMolecule();
+  CPPUNIT_ASSERT(TestMolecule != NULL);
+  for(int i=0;i<ATOM_COUNT;++i){
+    atom *_atom = World::getInstance().createAtom();
+    CPPUNIT_ASSERT(_atom != NULL);
+    _atom->setType(hydrogen);
+    TestMolecule->AddAtom(_atom);
+    atoms.push_back(_atom);
+    atomIds.push_back(_atom->getId());
+  }
+  CPPUNIT_ASSERT_EQUAL( (size_t)ATOM_COUNT, atoms.size());
+  CPPUNIT_ASSERT_EQUAL( (size_t)ATOM_COUNT, atomIds.size());
+  // create linear chain
+  for(int i=0;i<ATOM_COUNT-1;++i)
+    atoms[i]->addBond(WorldTime::getTime(), atoms[i+1]);
+
+  // create map as it should be
+  for(int i=0;i<ATOM_COUNT;++i) {
+    if (i != 0) // first has only one bond
+      comparisonMap.insert( std::make_pair(atomIds[i], atomIds[i-1]) );
+    if (i != ATOM_COUNT-1) // last has only one bond
+      comparisonMap.insert( std::make_pair(atomIds[i], atomIds[i+1]) );
+  }
+}
+
+void AdjacencyListTest::tearDown()
+{
+  comparisonMap.clear();
+
+  // destroy molecule and contained atoms
+  TestMolecule->removeAtomsinMolecule();
+  World::getInstance().destroyMolecule(TestMolecule);
+  // destroy World
+  World::purgeInstance();
+//  logger::purgeInstance();
+//  errorLogger::purgeInstance();
+}
+
+/** Unit tests for AdjacencyList::CreateExternalMap().
+ *
+ */
+void AdjacencyListTest::CreateExternalMapTest()
+{
+  std::stringstream input;
+  AdjacencyList fileChecker(input);
+  fileChecker.CreateExternalMap(atomIds);
+
+  // check size (it's 8*2 + 2*1 = 18 keys)
+  CPPUNIT_ASSERT_EQUAL( (size_t)18, fileChecker.ExternalAtomBondMap.size() );
+  CPPUNIT_ASSERT_EQUAL( (size_t)0, fileChecker.InternalAtomBondMap.size() );
+
+  // check equality
+  CPPUNIT_ASSERT( comparisonMap.size() == fileChecker.ExternalAtomBondMap.size() );
+//  std::cout << "comparisonMap: " << comparisonMap << std::endl;
+//  std::cout << "fileChecker.InternalAtomBondMap: " << fileChecker.InternalAtomBondMap << std::endl;
+  CPPUNIT_ASSERT( comparisonMap == fileChecker.ExternalAtomBondMap );
+
+  // check non-equality: more
+  comparisonMap.insert( std::make_pair( (atomId_t)10, (atomId_t)8) );
+  CPPUNIT_ASSERT( comparisonMap != fileChecker.ExternalAtomBondMap );
+  comparisonMap.erase((atomId_t)10);
+
+  // check non-equality: less
+  comparisonMap.erase((atomId_t)9);
+  CPPUNIT_ASSERT( comparisonMap != fileChecker.ExternalAtomBondMap );
+}
+
+/** Unit tests for AdjacencyList::ParseInInternalMap().
+ *
+ */
+void AdjacencyListTest::ParseInInternalMapTest()
+{
+  std::stringstream input(adjacencyfile);
+  AdjacencyList fileChecker(input);
+  std::vector<atomId_t> noids;
+  fileChecker.CreateExternalMap(noids);
+
+  // check size (it's 8*2 + 2*1 = 18 keys)
+  CPPUNIT_ASSERT_EQUAL( (size_t)0, fileChecker.ExternalAtomBondMap.size() );
+  CPPUNIT_ASSERT_EQUAL( (size_t)18, fileChecker.InternalAtomBondMap.size() );
+
+  // check equality
+  CPPUNIT_ASSERT( comparisonMap.size() == fileChecker.InternalAtomBondMap.size() );
+  CPPUNIT_ASSERT( comparisonMap == fileChecker.InternalAtomBondMap );
+
+  // check non-equality: more
+  comparisonMap.insert( std::make_pair( (atomId_t)10, (atomId_t)8) );
+  CPPUNIT_ASSERT( comparisonMap != fileChecker.InternalAtomBondMap );
+  comparisonMap.erase((atomId_t)10);
+
+  // check non-equality: less
+  comparisonMap.erase((atomId_t)9);
+  CPPUNIT_ASSERT( comparisonMap != fileChecker.InternalAtomBondMap );
+}
+
+/** Unit tests for AdjacencyList::CompareInternalExternalMap().
+ *
+ */
+void AdjacencyListTest::CompareInternalExternalMapTest()
+{
+  std::stringstream input(adjacencyfile);
+  AdjacencyList fileChecker(input);
+
+  // assert equality before parsing (empty sets should always return true)
+  CPPUNIT_ASSERT( fileChecker.ExternalAtomBondMap.size() != fileChecker.InternalAtomBondMap.size() );
+  CPPUNIT_ASSERT( fileChecker.ExternalAtomBondMap != fileChecker.InternalAtomBondMap );
+  CPPUNIT_ASSERT( fileChecker.CompareInternalExternalMap() );
+
+  // parse in external map
+  fileChecker.CreateExternalMap(atomIds);
+
+  // assert equality after parsing
+  CPPUNIT_ASSERT_EQUAL( fileChecker.ExternalAtomBondMap.size(), fileChecker.InternalAtomBondMap.size() );
+  CPPUNIT_ASSERT_EQUAL( fileChecker.ExternalAtomBondMap, fileChecker.InternalAtomBondMap );
+  CPPUNIT_ASSERT( fileChecker.CompareInternalExternalMap() );
+}
+
+/** Unit tests for AdjacencyList::operator()().
+ *
+ */
+void AdjacencyListTest::CheckAgainstSubsetTest()
+{
+  {
+    // parse right
+    std::stringstream input(adjacencyfile);
+    AdjacencyList fileChecker(input);
+    CPPUNIT_ASSERT( fileChecker.CheckAgainstSubset(atomIds) );
+  }
+  {
+    // parse wrong1 (more atoms in the world than in file, hence wrong)
+    std::stringstream input(wrongadjacencyfile1);
+    AdjacencyList fileChecker(input);
+    CPPUNIT_ASSERT( !fileChecker.CheckAgainstSubset(atomIds) );
+  }
+  {
+    // remove third atom (index starts at 0) and test for equality then
+    std::vector<atomId_t> validids;
+    std::remove_copy_if(atomIds.begin(), atomIds.end(), std::back_inserter(validids), boost::lambda::_1 == (atomId_t)2);
+    CPPUNIT_ASSERT_EQUAL( (size_t)ATOM_COUNT-1, validids.size() );
+    // parse wrong1 (more atoms in the world than in file, hence wrong)
+    std::stringstream input(wrongadjacencyfile1);
+    AdjacencyList fileChecker(input);
+    CPPUNIT_ASSERT( fileChecker.CheckAgainstSubset(validids) );
+  }
+  {
+    // parse wrong2 (there is no atom 10, but present in file. hence true)
+    std::stringstream input(wrongadjacencyfile2);
+    AdjacencyList fileChecker(input);
+    CPPUNIT_ASSERT( !fileChecker.CheckAgainstSubset(atomIds) );
+  }
+  {
+    // parse wrong3 (6 is not connected)
+    std::stringstream input(wrongadjacencyfile3);
+    AdjacencyList fileChecker(input);
+    CPPUNIT_ASSERT( !fileChecker.CheckAgainstSubset(atomIds) );
+  }
+}
Index: src/Graph/unittests/AdjacencyListUnitTest.hpp
===================================================================
--- src/Graph/unittests/AdjacencyListUnitTest.hpp	(revision 0fad93db3291c128f999fcbf427d65f1824b785b)
+++ src/Graph/unittests/AdjacencyListUnitTest.hpp	(revision 0fad93db3291c128f999fcbf427d65f1824b785b)
@@ -0,0 +1,54 @@
+/*
+ * AdjacencyListUnitTest.hpp
+ *
+ *  Created on: Oct 17, 2011
+ *      Author: heber
+ */
+
+#ifndef UNITTEST_HPP_
+#define UNITTEST_HPP_
+
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include <cppunit/extensions/HelperMacros.h>
+
+#include "Graph/AdjacencyList.hpp"
+#include "types.hpp"
+
+// we prefer enum over define
+enum { ATOM_COUNT = 10 };
+
+class atom;
+class molecule;
+class World;
+
+class AdjacencyListTest : public CppUnit::TestFixture
+{
+  CPPUNIT_TEST_SUITE( AdjacencyListTest );
+  CPPUNIT_TEST ( CreateExternalMapTest );
+  CPPUNIT_TEST ( ParseInInternalMapTest );
+  CPPUNIT_TEST ( CompareInternalExternalMapTest );
+  CPPUNIT_TEST ( CheckAgainstSubsetTest );
+  CPPUNIT_TEST_SUITE_END();
+
+public:
+  void setUp();
+  void tearDown();
+
+  void CreateExternalMapTest();
+  void ParseInInternalMapTest();
+  void CompareInternalExternalMapTest();
+  void CheckAgainstSubsetTest();
+
+private:
+  AdjacencyList::AtomBondMap comparisonMap;
+  std::vector<atom *> atoms;
+  std::vector<atomId_t> atomIds;
+  molecule * TestMolecule;
+};
+
+#endif /* UNITTEST_HPP_ */
Index: src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp
===================================================================
--- src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp	(revision 06f41f3c956f559b0c681f2d22c237c2160d0f8d)
+++ 	(revision )
@@ -1,281 +1,0 @@
-/*
- * Project: MoleCuilder
- * Description: creates and alters molecular systems
- * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
- * 
- *
- *   This file is part of MoleCuilder.
- *
- *    MoleCuilder is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 2 of the License, or
- *    (at your option) any later version.
- *
- *    MoleCuilder is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with MoleCuilder.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-/*
- * CheckAgainstAdjacencyFileUnitTest.cpp
- *
- *  Created on: Oct 17, 2011
- *      Author: heber
- */
-
-// include config.h
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "CheckAgainstAdjacencyFileUnitTest.hpp"
-
-#include <cppunit/CompilerOutputter.h>
-#include <cppunit/extensions/TestFactoryRegistry.h>
-#include <cppunit/ui/text/TestRunner.h>
-
-#include <boost/lambda/lambda.hpp>
-#include <iostream>
-#include <iterator>
-#include <iostream>
-#include <vector>
-
-#include "CodePatterns/Assert.hpp"
-#include "CodePatterns/Log.hpp"
-
-#include "Atom/atom.hpp"
-#include "Descriptors/AtomDescriptor.hpp"
-#include "Element/element.hpp"
-#include "Element/periodentafel.hpp"
-#include "Graph/CheckAgainstAdjacencyFile.hpp"
-#include "molecule.hpp"
-#include "World.hpp"
-#include "WorldTime.hpp"
-
-#ifdef HAVE_TESTRUNNER
-#include "UnitTestMain.hpp"
-#endif /*HAVE_TESTRUNNER*/
-
-/********************************************** Test classes **************************************/
-// Registers the fixture into the 'registry'
-CPPUNIT_TEST_SUITE_REGISTRATION( CheckAgainstAdjacencyFileTest );
-
-static std::string adjacencyfile ="\
-1 2\n\
-2 1 3\n\
-3 2 4\n\
-4 3 5\n\
-5 4 6\n\
-6 5 7\n\
-7 6 8\n\
-8 7 9\n\
-9 8 10\n\
-10 9\n";
-
-static std::string wrongadjacencyfile1 ="\
-1 2\n\
-2 1\n\
-4 5\n\
-5 4 6\n\
-6 5 7\n\
-7 6 8\n\
-8 7 9\n\
-9 8 10\n\
-10 9\n";
-
-static std::string wrongadjacencyfile2 ="\
-1 2\n\
-2 1 3\n\
-3 2 4\n\
-4 3 5\n\
-5 4 6\n\
-6 5 7\n\
-7 6 8\n\
-8 7 9\n\
-9 8 10\n\
-10 9 11\n\
-11 10";
-
-static std::string wrongadjacencyfile3 ="\
-1 2\n\
-2 1 3\n\
-3 2 4\n\
-4 3 5\n\
-5 4 7\n\
-6\n\
-7 5 8\n\
-8 7 9\n\
-9 8 10\n\
-10 9 11\n\
-11 10";
-
-// set up and tear down
-void CheckAgainstAdjacencyFileTest::setUp()
-{
-  // failing asserts should be thrown
-  ASSERT_DO(Assert::Throw);
-
-  const element *hydrogen = World::getInstance().getPeriode()->FindElement(1);
-  CPPUNIT_ASSERT(hydrogen != NULL);
-
-  TestMolecule = World::getInstance().createMolecule();
-  CPPUNIT_ASSERT(TestMolecule != NULL);
-  for(int i=0;i<ATOM_COUNT;++i){
-    atom *_atom = World::getInstance().createAtom();
-    CPPUNIT_ASSERT(_atom != NULL);
-    _atom->setType(hydrogen);
-    TestMolecule->AddAtom(_atom);
-    atoms.push_back(_atom);
-    atomIds.push_back(_atom->getId());
-  }
-  CPPUNIT_ASSERT_EQUAL( (size_t)ATOM_COUNT, atoms.size());
-  CPPUNIT_ASSERT_EQUAL( (size_t)ATOM_COUNT, atomIds.size());
-  // create linear chain
-  for(int i=0;i<ATOM_COUNT-1;++i)
-    atoms[i]->addBond(WorldTime::getTime(), atoms[i+1]);
-
-  // create map as it should be
-  for(int i=0;i<ATOM_COUNT;++i) {
-    if (i != 0) // first has only one bond
-      comparisonMap.insert( std::make_pair(atomIds[i], atomIds[i-1]) );
-    if (i != ATOM_COUNT-1) // last has only one bond
-      comparisonMap.insert( std::make_pair(atomIds[i], atomIds[i+1]) );
-  }
-}
-
-void CheckAgainstAdjacencyFileTest::tearDown()
-{
-  comparisonMap.clear();
-
-  // destroy molecule and contained atoms
-  TestMolecule->removeAtomsinMolecule();
-  World::getInstance().destroyMolecule(TestMolecule);
-  // destroy World
-  World::purgeInstance();
-//  logger::purgeInstance();
-//  errorLogger::purgeInstance();
-}
-
-/** Unit tests for CheckAgainstAdjacencyFile::CreateExternalMap().
- *
- */
-void CheckAgainstAdjacencyFileTest::CreateExternalMapTest()
-{
-  std::stringstream input;
-  CheckAgainstAdjacencyFile fileChecker(input);
-  fileChecker.CreateExternalMap(atomIds);
-
-  // check size (it's 8*2 + 2*1 = 18 keys)
-  CPPUNIT_ASSERT_EQUAL( (size_t)18, fileChecker.ExternalAtomBondMap.size() );
-  CPPUNIT_ASSERT_EQUAL( (size_t)0, fileChecker.InternalAtomBondMap.size() );
-
-  // check equality
-  CPPUNIT_ASSERT( comparisonMap.size() == fileChecker.ExternalAtomBondMap.size() );
-//  std::cout << "comparisonMap: " << comparisonMap << std::endl;
-//  std::cout << "fileChecker.InternalAtomBondMap: " << fileChecker.InternalAtomBondMap << std::endl;
-  CPPUNIT_ASSERT( comparisonMap == fileChecker.ExternalAtomBondMap );
-
-  // check non-equality: more
-  comparisonMap.insert( std::make_pair( (atomId_t)10, (atomId_t)8) );
-  CPPUNIT_ASSERT( comparisonMap != fileChecker.ExternalAtomBondMap );
-  comparisonMap.erase((atomId_t)10);
-
-  // check non-equality: less
-  comparisonMap.erase((atomId_t)9);
-  CPPUNIT_ASSERT( comparisonMap != fileChecker.ExternalAtomBondMap );
-}
-
-/** Unit tests for CheckAgainstAdjacencyFile::ParseInInternalMap().
- *
- */
-void CheckAgainstAdjacencyFileTest::ParseInInternalMapTest()
-{
-  std::stringstream input(adjacencyfile);
-  CheckAgainstAdjacencyFile fileChecker(input);
-  std::vector<atomId_t> noids;
-  fileChecker.CreateExternalMap(noids);
-
-  // check size (it's 8*2 + 2*1 = 18 keys)
-  CPPUNIT_ASSERT_EQUAL( (size_t)0, fileChecker.ExternalAtomBondMap.size() );
-  CPPUNIT_ASSERT_EQUAL( (size_t)18, fileChecker.InternalAtomBondMap.size() );
-
-  // check equality
-  CPPUNIT_ASSERT( comparisonMap.size() == fileChecker.InternalAtomBondMap.size() );
-  CPPUNIT_ASSERT( comparisonMap == fileChecker.InternalAtomBondMap );
-
-  // check non-equality: more
-  comparisonMap.insert( std::make_pair( (atomId_t)10, (atomId_t)8) );
-  CPPUNIT_ASSERT( comparisonMap != fileChecker.InternalAtomBondMap );
-  comparisonMap.erase((atomId_t)10);
-
-  // check non-equality: less
-  comparisonMap.erase((atomId_t)9);
-  CPPUNIT_ASSERT( comparisonMap != fileChecker.InternalAtomBondMap );
-}
-
-/** Unit tests for CheckAgainstAdjacencyFile::CompareInternalExternalMap().
- *
- */
-void CheckAgainstAdjacencyFileTest::CompareInternalExternalMapTest()
-{
-  std::stringstream input(adjacencyfile);
-  CheckAgainstAdjacencyFile fileChecker(input);
-
-  // assert equality before parsing (empty sets should always return true)
-  CPPUNIT_ASSERT( fileChecker.ExternalAtomBondMap.size() != fileChecker.InternalAtomBondMap.size() );
-  CPPUNIT_ASSERT( fileChecker.ExternalAtomBondMap != fileChecker.InternalAtomBondMap );
-  CPPUNIT_ASSERT( fileChecker.CompareInternalExternalMap() );
-
-  // parse in external map
-  fileChecker.CreateExternalMap(atomIds);
-
-  // assert equality after parsing
-  CPPUNIT_ASSERT_EQUAL( fileChecker.ExternalAtomBondMap.size(), fileChecker.InternalAtomBondMap.size() );
-  CPPUNIT_ASSERT_EQUAL( fileChecker.ExternalAtomBondMap, fileChecker.InternalAtomBondMap );
-  CPPUNIT_ASSERT( fileChecker.CompareInternalExternalMap() );
-}
-
-/** Unit tests for CheckAgainstAdjacencyFile::operator()().
- *
- */
-void CheckAgainstAdjacencyFileTest::operatorTest()
-{
-  {
-    // parse right
-    std::stringstream input(adjacencyfile);
-    CheckAgainstAdjacencyFile fileChecker(input);
-    CPPUNIT_ASSERT( fileChecker(atomIds) );
-  }
-  {
-    // parse wrong1 (more atoms in the world than in file, hence wrong)
-    std::stringstream input(wrongadjacencyfile1);
-    CheckAgainstAdjacencyFile fileChecker(input);
-    CPPUNIT_ASSERT( !fileChecker(atomIds) );
-  }
-  {
-    // remove third atom (index starts at 0) and test for equality then
-    std::vector<atomId_t> validids;
-    std::remove_copy_if(atomIds.begin(), atomIds.end(), std::back_inserter(validids), boost::lambda::_1 == (atomId_t)2);
-    CPPUNIT_ASSERT_EQUAL( (size_t)ATOM_COUNT-1, validids.size() );
-    // parse wrong1 (more atoms in the world than in file, hence wrong)
-    std::stringstream input(wrongadjacencyfile1);
-    CheckAgainstAdjacencyFile fileChecker(input);
-    CPPUNIT_ASSERT( fileChecker(validids) );
-  }
-  {
-    // parse wrong2 (there is no atom 10, but present in file. hence true)
-    std::stringstream input(wrongadjacencyfile2);
-    CheckAgainstAdjacencyFile fileChecker(input);
-    CPPUNIT_ASSERT( !fileChecker(atomIds) );
-  }
-  {
-    // parse wrong3 (6 is not connected)
-    std::stringstream input(wrongadjacencyfile3);
-    CheckAgainstAdjacencyFile fileChecker(input);
-    CPPUNIT_ASSERT( !fileChecker(atomIds) );
-  }
-}
Index: src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp
===================================================================
--- src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp	(revision 06f41f3c956f559b0c681f2d22c237c2160d0f8d)
+++ 	(revision )
@@ -1,54 +1,0 @@
-/*
- * CheckAgainstAdjacencyFileUnitTest.hpp
- *
- *  Created on: Oct 17, 2011
- *      Author: heber
- */
-
-#ifndef CHECKADJACENCYAGAINSTFILEUNITTEST_HPP_
-#define CHECKADJACENCYAGAINSTFILEUNITTEST_HPP_
-
-// include config.h
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include <cppunit/extensions/HelperMacros.h>
-
-#include "Graph/CheckAgainstAdjacencyFile.hpp"
-#include "types.hpp"
-
-// we prefer enum over define
-enum { ATOM_COUNT = 10 };
-
-class atom;
-class molecule;
-class World;
-
-class CheckAgainstAdjacencyFileTest : public CppUnit::TestFixture
-{
-  CPPUNIT_TEST_SUITE( CheckAgainstAdjacencyFileTest );
-  CPPUNIT_TEST ( CreateExternalMapTest );
-  CPPUNIT_TEST ( ParseInInternalMapTest );
-  CPPUNIT_TEST ( CompareInternalExternalMapTest );
-  CPPUNIT_TEST ( operatorTest );
-  CPPUNIT_TEST_SUITE_END();
-
-public:
-  void setUp();
-  void tearDown();
-
-  void CreateExternalMapTest();
-  void ParseInInternalMapTest();
-  void CompareInternalExternalMapTest();
-  void operatorTest();
-
-private:
-  CheckAgainstAdjacencyFile::AtomBondMap comparisonMap;
-  std::vector<atom *> atoms;
-  std::vector<atomId_t> atomIds;
-  molecule * TestMolecule;
-};
-
-#endif /* CHECKADJACENCYAGAINSTFILEUNITTEST_HPP_ */
Index: src/Graph/unittests/Makefile.am
===================================================================
--- src/Graph/unittests/Makefile.am	(revision 06f41f3c956f559b0c681f2d22c237c2160d0f8d)
+++ src/Graph/unittests/Makefile.am	(revision 0fad93db3291c128f999fcbf427d65f1824b785b)
@@ -3,14 +3,14 @@
 
 GRAPHTESTSSOURCES = \
-	../Graph/unittests/BondGraphUnitTest.cpp \
-	../Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp
+	../Graph/unittests/AdjacencyListUnitTest.cpp \
+	../Graph/unittests/BondGraphUnitTest.cpp
 
 GRAPHTESTSHEADERS = \
-	../Graph/unittests/BondGraphUnitTest.hpp \
-	../Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp
+	../Graph/unittests/AdjacencyListUnitTest.hpp \
+	../Graph/unittests/BondGraphUnitTest.hpp
 
 GRAPHTESTS = \
-	BondGraphUnitTest \
-	CheckAgainstAdjacencyFileUnitTest
+	AdjacencyListUnitTest \
+	BondGraphUnitTest
 
 
@@ -32,4 +32,9 @@
 
 
+AdjacencyListUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
+	../Graph/unittests/AdjacencyListUnitTest.cpp \
+	../Graph/unittests/AdjacencyListUnitTest.hpp
+AdjacencyListUnitTest_LDADD = ${ALLLIBS}
+
 BondGraphUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
 	../Graph/unittests/BondGraphUnitTest.cpp \
@@ -37,9 +42,4 @@
 BondGraphUnitTest_LDADD = ${GRAPHLIBS}
 
-CheckAgainstAdjacencyFileUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
-	../Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp \
-	../Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp
-CheckAgainstAdjacencyFileUnitTest_LDADD = ${ALLLIBS}
-
 
 
