Index: tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentResults.dat
===================================================================
--- tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentResults.dat	(revision 55e1bc203062d6ce285fbba9c783e28963932633)
+++ tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentResults.dat	(revision 10f0cb73e0cc1105d7dc5360f9c6409f9674a51e)
@@ -1,55 +1,43 @@
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-48
-49 0 0 0 36.426358155847325 36.426358155847325 36.426358155847325 5 0 0 0 -0 0 -0 0 -0 0 0 0 0 0 77.445322036743164 77.388835999999969 0 7.8627738952636719 7.8564910000000054 0 40 -235.26623779761212 246.41101401336471 358.47509627704221 -36.088771365833544 0 25.000000000000199 117.85654818238892 -804.063576722108 82 0 -11.213735660698733 -11.213686201564187 -11.211818041250009 -11.211238287978301 -11.207342398771985 -11.207283533407654 -1.0933565580029172 -1.0418457410864572 -0.96280469451579442 -0.86864019596123498 -0.79546383578164703 -0.78915191831965892 -0.66079260899812253 -0.61650440208268342 -0.59303541613526745 -0.57850804125844257 -0.55639991473225581 -0.52252266021682703 -0.51578516055584311 -0.50055160186799541 -0.47731016427733014 -0.46907418775422721 -0.4633720981687543 -0.45965581594822008 -0.41558433124368188 0.22460232435309146 0.24167380970174371 0.26182224693199957 0.274442732526264 0.28020298524191534 0.31283054229216412 0.31937217506900883 0.32133971832716679 0.34094920221577563 0.34482436417555035 0.34538585423647772 0.34777209804033848 0.36996262160125354 0.37463765894123519 0.39486177288607005 0.39829656586063866 0.44917858030586572 0.45357940281818476 0.47562273163070157 0.71019915355840946 0.74341576544094279 0.76679857970878484 0.78120179633625808 0.78947288105776592 0.81206184208848675 0.82868110808045881 0.86781581357762894 0.8898698455050984 0.90736803985763703 0.97284921241424505 0.9742263664119003 1.0060213828076012 1.0430327428137958 1.0604719987919966 1.086448150317062 1.1138988586528924 1.1687393472823846 1.1865287106484095 1.2137322884271204 1.2224336733525241 1.2249247349542112 1.239953568806935 1.2562177262849565 1.2697632858506627 1.2741567863399785 1.2827857535593581 1.291425613816672 1.2997480501685874 1.3010278180829917 1.3379360800772504 1.3605066896880424 1.5895522659846644 1.6472727641373173 1.6875539404938789 1.7309631776661789 1.8141290244265216 2.1272435408671169 20 0 3 0 -0.00012509334515584114 0.0015087214507278901 0.0045845539190643159 3 0 -0.00012509334515285742 0.0015087214507110147 -0.004584553918990153 3 0 0.00013337263984229686 -0.001501400083282256 0.0045814346558881169 3 0 0.00013337263984304626 -0.0015014000833115659 -0.0045814346559143182 3 0 0.00048156363748086406 -0.001645721351790197 -0.005055072534044136 3 0 0.00048156363747930975 -0.0016457213518115132 0.0050550725340263725 3 0 -0.00049137192787807038 0.0016390519061415532 -0.0050529276456749983 3 0 -0.00049137192788156758 0.0016390519061428854 0.0050529276456905414 3 0 -0.0040067522961751423 -0.00058363438772413012 0.0047413463251682053 3 0 -0.0040067522961684254 -0.00058363438772079945 -0.0047413463251397836 3 0 0.00063853645098665979 -0.0079332430106533458 3.8321933299573406e-16 3 0 0.0040299581693440389 0.0005952059311689073 0.0047401581713324425 3 0 0.0040299581693375441 0.00059520593117601273 -0.0047401581713160112 3 0 -0.00076672281155010236 -0.022807133844709337 3.0872407626121481e-13 3 0 0.0012330447135060485 0.022986169625903496 2.8943385893422099e-13 3 0 -0.0057654413217171907 0.016091364643127992 2.8355223916092093e-13 3 0 0.0053560609268483717 -0.016243775411925898 2.7456718060991478e-13 3 0 -0.0030371444042445184 -0.009641635987987951 2.0703183813532745e-13 3 0 0.0031400417293236949 0.0097895633045068653 2.3356021612383695e-13 3 0 -0.00084172903672774524 0.0077342437537346598 2.6666709962715304e-15
-50
-51 0 0 0 36.426358155847325 36.426358155847325 36.426358155847325 5 0 0 0 -0 0 -0 0 -0 0 0 0 0 0 136.02419996261597 135.98449900000003 0 13.569527149200439 13.564846999999986 0 41 -235.26624554400001 246.39985178249503 358.46384823231961 -36.088404132543936 0 25.000000000000274 117.85577875834709 -804.04154142616562 82 0 -11.213748168048063 -11.213741336723436 -11.211804872360092 -11.211226732809383 -11.207391225108708 -11.20734263112629 -1.0933729520219222 -1.0417072216139343 -0.96269564907059624 -0.86873761035590624 -0.79547341528046722 -0.78915861023481981 -0.66080645088876444 -0.61643536025671852 -0.59298692600050862 -0.5784748439895584 -0.55635281350455335 -0.52249684233704763 -0.51572670801877862 -0.50062466071792477 -0.47728351048914891 -0.46910057064818106 -0.46337537111880245 -0.45966029872841485 -0.41560185308238717 0.22459628051728889 0.24167336537868922 0.26181898203139281 0.2744414381427841 0.28019588636950521 0.31287990640604918 0.3194110983935961 0.32134168136363195 0.34090795796455925 0.34473873847822739 0.34538396408297134 0.34775830606940344 0.36994011607682936 0.37466665149262779 0.39485594235405325 0.39820980959688179 0.44899712743880421 0.45355908329097849 0.47571957540942689 0.71019140324562091 0.74365180588615287 0.76668504908120738 0.78109999743088787 0.78938033158359278 0.81212469840338397 0.82870058072791786 0.86766191497095002 0.88989831561536936 0.90726298515216774 0.97307548010179645 0.97391695376466647 1.005848511877006 1.0429850366146263 1.0604709308277072 1.0863461713486975 1.1138838089091077 1.1687411888113866 1.186467081828966 1.2138241533676322 1.2224444137330153 1.2249897788982633 1.2400350465182512 1.2561911607911709 1.269762377851624 1.2741505777239905 1.2827709378006171 1.2914235599332777 1.2996385955910565 1.3009793562357483 1.3380282564690518 1.3604522066896076 1.589571504466297 1.6472534519286248 1.6873789372956505 1.7309413070980395 1.8140639006071382 2.1270902367869331 20 0 3 0 0.00012104496852381741 0.001508901285365738 0.004584861516746308 3 0 0.00012104496852620439 0.001508901285335984 -0.0045848615167431994 3 0 -0.00047156073051340952 -0.0016374282019553377 0.0050542435477689551 3 0 -0.00047156073050974578 -0.001637428201932245 -0.0050542435478200254 3 0 -0.00012078543893273563 -0.0015090653758584871 -0.0045847080886787239 3 0 -0.00012078543893864757 -0.0015090653758575989 0.0045847080887257974 3 0 0.004008720741944638 -0.00059754349945895235 -0.0047376592469769996 3 0 0.0040087207419427506 -0.00059754349944340923 0.0047376592469503542 3 0 0.00047162701404146468 0.0016368798761363657 0.0050548114962731816 3 0 0.00047162701403813401 0.0016368798761301484 -0.0050548114962420954 3 0 -0.0005912005206991644 -0.0078931860589219749 -1.6531914313103288e-15 3 0 -0.0040180212892605982 0.00060364579043015176 -0.0047368267826364274 3 0 -0.0040180212892678147 0.00060364579043015176 0.0047368267826599642 3 0 0.00090777130757258018 -0.022795685522521481 2.9325596396833363e-13 3 0 0.006121625506069428 0.016252475757113305 2.7298547835770588e-13 3 0 -0.00090868768384366749 0.022794074805849829 2.7162703518545053e-13 3 0 0.0026127482050353201 -0.0098227257124949841 2.368063566387044e-13 3 0 -0.0061238165965233904 -0.016248779923828005 2.2988891121551182e-13 3 0 -0.0028149306445692801 0.0099771606747276476 2.0125472235104767e-13 3 0 0.00081443989712814968 0.0077258862336035961 -5.7836291277115049e-16
-52
-53 0 0 0 36.426358155847325 36.426358155847325 36.426358155847325 5 0 0 0 -0 0 -0 0 -0 0 0 0 0 0 136.64175200462341 136.47652899999991 0 13.551898956298828 13.54884699999991 0 0 0 0 0
+41 0 0 0 37.794519771578464 37.794519771578464 37.794519771578464 6 0 0 0 -0 0 -0 0 -0 0 0 0 0 0 0 132.89544486999512 132.864304 0 13.243814945220947 13.240827000000024 0 0 0 0 0
Index: tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb
===================================================================
--- tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb	(revision 10f0cb73e0cc1105d7dc5360f9c6409f9674a51e)
+++ tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb	(revision 10f0cb73e0cc1105d7dc5360f9c6409f9674a51e)
@@ -0,0 +1,42 @@
+REMARK created by molecuilder on Thu Apr 18 09:42:02 2013, time step 0
+ATOM      1 C01 0alk 01          5.890   6.513   5.890  0.00  0.00           C 0
+ATOM      2 C02 0alk 01          7.139   5.630   5.890  0.00  0.00           C 0
+ATOM      3 H01 0alk 01          5.890   7.142   5.000  0.00  0.00           H 0
+ATOM      4 H02 0alk 01          5.890   7.142   6.780  0.00  0.00           H 0
+ATOM      5 H03 0alk 01          7.139   5.000   5.000  0.00  0.00           H 0
+ATOM      6 H04 0alk 01          7.139   5.000   6.780  0.00  0.00           H 0
+ATOM      7 C03 0alk 01          8.388   6.513   5.890  0.00  0.00           C 0
+ATOM      8 C04 0alk 01          9.638   5.630   5.890  0.00  0.00           C 0
+ATOM      9 H05 0alk 01          8.388   7.142   5.000  0.00  0.00           H 0
+ATOM     10 H06 0alk 01          8.388   7.142   6.780  0.00  0.00           H 0
+ATOM     11 H07 0alk 01          9.638   5.000   5.000  0.00  0.00           H 0
+ATOM     12 H08 0alk 01          9.638   5.000   6.780  0.00  0.00           H 0
+ATOM     13 C05 0alk 01         10.887   6.513   5.890  0.00  0.00           C 0
+ATOM     14 C06 0alk 01         12.136   5.630   5.890  0.00  0.00           C 0
+ATOM     15 H09 0alk 01         10.887   7.142   5.000  0.00  0.00           H 0
+ATOM     16 H10 0alk 01         10.887   7.142   6.780  0.00  0.00           H 0
+ATOM     17 H11 0alk 01         12.136   5.000   5.000  0.00  0.00           H 0
+ATOM     18 H12 0alk 01         12.136   5.000   6.780  0.00  0.00           H 0
+ATOM     19 H13 0alk 01          5.000   5.884   5.890  0.00  0.00           H 0
+ATOM     20 H14 0alk 01         13.026   6.259   5.890  0.00  0.00           H 0
+CONECT    1    3    2    4   19                                                 
+CONECT    2    1    5    6    7                                                 
+CONECT    3    1                                                                
+CONECT    4    1                                                                
+CONECT    5    2                                                                
+CONECT    6    2                                                                
+CONECT    7    2    8    9   10                                                 
+CONECT    8    7   11   12   13                                                 
+CONECT    9    7                                                                
+CONECT   10    7                                                                
+CONECT   11    8                                                                
+CONECT   12    8                                                                
+CONECT   13    8   14   15   16                                                 
+CONECT   14   13   17   18   20                                                 
+CONECT   15   13                                                                
+CONECT   16   13                                                                
+CONECT   17   14                                                                
+CONECT   18   14                                                                
+CONECT   19    1                                                                
+CONECT   20   14                                                                
+END
