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Removed some more usages of Molecule

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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commit b84587f84550985fe02da53f97c1d439b18d2f9f 1 parent 04b1542
Rajarshi Guha authored egonw committed
3  src/test/org/openscience/cdk/ChangeEventPropagationTest.java
@@ -23,6 +23,7 @@
23 23
 import org.junit.Assert;
24 24
 import org.junit.BeforeClass;
25 25
 import org.junit.Test;
  26
+import org.openscience.cdk.interfaces.IAtomContainer;
26 27
 import org.openscience.cdk.interfaces.IAtomContainerSet;
27 28
 import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
28 29
 import org.openscience.cdk.interfaces.IChemObjectListener;
@@ -45,7 +46,7 @@
45 46
 	ChemSequence cs = new ChemSequence();
46 47
 	ChemModel cm = new ChemModel();
47 48
 	IAtomContainerSet som = new AtomContainerSet();
48  
-        Molecule mol = new Molecule();
  49
+        IAtomContainer mol = new AtomContainer();
49 50
 	Atom a1 = new Atom("C");
50 51
 	Atom a2 = new Atom("C");
51 52
 	Bond b1 = new Bond(a1, a2);
281  src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -23,13 +23,10 @@
23 23
  */
24 24
 package org.openscience.cdk.atomtype;
25 25
 
26  
-import java.util.HashMap;
27  
-import java.util.Iterator;
28  
-import java.util.Map;
29  
-
30 26
 import org.junit.Assert;
31 27
 import org.junit.Test;
32 28
 import org.openscience.cdk.Atom;
  29
+import org.openscience.cdk.AtomContainer;
33 30
 import org.openscience.cdk.Bond;
34 31
 import org.openscience.cdk.CDKConstants;
35 32
 import org.openscience.cdk.DefaultChemObjectBuilder;
@@ -52,6 +49,10 @@
52 49
 import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
53 50
 import org.openscience.cdk.tools.periodictable.PeriodicTable;
54 51
 
  52
+import java.util.HashMap;
  53
+import java.util.Iterator;
  54
+import java.util.Map;
  55
+
55 56
 /**
56 57
  * This class tests the matching of atom types defined in the
57 58
  * CDK atom type list. All tests in this class <b>must</b> use
@@ -79,7 +80,7 @@
79 80
     }
80 81
 
81 82
     @Test public void testFindMatchingAtomType_IAtomContainer_IAtom() throws Exception {
82  
-        IMolecule mol = new Molecule();
  83
+        IAtomContainer mol = new AtomContainer();
83 84
         IAtom atom = new Atom("C");
84 85
         final IAtomType.Hybridization thisHybridization = IAtomType.Hybridization.SP3;
85 86
         atom.setHybridization(thisHybridization);
@@ -90,7 +91,7 @@
90 91
     }
91 92
 
92 93
     @Test public void testFindMatchingAtomType_IAtomContainer() throws Exception {
93  
-        IMolecule mol = new Molecule();
  94
+        IAtomContainer mol = new AtomContainer();
94 95
         IAtom atom = new Atom("C");
95 96
         final IAtomType.Hybridization thisHybridization = IAtomType.Hybridization.SP3;
96 97
         atom.setHybridization(thisHybridization);
@@ -107,7 +108,7 @@
107 108
     }
108 109
 
109 110
     @Test public void testDummy() throws Exception {
110  
-        IMolecule mol = new Molecule();
  111
+        IAtomContainer mol = new AtomContainer();
111 112
         IAtom atom = new PseudoAtom("R");
112 113
         mol.addAtom(atom);
113 114
 
@@ -119,7 +120,7 @@
119 120
      * @cdk.bug 2445178
120 121
      */
121 122
     @Test public void testNonExistingType() throws Exception {
122  
-        IMolecule mol = new Molecule();
  123
+        IAtomContainer mol = new AtomContainer();
123 124
         IAtom atom = new Atom("Error");
124 125
         mol.addAtom(atom);
125 126
         CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(
@@ -128,7 +129,7 @@
128 129
     }
129 130
 
130 131
     @Test public void testEthene() throws Exception {
131  
-    	IMolecule mol = new Molecule();
  132
+    	IAtomContainer mol = new AtomContainer();
132 133
         IAtom atom = new Atom("C");
133 134
         IAtom atom2 = new Atom("C");
134 135
         mol.addAtom(atom);
@@ -140,7 +141,7 @@
140 141
     }
141 142
     
142 143
     @Test public void testEthyneKation() throws Exception {
143  
-    	IMolecule mol = new Molecule();
  144
+    	IAtomContainer mol = new AtomContainer();
144 145
         IAtom atom = new Atom("C");
145 146
         IAtom atom2 = new Atom("C"); atom2.setFormalCharge(+1);
146 147
         mol.addAtom(atom);
@@ -152,7 +153,7 @@
152 153
     }
153 154
     
154 155
     @Test public void testEthyneRadical() throws Exception {
155  
-    	IMolecule mol = new Molecule();
  156
+    	IAtomContainer mol = new AtomContainer();
156 157
         IAtom atom = new Atom("C");
157 158
         IAtom atom2 = new Atom("C");
158 159
         mol.addAtom(atom);
@@ -165,7 +166,7 @@
165 166
     }
166 167
     
167 168
     @Test public void testImine() throws Exception {
168  
-    	IMolecule mol = new Molecule();
  169
+    	IAtomContainer mol = new AtomContainer();
169 170
         IAtom atom = new Atom("C");
170 171
         IAtom atom2 = new Atom("N");
171 172
         mol.addAtom(atom);
@@ -177,7 +178,7 @@
177 178
     }
178 179
     
179 180
     @Test public void testImineRadical() throws Exception {
180  
-    	IMolecule mol = new Molecule();
  181
+    	IAtomContainer mol = new AtomContainer();
181 182
         IAtom atom = new Atom("C");
182 183
         IAtom atom2 = new Atom("N");
183 184
         mol.addAtom(atom);
@@ -190,7 +191,7 @@
190 191
     }
191 192
     
192 193
     @Test public void testEtheneRadical() throws Exception {
193  
-    	IMolecule mol = new Molecule();
  194
+    	IAtomContainer mol = new AtomContainer();
194 195
         IAtom atom = new Atom("C");
195 196
         IAtom atom2 = new Atom("C");
196 197
         mol.addAtom(atom);
@@ -203,7 +204,7 @@
203 204
     }
204 205
     
205 206
     @Test public void testGuanineMethyl() throws Exception {
206  
-    	IMolecule mol = new Molecule();
  207
+    	IAtomContainer mol = new AtomContainer();
207 208
         IAtom atom1 = new Atom("C");
208 209
         IAtom atom2 = new Atom("N");
209 210
         IAtom atom3 = new Atom("C");
@@ -249,7 +250,7 @@
249 250
     }
250 251
     
251 252
     @Test public void testPropyne() throws Exception {
252  
-    	IMolecule mol = new Molecule();
  253
+    	IAtomContainer mol = new AtomContainer();
253 254
         IAtom atom = new Atom("C");
254 255
         IAtom atom2 = new Atom("C");
255 256
         IAtom atom3 = new Atom("C");
@@ -264,7 +265,7 @@
264 265
     }
265 266
     
266 267
     @Test public void testFormaldehyde() throws Exception {
267  
-    	IMolecule mol = new Molecule();
  268
+    	IAtomContainer mol = new AtomContainer();
268 269
         IAtom atom = new Atom("O");
269 270
         IAtom atom2 = new Atom("C");
270 271
         mol.addAtom(atom);
@@ -276,7 +277,7 @@
276 277
     }
277 278
 
278 279
     @Test public void testCarboxylate() throws Exception {
279  
-        IMolecule mol = new Molecule();
  280
+        IAtomContainer mol = new AtomContainer();
280 281
         IAtom atom = new Atom("O");
281 282
         IAtom atom1 = new Atom("C");
282 283
         IAtom atom2 = new Atom("O"); atom2.setFormalCharge(-1);
@@ -294,7 +295,7 @@
294 295
     }
295 296
 
296 297
     @Test public void testFormaldehydeRadicalKation() throws Exception {
297  
-    	IMolecule mol = new Molecule();
  298
+    	IAtomContainer mol = new AtomContainer();
298 299
         IAtom atom = new Atom("O"); atom.setFormalCharge(+1);
299 300
         IAtom atom2 = new Atom("C");
300 301
         mol.addAtom(atom);
@@ -332,7 +333,7 @@
332 333
     }
333 334
     
334 335
     @Test public void testMethanol() throws Exception {
335  
-    	IMolecule mol = new Molecule();
  336
+    	IAtomContainer mol = new AtomContainer();
336 337
         IAtom atom = new Atom("O");
337 338
         IAtom atom2 = new Atom("C");
338 339
         mol.addAtom(atom);
@@ -344,7 +345,7 @@
344 345
     }
345 346
     
346 347
     @Test public void testLithiumMethanoxide() throws Exception {
347  
-    	IMolecule mol = new Molecule();
  348
+    	IAtomContainer mol = new AtomContainer();
348 349
         IAtom atom = new Atom("O");
349 350
         IAtom atom2 = new Atom("C");
350 351
         IAtom atom3 = new Atom("Li");
@@ -359,7 +360,7 @@
359 360
     }
360 361
     
361 362
     @Test public void testHCN() throws Exception {
362  
-    	IMolecule mol = new Molecule();
  363
+    	IAtomContainer mol = new AtomContainer();
363 364
         IAtom atom = new Atom("N");
364 365
         IAtom atom2 = new Atom("C");
365 366
         mol.addAtom(atom);
@@ -371,7 +372,7 @@
371 372
     }
372 373
     
373 374
     @Test public void testHNO2() throws Exception {
374  
-    	IMolecule mol = new Molecule();
  375
+    	IAtomContainer mol = new AtomContainer();
375 376
         IAtom atom = new Atom("N");
376 377
         IAtom atom2 = new Atom("O");
377 378
         IAtom atom3 = new Atom("O");
@@ -389,7 +390,7 @@
389 390
     }
390 391
     
391 392
     @Test public void testNitromethane() throws Exception {
392  
-    	IMolecule mol = new Molecule();
  393
+    	IAtomContainer mol = new AtomContainer();
393 394
         IAtom atom = new Atom("N");
394 395
         IAtom atom2 = new Atom("O");
395 396
         IAtom atom3 = new Atom("O");
@@ -407,7 +408,7 @@
407 408
     }
408 409
     
409 410
     @Test public void testMethylAmine() throws Exception {
410  
-    	IMolecule mol = new Molecule();
  411
+    	IAtomContainer mol = new AtomContainer();
411 412
         IAtom atom = new Atom("N");
412 413
         IAtom atom2 = new Atom("C");
413 414
         mol.addAtom(atom);
@@ -419,7 +420,7 @@
419 420
     }
420 421
     
421 422
     @Test public void testMethylAmineRadical() throws Exception {
422  
-    	IMolecule mol = new Molecule();
  423
+    	IAtomContainer mol = new AtomContainer();
423 424
         IAtom atom = new Atom("N");
424 425
         IAtom atom2 = new Atom("C");
425 426
         mol.addAtom(atom);
@@ -433,7 +434,7 @@
433 434
     }
434 435
     
435 436
     @Test public void testMethyleneImine() throws Exception {
436  
-    	IMolecule mol = new Molecule();
  437
+    	IAtomContainer mol = new AtomContainer();
437 438
         IAtom atom = new Atom("N");
438 439
         IAtom atom2 = new Atom("C");
439 440
         mol.addAtom(atom);
@@ -445,7 +446,7 @@
445 446
     }
446 447
     
447 448
     @Test public void testEthene_withHybridInfo() throws Exception {
448  
-    	IMolecule mol = new Molecule();
  449
+    	IAtomContainer mol = new AtomContainer();
449 450
         IAtom atom = new Atom("C");
450 451
         IAtom atom2 = new Atom("C");
451 452
         final IAtomType.Hybridization thisHybridization = IAtomType.Hybridization.SP2;
@@ -562,7 +563,7 @@ public void testTetrahydropyran() throws Exception {
562 563
     }
563 564
 
564 565
     @Test public void testDMSOCharged() throws Exception {
565  
-    	IMolecule mol = new Molecule();
  566
+    	IAtomContainer mol = new AtomContainer();
566 567
         IAtom atom = new Atom("O"); atom.setFormalCharge(-1);
567 568
         IAtom atom2 = new Atom("S"); atom2.setFormalCharge(1);
568 569
         IAtom atom3 = new Atom("C");
@@ -580,7 +581,7 @@ public void testTetrahydropyran() throws Exception {
580 581
     }
581 582
     
582 583
     @Test public void testDMSO() throws Exception {
583  
-        IMolecule mol = new Molecule();
  584
+        IAtomContainer mol = new AtomContainer();
584 585
         IAtom atom = new Atom("O");
585 586
         IAtom atom2 = new Atom("S");
586 587
         IAtom atom3 = new Atom("C");
@@ -598,7 +599,7 @@ public void testTetrahydropyran() throws Exception {
598 599
     }
599 600
     
600 601
     @Test public void testDMSOO() throws Exception {
601  
-        IMolecule mol = new Molecule();
  602
+        IAtomContainer mol = new AtomContainer();
602 603
         IAtom atom = new Atom("O");
603 604
         IAtom atom1 = new Atom("O");
604 605
         IAtom atom2 = new Atom("S");
@@ -619,7 +620,7 @@ public void testTetrahydropyran() throws Exception {
619 620
     }
620 621
     
621 622
     @Test public void testStrioxide() throws Exception {
622  
-        IMolecule mol = new Molecule();
  623
+        IAtomContainer mol = new AtomContainer();
623 624
         IAtom atom = new Atom("O");
624 625
         IAtom atom1 = new Atom("O");
625 626
         IAtom atom2 = new Atom("S");
@@ -637,7 +638,7 @@ public void testTetrahydropyran() throws Exception {
637 638
     }
638 639
 
639 640
     @Test public void testAmide() throws Exception {
640  
-    	IMolecule mol = new Molecule();
  641
+    	IAtomContainer mol = new AtomContainer();
641 642
         IAtom atom = new Atom("O");
642 643
         IAtom atom2 = new Atom("C");
643 644
         IAtom atom3 = new Atom("N");
@@ -653,7 +654,7 @@ public void testTetrahydropyran() throws Exception {
653 654
     
654 655
 
655 656
     @Test public void testAmineOxide() throws Exception {
656  
-        IMolecule mol = new Molecule();
  657
+        IAtomContainer mol = new AtomContainer();
657 658
         IAtom atom = new Atom("O");
658 659
         IAtom atom2 = new Atom("N");
659 660
         IAtom atom3 = new Atom("C");
@@ -674,7 +675,7 @@ public void testTetrahydropyran() throws Exception {
674 675
     }
675 676
 
676 677
     @Test public void testThioAmide() throws Exception {
677  
-        IMolecule mol = new Molecule();
  678
+        IAtomContainer mol = new AtomContainer();
678 679
         IAtom atom = new Atom("S");
679 680
         IAtom atom2 = new Atom("C");
680 681
         IAtom atom3 = new Atom("N");
@@ -715,7 +716,7 @@ public void testTetrahydropyran() throws Exception {
715 716
     }
716 717
     
717 718
     @Test public void testAmide3() throws Exception {
718  
-        IMolecule mol = new Molecule();
  719
+        IAtomContainer mol = new AtomContainer();
719 720
         IAtom atom = new Atom("O");
720 721
         IAtom atom1 = new Atom("C");
721 722
         IAtom atom2 = new Atom("N");
@@ -736,7 +737,7 @@ public void testTetrahydropyran() throws Exception {
736 737
     }
737 738
     
738 739
     @Test public void testLactam() throws Exception {
739  
-        IMolecule mol = new Molecule();
  740
+        IAtomContainer mol = new AtomContainer();
740 741
         IAtom atom = new Atom("O");
741 742
         IAtom atom1 = new Atom("C");
742 743
         IAtom atom2 = new Atom("N");
@@ -761,7 +762,7 @@ public void testTetrahydropyran() throws Exception {
761 762
     }
762 763
     
763 764
     @Test public void testThioAcetone() throws Exception {
764  
-    	IMolecule mol = new Molecule();
  765
+    	IAtomContainer mol = new AtomContainer();
765 766
         IAtom atom = new Atom("S");
766 767
         IAtom atom2 = new Atom("C");
767 768
         IAtom atom3 = new Atom("C");
@@ -779,7 +780,7 @@ public void testTetrahydropyran() throws Exception {
779 780
     }
780 781
 
781 782
     @Test public void testSulphuricAcid() throws Exception {
782  
-    	IMolecule mol = new Molecule();
  783
+    	IAtomContainer mol = new AtomContainer();
783 784
         IAtom atom = new Atom("O");
784 785
         IAtom atom2 = new Atom("S");
785 786
         IAtom atom3 = new Atom("O");
@@ -829,7 +830,7 @@ public void testTetrahydropyran() throws Exception {
829 830
     }
830 831
 
831 832
     @Test public void testSulphuricAcid_Charged() throws Exception {
832  
-    	IMolecule mol = new Molecule();
  833
+    	IAtomContainer mol = new AtomContainer();
833 834
         IAtom atom = new Atom("O");
834 835
         IAtom atom2 = new Atom("S");
835 836
         IAtom atom3 = new Atom("O");
@@ -850,7 +851,7 @@ public void testTetrahydropyran() throws Exception {
850 851
     }
851 852
 
852 853
     @Test public void testSF6() throws Exception {
853  
-    	IMolecule mol = new Molecule();
  854
+    	IAtomContainer mol = new AtomContainer();
854 855
         IAtom atom = new Atom("F");
855 856
         IAtom atom2 = new Atom("S");
856 857
         IAtom atom3 = new Atom("F");
@@ -877,7 +878,7 @@ public void testTetrahydropyran() throws Exception {
877 878
     }
878 879
 
879 880
     @Test public void testMnF4() throws Exception {
880  
-    	IMolecule mol = new Molecule();
  881
+    	IAtomContainer mol = new AtomContainer();
881 882
         IAtom atom = new Atom("F");
882 883
         IAtom atom2 = new Atom("Mn");
883 884
         IAtom atom3 = new Atom("F");
@@ -894,7 +895,7 @@ public void testTetrahydropyran() throws Exception {
894 895
     }
895 896
 
896 897
     @Test public void testCrF6() throws Exception {
897  
-    	IMolecule mol = new Molecule();
  898
+    	IAtomContainer mol = new AtomContainer();
898 899
         IAtom atom = new Atom("F");
899 900
         IAtom atom2 = new Atom("Cr");
900 901
         IAtom atom3 = new Atom("F");
@@ -921,7 +922,7 @@ public void testTetrahydropyran() throws Exception {
921 922
     }
922 923
 
923 924
     @Test public void testXeF4() throws Exception {
924  
-        IMolecule mol = new Molecule();
  925
+        IAtomContainer mol = new AtomContainer();
925 926
           IAtom atom = new Atom("F");
926 927
           IAtom atom2 = new Atom("Xe");
927 928
           IAtom atom3 = new Atom("F");
@@ -942,7 +943,7 @@ public void testTetrahydropyran() throws Exception {
942 943
       }
943 944
 
944 945
     @Test public void testPhosphate() throws Exception {
945  
-    	IMolecule mol = new Molecule();
  946
+    	IAtomContainer mol = new AtomContainer();
946 947
         IAtom atom = new Atom("O");
947 948
         IAtom atom2 = new Atom("P");
948 949
         IAtom atom3 = new Atom("O");
@@ -966,7 +967,7 @@ public void testTetrahydropyran() throws Exception {
966 967
      * @cdk.inchi InChI=1/C3H10OP/c1-5(2,3)4/h4H,1-3H3/q+1
967 968
      */
968 969
     @Test public void testHydroxyTriMethylPhophanium() throws Exception {
969  
-        IMolecule mol = new Molecule();
  970
+        IAtomContainer mol = new AtomContainer();
970 971
         IAtom atom = new Atom("C");
971 972
         IAtom atom2 = new Atom("P");
972 973
         atom2.setFormalCharge(+1);
@@ -988,7 +989,7 @@ public void testTetrahydropyran() throws Exception {
988 989
     }
989 990
 
990 991
     @Test public void testPhosphateCharged() throws Exception {
991  
-        IMolecule mol = new Molecule();
  992
+        IAtomContainer mol = new AtomContainer();
992 993
         IAtom atom = new Atom("O"); atom.setFormalCharge(-1);
993 994
         IAtom atom2 = new Atom("P"); atom2.setFormalCharge(1);
994 995
         IAtom atom3 = new Atom("O");
@@ -1009,7 +1010,7 @@ public void testTetrahydropyran() throws Exception {
1009 1010
     }
1010 1011
 
1011 1012
     @Test public void testPhosphorusTriradical() throws Exception {
1012  
-    	IMolecule mol = new Molecule();
  1013
+    	IAtomContainer mol = new AtomContainer();
1013 1014
         IAtom atom = new Atom("P");
1014 1015
         mol.addAtom(atom);
1015 1016
         mol.addSingleElectron(0);
@@ -1021,7 +1022,7 @@ public void testTetrahydropyran() throws Exception {
1021 1022
     }
1022 1023
 
1023 1024
     @Test public void testAmmonia() throws Exception {
1024  
-    	IMolecule mol = new Molecule();
  1025
+    	IAtomContainer mol = new AtomContainer();
1025 1026
         IAtom atom = new Atom("H");
1026 1027
         IAtom atom2 = new Atom("N");
1027 1028
         IAtom atom3 = new Atom("H");
@@ -1043,7 +1044,7 @@ public void testTetrahydropyran() throws Exception {
1043 1044
     }
1044 1045
 
1045 1046
     @Test public void testNitrogenRadical() throws Exception {
1046  
-    	IMolecule mol = new Molecule();
  1047
+    	IAtomContainer mol = new AtomContainer();
1047 1048
         IAtom atom = new Atom("H");
1048 1049
         IAtom atom2 = new Atom("N");
1049 1050
         IAtom atom3 = new Atom("H");
@@ -1058,7 +1059,7 @@ public void testTetrahydropyran() throws Exception {
1058 1059
     }
1059 1060
 
1060 1061
     @Test public void testTMS() throws Exception {
1061  
-    	IMolecule mol = new Molecule();
  1062
+    	IAtomContainer mol = new AtomContainer();
1062 1063
         IAtom atom = new Atom("C");
1063 1064
         IAtom atom2 = new Atom("Si");
1064 1065
         IAtom atom3 = new Atom("C");
@@ -1079,7 +1080,7 @@ public void testTetrahydropyran() throws Exception {
1079 1080
     }
1080 1081
 
1081 1082
     @Test public void testTinCompound() throws Exception {
1082  
-    	IMolecule mol = new Molecule();
  1083
+    	IAtomContainer mol = new AtomContainer();
1083 1084
         IAtom atom = new Atom("C");
1084 1085
         IAtom atom2 = new Atom("Sn");
1085 1086
         IAtom atom3 = new Atom("C");
@@ -1100,7 +1101,7 @@ public void testTetrahydropyran() throws Exception {
1100 1101
     }
1101 1102
 
1102 1103
     @Test public void testArsenicPlus() throws Exception {
1103  
-    	IMolecule mol = new Molecule();
  1104
+    	IAtomContainer mol = new AtomContainer();
1104 1105
         IAtom atom = new Atom("C");
1105 1106
         IAtom atom2 = new Atom("As"); atom2.setFormalCharge(+1);
1106 1107
         IAtom atom3 = new Atom("C");
@@ -1121,7 +1122,7 @@ public void testTetrahydropyran() throws Exception {
1121 1122
     }
1122 1123
 
1123 1124
     @Test public void testPhosphine() throws Exception {
1124  
-    	IMolecule mol = new Molecule();
  1125
+    	IAtomContainer mol = new AtomContainer();
1125 1126
         IAtom atom = new Atom("H");
1126 1127
         IAtom atom2 = new Atom("P");
1127 1128
         IAtom atom3 = new Atom("H");
@@ -1142,7 +1143,7 @@ public void testTetrahydropyran() throws Exception {
1142 1143
      * @cdk.inchi InChI=1S/HO3P/c1-4(2)3/h(H-,1,2,3)/p+1
1143 1144
      */
1144 1145
     @Test public void testPhosphorousAcid() throws Exception {
1145  
-        IMolecule mol = new Molecule();
  1146
+        IAtomContainer mol = new AtomContainer();
1146 1147
         IChemObjectBuilder builder = mol.getBuilder();
1147 1148
         IAtom a1 = builder.newInstance(IAtom.class,"P");
1148 1149
         a1.setFormalCharge(1);
@@ -1175,7 +1176,7 @@ public void testTetrahydropyran() throws Exception {
1175 1176
     }
1176 1177
 
1177 1178
     @Test public void testDiethylPhosphine() throws Exception {
1178  
-    	IMolecule mol = new Molecule();
  1179
+    	IAtomContainer mol = new AtomContainer();
1179 1180
         IAtom atom = new Atom("C");
1180 1181
         IAtom atom2 = new Atom("P");
1181 1182
         IAtom atom3 = new Atom("C");
@@ -1193,7 +1194,7 @@ public void testTetrahydropyran() throws Exception {
1193 1194
      * @cdk.inchi InChI=1/C2H5P/c1-3-2/h1H2,2H3
1194 1195
      */
1195 1196
     @Test public void testPhosphorCompound() throws Exception {
1196  
-    	IMolecule mol = new Molecule();
  1197
+    	IAtomContainer mol = new AtomContainer();
1197 1198
         IAtom atom = new Atom("C");
1198 1199
         IAtom atom2 = new Atom("P");
1199 1200
         IAtom atom3 = new Atom("C");
@@ -1208,7 +1209,7 @@ public void testTetrahydropyran() throws Exception {
1208 1209
     }
1209 1210
 
1210 1211
     @Test public void testCarbokation() throws Exception {
1211  
-    	IMolecule mol = new Molecule();
  1212
+    	IAtomContainer mol = new AtomContainer();
1212 1213
         IAtom atom = new Atom("H");
1213 1214
         IAtom atom2 = new Atom("C"); atom2.setFormalCharge(+1);
1214 1215
         IAtom atom3 = new Atom("H");
@@ -1226,7 +1227,7 @@ public void testTetrahydropyran() throws Exception {
1226 1227
     }
1227 1228
 
1228 1229
     @Test public void testCarbokation_implicitHydrogen() throws Exception {
1229  
-    	IMolecule mol = new Molecule();
  1230
+    	IAtomContainer mol = new AtomContainer();
1230 1231
         IAtom atom2 = new Atom("C"); atom2.setFormalCharge(+1);
1231 1232
         mol.addAtom(atom2);
1232 1233
 
@@ -1235,7 +1236,7 @@ public void testTetrahydropyran() throws Exception {
1235 1236
     }
1236 1237
 
1237 1238
     @Test public void testHydrogen() throws Exception {
1238  
-    	IMolecule mol = new Molecule();
  1239
+    	IAtomContainer mol = new AtomContainer();
1239 1240
         IAtom atom = new Atom("H");
1240 1241
         mol.addAtom(atom);
1241 1242
 
@@ -1244,7 +1245,7 @@ public void testTetrahydropyran() throws Exception {
1244 1245
     }
1245 1246
     
1246 1247
     @Test public void testHydroxyl() throws Exception {
1247  
-    	IMolecule mol = new Molecule();
  1248
+    	IAtomContainer mol = new AtomContainer();
1248 1249
         IAtom atom = new Atom("H");
1249 1250
         IAtom oxygen = new Atom("O");
1250 1251
         oxygen.setFormalCharge(-1);
@@ -1257,7 +1258,7 @@ public void testTetrahydropyran() throws Exception {
1257 1258
     }
1258 1259
     
1259 1260
     @Test public void testHydroxyl2() throws Exception {
1260  
-        IMolecule mol = new Molecule();
  1261
+        IAtomContainer mol = new AtomContainer();
1261 1262
           IAtom oxygen = new Atom("O");
1262 1263
           oxygen.setFormalCharge(-1);
1263 1264
           mol.addAtom(oxygen);
@@ -1267,7 +1268,7 @@ public void testTetrahydropyran() throws Exception {
1267 1268
       }
1268 1269
       
1269 1270
     @Test public void testHydroxonium() throws Exception {
1270  
-    	IMolecule mol = new Molecule();
  1271
+    	IAtomContainer mol = new AtomContainer();
1271 1272
         IAtom atom = new Atom("H");
1272 1273
         IAtom atom1 = new Atom("H");
1273 1274
         IAtom atom2 = new Atom("H");
@@ -1286,7 +1287,7 @@ public void testTetrahydropyran() throws Exception {
1286 1287
     }
1287 1288
     
1288 1289
     @Test public void testPositiveCarbonyl() throws Exception {
1289  
-    	IMolecule mol = new Molecule();
  1290
+    	IAtomContainer mol = new AtomContainer();
1290 1291
         IAtom atom = new Atom("H");
1291 1292
         IAtom atom1 = new Atom("H");
1292 1293
         IAtom atom2 = new Atom("H");
@@ -1308,7 +1309,7 @@ public void testTetrahydropyran() throws Exception {
1308 1309
     }
1309 1310
     
1310 1311
     @Test public void testProton() throws Exception {
1311  
-    	IMolecule mol = new Molecule();
  1312
+    	IAtomContainer mol = new AtomContainer();
1312 1313
         IAtom atom = new Atom("H");
1313 1314
         atom.setFormalCharge(1);
1314 1315
         mol.addAtom(atom);
@@ -1318,7 +1319,7 @@ public void testTetrahydropyran() throws Exception {
1318 1319
     }
1319 1320
 
1320 1321
     @Test public void testHalides() throws Exception {
1321  
-        IMolecule mol = new Molecule();
  1322
+        IAtomContainer mol = new AtomContainer();
1322 1323
 
1323 1324
         IAtom atom = new Atom("Cl");
1324 1325
         atom.setFormalCharge(-1);
@@ -1349,7 +1350,7 @@ public void testTetrahydropyran() throws Exception {
1349 1350
     }
1350 1351
     
1351 1352
     @Test public void testHalogens() throws Exception {
1352  
-        IMolecule mol = new Molecule();
  1353
+        IAtomContainer mol = new AtomContainer();
1353 1354
 
1354 1355
         IAtom atom = new Atom("Cl");
1355 1356
         IAtom hydrogen = new Atom("H");
@@ -1385,7 +1386,7 @@ public void testTetrahydropyran() throws Exception {
1385 1386
     }
1386 1387
 
1387 1388
     @Test public void testFluorRadical() throws Exception {
1388  
-        IMolecule mol = new Molecule();
  1389
+        IAtomContainer mol = new AtomContainer();
1389 1390
         IAtom atom = new Atom("F");
1390 1391
         mol.addAtom(atom);
1391 1392
         mol.addSingleElectron(0);
@@ -1395,7 +1396,7 @@ public void testTetrahydropyran() throws Exception {
1395 1396
     }
1396 1397
     
1397 1398
     @Test public void testChlorRadical() throws Exception {
1398  
-        IMolecule mol = new Molecule();
  1399
+        IAtomContainer mol = new AtomContainer();
1399 1400
         IAtom atom = new Atom("Cl");
1400 1401
         mol.addAtom(atom);
1401 1402
         mol.addSingleElectron(0);
@@ -1405,7 +1406,7 @@ public void testTetrahydropyran() throws Exception {
1405 1406
     }
1406 1407
     
1407 1408
     @Test public void testBromRadical() throws Exception {
1408  
-        IMolecule mol = new Molecule();
  1409
+        IAtomContainer mol = new AtomContainer();
1409 1410
         IAtom atom = new Atom("Br");
1410 1411
         mol.addAtom(atom);
1411 1412
         mol.addSingleElectron(0);
@@ -1415,7 +1416,7 @@ public void testTetrahydropyran() throws Exception {
1415 1416
     }
1416 1417
     
1417 1418
     @Test public void testIodRadical() throws Exception {
1418  
-        IMolecule mol = new Molecule();
  1419
+        IAtomContainer mol = new AtomContainer();
1419 1420
         IAtom atom = new Atom("I");
1420 1421
         mol.addAtom(atom);
1421 1422
         mol.addSingleElectron(0);
@@ -1425,7 +1426,7 @@ public void testTetrahydropyran() throws Exception {
1425 1426
     }
1426 1427
 
1427 1428
     @Test public void testIMinusF2() throws Exception {
1428  
-        IMolecule mol = new Molecule();
  1429
+        IAtomContainer mol = new AtomContainer();
1429 1430
         IAtom atom = new Atom("F");
1430 1431
         IAtom atom2 = new Atom("I");
1431 1432
         IAtom atom3 = new Atom("F");
@@ -1441,7 +1442,7 @@ public void testTetrahydropyran() throws Exception {
1441 1442
     }
1442 1443
 
1443 1444
     @Test public void testHydride() throws Exception {
1444  
-    	IMolecule mol = new Molecule();
  1445
+    	IAtomContainer mol = new AtomContainer();
1445 1446
         IAtom atom = new Atom("H");
1446 1447
         atom.setFormalCharge(-1);
1447 1448
         mol.addAtom(atom);
@@ -1451,7 +1452,7 @@ public void testTetrahydropyran() throws Exception {
1451 1452
     }
1452 1453
 
1453 1454
     @Test public void testHydrogenRadical() throws Exception {
1454  
-    	IMolecule mol = new Molecule();
  1455
+    	IAtomContainer mol = new AtomContainer();
1455 1456
         IAtom atom = new Atom("H");
1456 1457
         mol.addAtom(atom);
1457 1458
         mol.addSingleElectron(0);
@@ -1461,7 +1462,7 @@ public void testTetrahydropyran() throws Exception {
1461 1462
     }
1462 1463
 
1463 1464
     @Test public void testAzide() throws Exception {
1464  
-    	IMolecule mol = new Molecule();
  1465
+    	IAtomContainer mol = new AtomContainer();
1465 1466
         IAtom atom = new Atom("C");
1466 1467
         IAtom atom2 = new Atom("N"); atom2.setFormalCharge(-1);
1467 1468
         IAtom atom3 = new Atom("N"); atom3.setFormalCharge(+1);
@@ -1479,7 +1480,7 @@ public void testTetrahydropyran() throws Exception {
1479 1480
     }
1480 1481
     
1481 1482
     @Test public void testAzide2() throws Exception {
1482  
-    	IMolecule mol = new Molecule();
  1483
+    	IAtomContainer mol = new AtomContainer();
1483 1484
         IAtom atom = new Atom("C");
1484 1485
         IAtom atom2 = new Atom("N");
1485 1486
         IAtom atom3 = new Atom("N"); atom3.setFormalCharge(+1);
@@ -1497,7 +1498,7 @@ public void testTetrahydropyran() throws Exception {
1497 1498
     }
1498 1499
     
1499 1500
     @Test public void testMercuryComplex() throws Exception {
1500  
-    	IMolecule mol = new Molecule();
  1501
+    	IAtomContainer mol = new AtomContainer();
1501 1502
         
1502 1503
         IAtom atom = new Atom("Hg");
1503 1504
         atom.setFormalCharge(-1);
@@ -1607,7 +1608,7 @@ public void test_Hg_2() throws Exception {
1607 1608
 
1608 1609
     	
1609 1610
     @Test public void testPoloniumComplex() throws Exception {
1610  
-    	IMolecule mol = new Molecule();
  1611
+    	IAtomContainer mol = new AtomContainer();
1611 1612
         
1612 1613
         IAtom atom = new Atom("O");
1613 1614
         IAtom atom1 = new Atom("Po");
@@ -1625,7 +1626,7 @@ public void test_Hg_2() throws Exception {
1625 1626
     }
1626 1627
     	
1627 1628
     @Test public void testStronglyBoundKations() throws Exception {
1628  
-    	IMolecule mol = new Molecule();
  1629
+    	IAtomContainer mol = new AtomContainer();
1629 1630
     	mol.addAtom(new Atom("C"));
1630 1631
     	mol.addAtom(new Atom("O")); mol.getAtom(1).setFormalCharge(+1);
1631 1632
     	mol.addBond(0,1, IBond.Order.DOUBLE);    	
@@ -1638,7 +1639,7 @@ public void test_Hg_2() throws Exception {
1638 1639
      }
1639 1640
 
1640 1641
     @Test public void testMetallics() throws Exception {
1641  
-        IMolecule mol = new Molecule();
  1642
+        IAtomContainer mol = new AtomContainer();
1642 1643
 
1643 1644
         IAtom atom = new Atom("W");
1644 1645
         mol.addAtom(atom);
@@ -1659,7 +1660,7 @@ public void test_Hg_2() throws Exception {
1659 1660
     }
1660 1661
 
1661 1662
     @Test public void testSalts() throws Exception {
1662  
-    	IMolecule mol = new Molecule();
  1663
+    	IAtomContainer mol = new AtomContainer();
1663 1664
         
1664 1665
         IAtom atom = new Atom("Na");
1665 1666
         atom.setFormalCharge(+1);
@@ -1854,7 +1855,7 @@ public void fix_Ca_1() throws Exception {
1854 1855
     }
1855 1856
     
1856 1857
     @Test public void testPerchlorate() throws Exception {
1857  
-    	IMolecule mol = new Molecule();
  1858
+    	IAtomContainer mol = new AtomContainer();
1858 1859
         IAtom atom = new Atom("O");
1859 1860
         IAtom atom2 = new Atom("Cl");
1860 1861
         IAtom atom3 = new Atom("O");
@@ -1880,7 +1881,7 @@ public void fix_Ca_1() throws Exception {
1880 1881
      * Gallium tetrahydroxide.
1881 1882
      */
1882 1883
     @Test public void testGallate() throws Exception {
1883  
-        IMolecule mol = new Molecule();
  1884
+        IAtomContainer mol = new AtomContainer();
1884 1885
           IAtom atom = new Atom("O"); atom.setFormalCharge(-1);
1885 1886
           IAtom atom2 = new Atom("Ga"); atom2.setFormalCharge(+3);
1886 1887
           IAtom atom3 = new Atom("O"); atom3.setFormalCharge(-1);
@@ -1902,7 +1903,7 @@ public void fix_Ca_1() throws Exception {
1902 1903
      * Gallium trihydroxide.
1903 1904
      */
1904 1905
     @Test public void testGallateCovalent() throws Exception {
1905  
-        IMolecule mol = new Molecule();
  1906
+        IAtomContainer mol = new AtomContainer();
1906 1907
         IAtom atom = new Atom("O");
1907 1908
         IAtom atom2 = new Atom("Ga");
1908 1909
         IAtom atom3 = new Atom("O");
@@ -1919,7 +1920,7 @@ public void fix_Ca_1() throws Exception {
1919 1920
     }
1920 1921
 
1921 1922
     @Test public void testPerchlorate_ChargedBonds() throws Exception {
1922  
-    	IMolecule mol = new Molecule();
  1923
+    	IAtomContainer mol = new AtomContainer();
1923 1924
         IAtom atom = new Atom("O");
1924 1925
         IAtom atom2 = new Atom("Cl");
1925 1926
         IAtom atom3 = new Atom("O");
@@ -1942,7 +1943,7 @@ public void fix_Ca_1() throws Exception {
1942 1943
     }
1943 1944
 
1944 1945
     @Test public void testChlorate() throws Exception {
1945  
-    	IMolecule mol = new Molecule();
  1946
+    	IAtomContainer mol = new AtomContainer();
1946 1947
         IAtom atom = new Atom("O");
1947 1948
         IAtom atom2 = new Atom("Cl");
1948 1949
         IAtom atom3 = new Atom("O");
@@ -1962,7 +1963,7 @@ public void fix_Ca_1() throws Exception {
1962 1963
     }
1963 1964
 
1964 1965
     @Test public void testOxide() throws Exception {
1965  
-    	IMolecule mol = new Molecule();
  1966
+    	IAtomContainer mol = new AtomContainer();
1966 1967
         IAtom atom = new Atom("O"); atom.setFormalCharge(-2);
1967 1968
         mol.addAtom(atom);
1968 1969
 
@@ -2232,7 +2233,7 @@ public void testPyridineWithSP2() throws Exception {
2232 2233
                 "C.sp2",
2233 2234
                 "C.sp2"
2234 2235
         };
2235  
-        IMolecule mol = new Molecule();
  2236
+        IAtomContainer mol = new AtomContainer();
2236 2237
         IAtom a1 = mol.getBuilder().newInstance(IAtom.class,"N");
2237 2238
         IAtom a2 = mol.getBuilder().newInstance(IAtom.class,"C");
2238 2239
         IAtom a3 = mol.getBuilder().newInstance(IAtom.class,"C");
@@ -2296,7 +2297,7 @@ public void testPyridineWithSP2() throws Exception {
2296 2297
 	}
2297 2298
 
2298 2299
     @Test public void testPyridineOxide() throws Exception {
2299  
-        Molecule mol = new Molecule();
  2300
+        IAtomContainer mol = new AtomContainer();
2300 2301
         mol.addAtom(new Atom("C")); // 0
2301 2302
         mol.addAtom(new Atom("N")); // 1
2302 2303
         mol.addAtom(new Atom("C")); // 2
@@ -2326,7 +2327,7 @@ public void testPyridineWithSP2() throws Exception {
2326 2327
     }
2327 2328
 
2328 2329
     @Test public void testPyridineOxide_SP2() throws Exception {
2329  
-        Molecule mol = new Molecule();
  2330
+        IAtomContainer mol = new AtomContainer();
2330 2331
         mol.addAtom(new Atom("C")); // 0
2331 2332
         mol.getAtom(0).setHybridization(Hybridization.SP2);
2332 2333
         mol.addAtom(new Atom("N")); // 1
@@ -2479,7 +2480,7 @@ public void testPyridineWithSP2() throws Exception {
2479 2480
 
2480 2481
 
2481 2482
     @Test public void testHaloniumsCl() throws Exception {
2482  
-    	IMolecule mol = new Molecule();
  2483
+    	IAtomContainer mol = new AtomContainer();
2483 2484
 
2484 2485
     	IAtom carbon1 = new Atom("C");
2485 2486
     	IAtom carbon2 = new Atom("C");
@@ -2498,7 +2499,7 @@ public void testPyridineWithSP2() throws Exception {
2498 2499
 
2499 2500
 
2500 2501
     @Test public void testHaloniumsBr() throws Exception {
2501  
-    	IMolecule mol = new Molecule();
  2502
+    	IAtomContainer mol = new AtomContainer();
2502 2503
 
2503 2504
     	IAtom carbon1 = new Atom("C");
2504 2505
     	IAtom carbon2 = new Atom("C");
@@ -2517,7 +2518,7 @@ public void testPyridineWithSP2() throws Exception {
2517 2518
 
2518 2519
 
2519 2520
     @Test public void testHaloniumsI() throws Exception {
2520  
-    	IMolecule mol = new Molecule();
  2521
+    	IAtomContainer mol = new AtomContainer();
2521 2522
 
2522 2523
     	IAtom carbon1 = new Atom("C");
2523 2524
     	IAtom carbon2 = new Atom("C");
@@ -2535,7 +2536,7 @@ public void testPyridineWithSP2() throws Exception {
2535 2536
     }
2536 2537
     
2537 2538
     @Test public void testRearrangementCarbokation() throws Exception {
2538  
-    	IMolecule mol = new Molecule();
  2539
+    	IAtomContainer mol = new AtomContainer();
2539 2540
 
2540 2541
     	IAtom carbon1 = new Atom("C");
2541 2542
     	carbon1.setFormalCharge(+1);
@@ -2553,7 +2554,7 @@ public void testPyridineWithSP2() throws Exception {
2553 2554
     }
2554 2555
     
2555 2556
     @Test public void testChargedSpecies() throws Exception {
2556  
-    	IMolecule mol = new Molecule();
  2557
+    	IAtomContainer mol = new AtomContainer();
2557 2558
 
2558 2559
     	IAtom atom1 = new Atom("C");
2559 2560
     	atom1.setFormalCharge(-1);
@@ -2570,7 +2571,7 @@ public void testPyridineWithSP2() throws Exception {
2570 2571
     
2571 2572
 //    [O+]=C-[C-]
2572 2573
     @Test public void testChargedSpecies2() throws Exception {
2573  
-    	IMolecule mol = new Molecule();
  2574
+    	IAtomContainer mol = new AtomContainer();
2574 2575
 
2575 2576
     	IAtom atom1 = new Atom("O");
2576 2577
     	atom1.setFormalCharge(1);
@@ -2590,7 +2591,7 @@ public void testPyridineWithSP2() throws Exception {
2590 2591
     
2591 2592
 //    [C-]=C-C
2592 2593
     @Test public void testChargedSpecies3() throws Exception {
2593  
-    	IMolecule mol = new Molecule();
  2594
+    	IAtomContainer mol = new AtomContainer();
2594 2595
 
2595 2596
     	IAtom atom1 = new Atom("C");
2596 2597
     	atom1.setFormalCharge(-1);
@@ -2609,7 +2610,7 @@ public void testPyridineWithSP2() throws Exception {
2609 2610
 
2610 2611
     // [C-]#[N+]C
2611 2612
     @Test public void testIsonitrile() throws Exception {
2612  
-        IMolecule mol = new Molecule();
  2613
+        IAtomContainer mol = new AtomContainer();
2613 2614
 
2614 2615
         IAtom atom1 = new Atom("C");
2615 2616
         IAtom atom2 = new Atom("N");
@@ -2629,7 +2630,7 @@ public void testPyridineWithSP2() throws Exception {
2629 2630
     }
2630 2631
     
2631 2632
     @Test public void testNobleGases() throws Exception {
2632  
-    	IMolecule mol = new Molecule();
  2633
+    	IAtomContainer mol = new AtomContainer();
2633 2634
 
2634 2635
     	mol.addAtom(new Atom("He"));
2635 2636
     	mol.addAtom(new Atom("Ne"));
@@ -2643,7 +2644,7 @@ public void testPyridineWithSP2() throws Exception {
2643 2644
     }
2644 2645
     
2645 2646
     @Test public void testZincChloride() throws Exception {
2646  
-    	IMolecule mol = new Molecule();
  2647
+    	IAtomContainer mol = new AtomContainer();
2647 2648
     	mol.addAtom(new Atom("Zn"));
2648 2649
     	mol.addAtom(new Atom("Cl"));
2649 2650
     	mol.addAtom(new Atom("Cl"));
@@ -2655,7 +2656,7 @@ public void testPyridineWithSP2() throws Exception {
2655 2656
     }
2656 2657
     
2657 2658
     @Test public void testZinc() throws Exception {
2658  
-    	IMolecule mol = new Molecule();
  2659
+    	IAtomContainer mol = new AtomContainer();
2659 2660
     	mol.addAtom(new Atom("Zn")); mol.getAtom(0).setFormalCharge(+2);
2660 2661
 
2661 2662
     	String[] expectedTypes = {"Zn.2plus"}; 
@@ -2663,7 +2664,7 @@ public void testPyridineWithSP2() throws Exception {
2663 2664
     }
2664 2665
 
2665 2666
     @Test public void testSilicon() throws Exception {
2666  
-    	IMolecule mol = new Molecule();
  2667
+    	IAtomContainer mol = new AtomContainer();
2667 2668
     	IAtom a1 = mol.getBuilder().newInstance(IAtom.class,"Si"); mol.addAtom(a1);
2668 2669
     	IAtom a2 = mol.getBuilder().newInstance(IAtom.class,"O"); mol.addAtom(a2);
2669 2670
     	IAtom a3 = mol.getBuilder().newInstance(IAtom.class,"O"); mol.addAtom(a3);
@@ -2704,7 +2705,7 @@ public void testPyridineWithSP2() throws Exception {
2704 2705
     }
2705 2706
     
2706 2707
     @Test public void testScandium() throws Exception {
2707  
-    	IMolecule mol = new Molecule();
  2708
+    	IAtomContainer mol = new AtomContainer();
2708 2709
     	mol.addAtom(new Atom("Sc")); mol.getAtom(0).setFormalCharge(-3);
2709 2710
     	mol.addAtom(new Atom("O")); mol.addBond(0,1,IBond.Order.SINGLE);
2710 2711
     	mol.addAtom(new Atom("H")); mol.addBond(1,2,IBond.Order.SINGLE);
@@ -2726,7 +2727,7 @@ public void testPyridineWithSP2() throws Exception {
2726 2727
     }
2727 2728
     
2728 2729
     @Test public void testVanadium() throws Exception {
2729  
-    	IMolecule mol = new Molecule();
  2730
+    	IAtomContainer mol = new AtomContainer();
2730 2731
     	mol.addAtom(new Atom("V")); mol.getAtom(0).setFormalCharge(-3);
2731 2732
     	mol.addAtom(new Atom("C")); mol.addBond(0,1,IBond.Order.SINGLE);
2732 2733
     	mol.addAtom(new Atom("N")); mol.addBond(1,2,IBond.Order.TRIPLE);
@@ -2748,7 +2749,7 @@ public void testPyridineWithSP2() throws Exception {
2748 2749
     }
2749 2750
     
2750 2751
     @Test public void testTitanium() throws Exception {
2751  
-    	IMolecule mol = new Molecule();
  2752
+    	IAtomContainer mol = new AtomContainer();
2752 2753
     	mol.addAtom(new Atom("Ti")); mol.getAtom(0).setFormalCharge(-3);
2753 2754
     	mol.addAtom(new Atom("C")); mol.addBond(0,1,IBond.Order.SINGLE);
2754 2755
     	mol.addAtom(new Atom("N")); mol.addBond(1,2,IBond.Order.TRIPLE);
@@ -2770,7 +2771,7 @@ public void testPyridineWithSP2() throws Exception {
2770 2771
     }
2771 2772
     
2772 2773
     @Test public void testBoronTetraFluoride() throws Exception {
2773  
-    	IMolecule mol = new Molecule();
  2774
+    	IAtomContainer mol = new AtomContainer();
2774 2775
     	mol.addAtom(new Atom("B")); mol.getAtom(0).setFormalCharge(-1);
2775 2776
     	mol.addAtom(new Atom("F"));
2776 2777
     	mol.addAtom(new Atom("F"));
@@ -2786,7 +2787,7 @@ public void testPyridineWithSP2() throws Exception {
2786 2787
     }
2787 2788
     
2788 2789
     @Test public void testBerylliumTetraFluoride() throws Exception {
2789  
-    	IMolecule mol = new Molecule();
  2790
+    	IAtomContainer mol = new AtomContainer();
2790 2791
     	mol.addAtom(new Atom("Be")); mol.getAtom(0).setFormalCharge(-2);
2791 2792
     	mol.addAtom(new Atom("F"));
2792 2793
     	mol.addAtom(new Atom("F"));
@@ -2802,7 +2803,7 @@ public void testPyridineWithSP2() throws Exception {
2802 2803
     }
2803 2804
 
2804 2805
     @Test public void testArsine() throws Exception {
2805  
-    	IMolecule mol = new Molecule();
  2806
+    	IAtomContainer mol = new AtomContainer();
2806 2807
     	mol.addAtom(new Atom("As"));
2807 2808
     	mol.addAtom(new Atom("H"));
2808 2809
     	mol.addAtom(new Atom("H"));
@@ -2816,7 +2817,7 @@ public void testPyridineWithSP2() throws Exception {
2816 2817
     }
2817 2818
     
2818 2819
     @Test public void testBoron() throws Exception {
2819  
-    	IMolecule mol = new Molecule();
  2820
+    	IAtomContainer mol = new AtomContainer();
2820 2821
     	mol.addAtom(new Atom("B"));
2821 2822
     	mol.addAtom(new Atom("H"));
2822 2823
     	mol.addAtom(new Atom("H"));
@@ -2830,7 +2831,7 @@ public void testPyridineWithSP2() throws Exception {
2830 2831
     }
2831 2832
 
2832 2833
     @Test public void testCarbonMonoxide() throws Exception {
2833  
-    	IMolecule mol = new Molecule();
  2834
+    	IAtomContainer mol = new AtomContainer();
2834 2835
     	mol.addAtom(new Atom("C")); mol.getAtom(0).setFormalCharge(-1);
2835 2836
     	mol.addAtom(new Atom("O")); mol.getAtom(1).setFormalCharge(1);
2836 2837
     	mol.addBond(0,1,IBond.Order.TRIPLE);
@@ -2840,7 +2841,7 @@ public void testPyridineWithSP2() throws Exception {
2840 2841
     }
2841 2842
 
2842 2843
     @Test public void testTitaniumFourCoordinate() throws Exception {
2843  
-    	IMolecule mol = new Molecule();
  2844
+    	IAtomContainer mol = new AtomContainer();
2844 2845
     	mol.addAtom(new Atom("Ti"));
2845 2846
     	mol.addAtom(new Atom("Cl")); mol.addBond(0,1,IBond.Order.SINGLE);
2846 2847
     	mol.addAtom(new Atom("Cl")); mol.addBond(0,2,IBond.Order.SINGLE);
@@ -2855,7 +2856,7 @@ public void testPyridineWithSP2() throws Exception {
2855 2856
      * @cdk.bug 1872969
2856 2857
      */
2857 2858
     @Test public void bug1872969() throws Exception {
2858  
-    	IMolecule mol = new Molecule();
  2859
+    	IAtomContainer mol = new AtomContainer();
2859 2860
     	mol.addAtom(new Atom("C"));
2860 2861
     	mol.addAtom(new Atom("S"));
2861 2862
     	mol.addAtom(new Atom("O"));
@@ -2900,7 +2901,7 @@ public void testPyridineWithSP2() throws Exception {
2900 2901
     }
2901 2902
     
2902 2903
     @Test public void testAssumeExplicitHydrogens() throws Exception {