Index: tests/regression/Atoms/Saturate/post/saturated_cholesterol_H48_50_53_67_73.pdb
===================================================================
--- tests/regression/Atoms/Saturate/post/saturated_cholesterol_H48_50_53_67_73.pdb	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
+++ tests/regression/Atoms/Saturate/post/saturated_cholesterol_H48_50_53_67_73.pdb	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
@@ -0,0 +1,150 @@
+REMARK created by molecuilder on Mon Sep 12 15:10:27 2016, time step 0
+ATOM      1 C01 0non 01         13.068   4.685   8.414  0.00  0.00           C 0
+ATOM      2 C02 0non 01         11.975   5.754   8.354  0.00  0.00           C 0
+ATOM      3 C03 0non 01         12.194   6.668   7.119  0.00  0.00           C 0
+ATOM      4 C04 0non 01         10.624   5.104   8.072  0.00  0.00           C 0
+ATOM      5 C05 0non 01         12.056   6.648   9.577  0.00  0.00           C 0
+ATOM      6 C06 0non 01         13.650   7.098   7.126  0.00  0.00           C 0
+ATOM      7 C07 0non 01         11.782   5.741   5.969  0.00  0.00           C 0
+ATOM      8 C08 0non 01          9.493   5.960   8.647  0.00  0.00           C 0
+ATOM      9 C09 0non 01         10.514   5.039   6.528  0.00  0.00           C 0
+ATOM     10 C10 0non 01         13.494   7.182   9.650  0.00  0.00           C 0
+ATOM     11 C11 0non 01         13.874   7.948   8.389  0.00  0.00           C 0
+ATOM     12 C12 0non 01         13.914   7.989   5.905  0.00  0.00           C 0
+ATOM     13 C13 0non 01          9.475   7.319   7.945  0.00  0.00           C 0
+ATOM     14 C14 0non 01          8.155   5.253   8.426  0.00  0.00           C 0
+ATOM     15 C15 0non 01         15.345   8.336   8.478  0.00  0.00           C 0
+ATOM     16 C16 0non 01         15.263   8.633   6.025  0.00  0.00           C 0
+ATOM     17 C17 0non 01          8.320   8.161   8.492  0.00  0.00           C 0
+ATOM     18 C18 0non 01         15.475   9.512   9.449  0.00  0.00           C 0
+ATOM     19 C19 0non 01         15.898   8.760   7.144  0.00  0.00           C 0
+ATOM     20 C20 0non 01         16.186   7.179   9.011  0.00  0.00           C 0
+ATOM     21 C21 0non 01          8.301   9.520   7.789  0.00  0.00           C 0
+ATOM     22 C22 0non 01         17.293   9.364   7.151  0.00  0.00           C 0
+ATOM     23 C23 0non 01         17.614   7.279   8.476  0.00  0.00           C 0
+ATOM     24 C24 0non 01          7.146  10.361   8.337  0.00  0.00           C 0
+ATOM     25 C25 0non 01         18.046   8.733   8.331  0.00  0.00           C 0
+ATOM     26 C26 0non 01          7.127  11.720   7.634  0.00  0.00           C 0
+ATOM     27 C27 0non 01          5.823   9.637   8.083  0.00  0.00           C 0
+ATOM     28 O01 0non 01         19.452   8.787   8.082  0.00  0.00           O 0
+ATOM     29 H01 0non 01         12.905   4.048   9.284  0.00  0.00           H 0
+ATOM     30 H02 0non 01         13.033   4.078   7.509  0.00  0.00           H 0
+ATOM     31 H03 0non 01         14.043   5.165   8.492  0.00  0.00           H 0
+ATOM     32 H04 0non 01         11.541   7.539   7.169  0.00  0.00           H 0
+ATOM     33 H05 0non 01         10.591   4.101   8.497  0.00  0.00           H 0
+ATOM     34 H06 0non 01         11.356   7.478   9.479  0.00  0.00           H 0
+ATOM     35 H07 0non 01         11.828   6.072  10.474  0.00  0.00           H 0
+ATOM     36 H08 0non 01         14.307   6.229   7.126  0.00  0.00           H 0
+ATOM     37 H09 0non 01         11.541   6.318   5.076  0.00  0.00           H 0
+ATOM     38 H10 0non 01         12.566   5.014   5.760  0.00  0.00           H 0
+ATOM     39 H11 0non 01          9.656   6.106   9.715  0.00  0.00           H 0
+ATOM     40 H12 0non 01         10.486   4.000   6.199  0.00  0.00           H 0
+ATOM     41 H13 0non 01          9.618   5.562   6.194  0.00  0.00           H 0
+ATOM     42 H14 0non 01         13.579   7.855  10.503  0.00  0.00           H 0
+ATOM     43 H15 0non 01         14.177   6.344   9.792  0.00  0.00           H 0
+ATOM     44 H16 0non 01         13.271   8.854   8.320  0.00  0.00           H 0
+ATOM     45 H17 0non 01         13.882   7.382   5.000  0.00  0.00           H 0
+ATOM     46 H18 0non 01         13.148   8.762   5.848  0.00  0.00           H 0
+ATOM     47 H19 0non 01         10.418   7.835   8.126  0.00  0.00           H 0
+ATOM     48 H20 0non 01          9.341   7.172   6.873  0.00  0.00           H 0
+ATOM     49 H22 0non 01          7.942   5.204   7.359  0.00  0.00           H 0
+ATOM     50 H24 0non 01         15.735   8.998   5.126  0.00  0.00           H 0
+ATOM     51 H25 0non 01          7.377   7.645   8.311  0.00  0.00           H 0
+ATOM     52 H27 0non 01         15.357   9.154  10.471  0.00  0.00           H 0
+ATOM     53 H28 0non 01         16.458   9.970   9.335  0.00  0.00           H 0
+ATOM     54 H29 0non 01         14.703  10.250   9.231  0.00  0.00           H 0
+ATOM     55 H30 0non 01         16.205   7.217  10.101  0.00  0.00           H 0
+ATOM     56 H31 0non 01         15.745   6.235   8.692  0.00  0.00           H 0
+ATOM     57 H32 0non 01          9.244  10.035   7.970  0.00  0.00           H 0
+ATOM     58 H33 0non 01          8.167   9.373   6.718  0.00  0.00           H 0
+ATOM     59 H34 0non 01         17.803   9.131   6.216  0.00  0.00           H 0
+ATOM     60 H35 0non 01         17.230  10.444   7.284  0.00  0.00           H 0
+ATOM     61 H36 0non 01         18.290   6.773   9.165  0.00  0.00           H 0
+ATOM     62 H37 0non 01         17.665   6.790   7.503  0.00  0.00           H 0
+ATOM     63 H38 0non 01          7.280  10.508   9.409  0.00  0.00           H 0
+ATOM     64 H39 0non 01         17.817   9.283   9.244  0.00  0.00           H 0
+ATOM     65 H41 0non 01          8.070  12.236   7.815  0.00  0.00           H 0
+ATOM     66 H42 0non 01          6.994  11.573   6.563  0.00  0.00           H 0
+ATOM     67 H43 0non 01          5.836   8.669   8.583  0.00  0.00           H 0
+ATOM     68 H44 0non 01          5.000  10.236   8.473  0.00  0.00           H 0
+ATOM     69 H45 0non 01          5.689   9.490   7.011  0.00  0.00           H 0
+ATOM     70 H01 0cho 01          7.288   5.861   8.977  0.00  0.00           H 0
+ATOM     71 H02 0cho 01          8.211   4.148   8.872  0.00  0.00           H 0
+ATOM     72 H03 0cho 01          8.466   8.322   9.665  0.00  0.00           H 0
+ATOM     73 H04 0cho 01          6.226  12.376   8.061  0.00  0.00           H 0
+ATOM     74 H05 0cho 01         20.324   8.821   7.928  0.00  0.00           H 0
+CONECT    1   30   29    2   31                                                 
+CONECT    2    1    4    3    5                                                 
+CONECT    3    2    7   32    6                                                 
+CONECT    4    2    8   33    9                                                 
+CONECT    5    2   34   35   10                                                 
+CONECT    6    3   36   12   11                                                 
+CONECT    7    3    9   37   38                                                 
+CONECT    8    4   14   39   13                                                 
+CONECT    9    4    7   41   40                                                 
+CONECT   10    5   43   11   42                                                 
+CONECT   11    6   10   44   15                                                 
+CONECT   12    6   46   45   16                                                 
+CONECT   13    8   48   17   47                                                 
+CONECT   14    8   49   70   71                                                 
+CONECT   15   11   20   19   18                                                 
+CONECT   16   12   50   19                                                      
+CONECT   17   13   51   21   72                                                 
+CONECT   18   15   54   52   53                                                 
+CONECT   19   15   16   22                                                      
+CONECT   20   15   56   55   23                                                 
+CONECT   21   17   58   24   57                                                 
+CONECT   22   19   59   25   60                                                 
+CONECT   23   20   62   25   61                                                 
+CONECT   24   21   27   63   26                                                 
+CONECT   25   22   23   64   28                                                 
+CONECT   26   24   66   65   73                                                 
+CONECT   27   24   67   69   68                                                 
+CONECT   28   25   74                                                           
+CONECT   29    1                                                                
+CONECT   30    1                                                                
+CONECT   31    1                                                                
+CONECT   32    3                                                                
+CONECT   33    4                                                                
+CONECT   34    5                                                                
+CONECT   35    5                                                                
+CONECT   36    6                                                                
+CONECT   37    7                                                                
+CONECT   38    7                                                                
+CONECT   39    8                                                                
+CONECT   40    9                                                                
+CONECT   41    9                                                                
+CONECT   42   10                                                                
+CONECT   43   10                                                                
+CONECT   44   11                                                                
+CONECT   45   12                                                                
+CONECT   46   12                                                                
+CONECT   47   13                                                                
+CONECT   48   13                                                                
+CONECT   49   14                                                                
+CONECT   50   16                                                                
+CONECT   51   17                                                                
+CONECT   52   18                                                                
+CONECT   53   18                                                                
+CONECT   54   18                                                                
+CONECT   55   20                                                                
+CONECT   56   20                                                                
+CONECT   57   21                                                                
+CONECT   58   21                                                                
+CONECT   59   22                                                                
+CONECT   60   22                                                                
+CONECT   61   23                                                                
+CONECT   62   23                                                                
+CONECT   63   24                                                                
+CONECT   64   25                                                                
+CONECT   65   26                                                                
+CONECT   66   26                                                                
+CONECT   67   27                                                                
+CONECT   68   27                                                                
+CONECT   69   27                                                                
+CONECT   70   14                                                                
+CONECT   71   14                                                                
+CONECT   72   17                                                                
+CONECT   73   26                                                                
+CONECT   74   28                                                                
+END
Index: tests/regression/Atoms/Saturate/post/saturated_water.pdb
===================================================================
--- tests/regression/Atoms/Saturate/post/saturated_water.pdb	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
+++ tests/regression/Atoms/Saturate/post/saturated_water.pdb	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
@@ -0,0 +1,8 @@
+REMARK created by molecuilder on Fri Feb  6 23:34:57 2015, time step 0
+ATOM      1 O01 0non 01          4.494   5.000   5.000  0.00  0.00           O 0
+ATOM      2 H01 0non 01          5.253   5.000   5.504  0.00  0.00           H 0
+ATOM      3 H02 0non 01          5.253   5.000   4.496  0.00  0.00           H 0
+CONECT    1    2    3                                                           
+CONECT    2    1                                                                
+CONECT    3    1                                                                
+END
Index: tests/regression/Atoms/Saturate/post/saturated_water_H1.pdb
===================================================================
--- tests/regression/Atoms/Saturate/post/saturated_water_H1.pdb	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
+++ tests/regression/Atoms/Saturate/post/saturated_water_H1.pdb	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
@@ -0,0 +1,8 @@
+REMARK created by molecuilder on Mon Sep 12 14:44:15 2016, time step 0
+ATOM      1 O01 0non 01          4.494   5.000   5.000  0.00  0.00           O 0
+ATOM      2 H01 0non 01          5.253   5.000   5.504  0.00  0.00           H 0
+ATOM      3 H01 0wat 01          3.755   5.000   4.510  0.00  0.00           H 0
+CONECT    1    2    3                                                           
+CONECT    2    1                                                                
+CONECT    3    1                                                                
+END
Index: tests/regression/Atoms/Saturate/pre/cholesterol.pdb
===================================================================
--- tests/regression/Atoms/Saturate/pre/cholesterol.pdb	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
+++ tests/regression/Atoms/Saturate/pre/cholesterol.pdb	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
@@ -0,0 +1,150 @@
+REMARK created by molecuilder on Mon Sep 12 15:00:29 2016, time step 0
+ATOM      1 C01 0non 01         13.068   4.685   8.414  0.00  0.00           C 0
+ATOM      2 C02 0non 01         11.975   5.754   8.354  0.00  0.00           C 0
+ATOM      3 C03 0non 01         12.194   6.668   7.119  0.00  0.00           C 0
+ATOM      4 C04 0non 01         10.624   5.104   8.072  0.00  0.00           C 0
+ATOM      5 C05 0non 01         12.056   6.648   9.577  0.00  0.00           C 0
+ATOM      6 C06 0non 01         13.650   7.098   7.126  0.00  0.00           C 0
+ATOM      7 C07 0non 01         11.782   5.741   5.969  0.00  0.00           C 0
+ATOM      8 C08 0non 01          9.493   5.960   8.647  0.00  0.00           C 0
+ATOM      9 C09 0non 01         10.514   5.039   6.528  0.00  0.00           C 0
+ATOM     10 C10 0non 01         13.494   7.182   9.650  0.00  0.00           C 0
+ATOM     11 C11 0non 01         13.874   7.948   8.389  0.00  0.00           C 0
+ATOM     12 C12 0non 01         13.914   7.989   5.905  0.00  0.00           C 0
+ATOM     13 C13 0non 01          9.475   7.319   7.945  0.00  0.00           C 0
+ATOM     14 C14 0non 01          8.155   5.253   8.426  0.00  0.00           C 0
+ATOM     15 C15 0non 01         15.345   8.336   8.478  0.00  0.00           C 0
+ATOM     16 C16 0non 01         15.263   8.633   6.025  0.00  0.00           C 0
+ATOM     17 C17 0non 01          8.320   8.161   8.492  0.00  0.00           C 0
+ATOM     18 C18 0non 01         15.475   9.512   9.449  0.00  0.00           C 0
+ATOM     19 C19 0non 01         15.898   8.760   7.144  0.00  0.00           C 0
+ATOM     20 C20 0non 01         16.186   7.179   9.011  0.00  0.00           C 0
+ATOM     21 C21 0non 01          8.301   9.520   7.789  0.00  0.00           C 0
+ATOM     22 C22 0non 01         17.293   9.364   7.151  0.00  0.00           C 0
+ATOM     23 C23 0non 01         17.614   7.279   8.476  0.00  0.00           C 0
+ATOM     24 C24 0non 01          7.146  10.361   8.337  0.00  0.00           C 0
+ATOM     25 C25 0non 01         18.046   8.733   8.331  0.00  0.00           C 0
+ATOM     26 C26 0non 01          7.127  11.720   7.634  0.00  0.00           C 0
+ATOM     27 C27 0non 01          5.823   9.637   8.083  0.00  0.00           C 0
+ATOM     28 O01 0non 01         19.452   8.787   8.082  0.00  0.00           O 0
+ATOM     29 H01 0non 01         12.905   4.048   9.284  0.00  0.00           H 0
+ATOM     30 H02 0non 01         13.033   4.078   7.509  0.00  0.00           H 0
+ATOM     31 H03 0non 01         14.043   5.165   8.492  0.00  0.00           H 0
+ATOM     32 H04 0non 01         11.541   7.539   7.169  0.00  0.00           H 0
+ATOM     33 H05 0non 01         10.591   4.101   8.497  0.00  0.00           H 0
+ATOM     34 H06 0non 01         11.356   7.478   9.479  0.00  0.00           H 0
+ATOM     35 H07 0non 01         11.828   6.072  10.474  0.00  0.00           H 0
+ATOM     36 H08 0non 01         14.307   6.229   7.126  0.00  0.00           H 0
+ATOM     37 H09 0non 01         11.541   6.318   5.076  0.00  0.00           H 0
+ATOM     38 H10 0non 01         12.566   5.014   5.760  0.00  0.00           H 0
+ATOM     39 H11 0non 01          9.656   6.106   9.715  0.00  0.00           H 0
+ATOM     40 H12 0non 01         10.486   4.000   6.199  0.00  0.00           H 0
+ATOM     41 H13 0non 01          9.618   5.562   6.194  0.00  0.00           H 0
+ATOM     42 H14 0non 01         13.579   7.855  10.503  0.00  0.00           H 0
+ATOM     43 H15 0non 01         14.177   6.344   9.792  0.00  0.00           H 0
+ATOM     44 H16 0non 01         13.271   8.854   8.320  0.00  0.00           H 0
+ATOM     45 H17 0non 01         13.882   7.382   5.000  0.00  0.00           H 0
+ATOM     46 H18 0non 01         13.148   8.762   5.848  0.00  0.00           H 0
+ATOM     47 H19 0non 01         10.418   7.835   8.126  0.00  0.00           H 0
+ATOM     48 H20 0non 01          9.341   7.172   6.873  0.00  0.00           H 0
+ATOM     49 H21 0non 01          7.363   5.809   8.930  0.00  0.00           H 0
+ATOM     50 H22 0non 01          7.942   5.204   7.359  0.00  0.00           H 0
+ATOM     51 H23 0non 01          8.206   4.244   8.834  0.00  0.00           H 0
+ATOM     52 H24 0non 01         15.735   8.998   5.126  0.00  0.00           H 0
+ATOM     53 H25 0non 01          7.377   7.645   8.311  0.00  0.00           H 0
+ATOM     54 H26 0non 01          8.454   8.308   9.564  0.00  0.00           H 0
+ATOM     55 H27 0non 01         15.357   9.154  10.471  0.00  0.00           H 0
+ATOM     56 H28 0non 01         16.458   9.970   9.335  0.00  0.00           H 0
+ATOM     57 H29 0non 01         14.703  10.250   9.231  0.00  0.00           H 0
+ATOM     58 H30 0non 01         16.205   7.217  10.101  0.00  0.00           H 0
+ATOM     59 H31 0non 01         15.745   6.235   8.692  0.00  0.00           H 0
+ATOM     60 H32 0non 01          9.244  10.035   7.970  0.00  0.00           H 0
+ATOM     61 H33 0non 01          8.167   9.373   6.718  0.00  0.00           H 0
+ATOM     62 H34 0non 01         17.803   9.131   6.216  0.00  0.00           H 0
+ATOM     63 H35 0non 01         17.230  10.444   7.284  0.00  0.00           H 0
+ATOM     64 H36 0non 01         18.290   6.773   9.165  0.00  0.00           H 0
+ATOM     65 H37 0non 01         17.665   6.790   7.503  0.00  0.00           H 0
+ATOM     66 H38 0non 01          7.280  10.508   9.409  0.00  0.00           H 0
+ATOM     67 H39 0non 01         17.817   9.283   9.244  0.00  0.00           H 0
+ATOM     68 H40 0non 01          6.305  12.319   8.024  0.00  0.00           H 0
+ATOM     69 H41 0non 01          8.070  12.236   7.815  0.00  0.00           H 0
+ATOM     70 H42 0non 01          6.994  11.573   6.563  0.00  0.00           H 0
+ATOM     71 H43 0non 01          5.836   8.669   8.583  0.00  0.00           H 0
+ATOM     72 H44 0non 01          5.000  10.236   8.473  0.00  0.00           H 0
+ATOM     73 H45 0non 01          5.689   9.490   7.011  0.00  0.00           H 0
+ATOM     74 H46 0non 01         19.683   9.721   7.987  0.00  0.00           H 0
+CONECT    1   30   29    2   31                                                 
+CONECT    2    1    4    3    5                                                 
+CONECT    3    2    7   32    6                                                 
+CONECT    4    2    8   33    9                                                 
+CONECT    5    2   34   35   10                                                 
+CONECT    6    3   36   12   11                                                 
+CONECT    7    3    9   37   38                                                 
+CONECT    8    4   14   39   13                                                 
+CONECT    9    4    7   41   40                                                 
+CONECT   10    5   43   11   42                                                 
+CONECT   11    6   10   44   15                                                 
+CONECT   12    6   46   45   16                                                 
+CONECT   13    8   48   17   47                                                 
+CONECT   14    8   51   50   49                                                 
+CONECT   15   11   20   19   18                                                 
+CONECT   16   12   52   19                                                      
+CONECT   17   13   53   21   54                                                 
+CONECT   18   15   57   55   56                                                 
+CONECT   19   15   16   22                                                      
+CONECT   20   15   59   58   23                                                 
+CONECT   21   17   61   24   60                                                 
+CONECT   22   19   62   25   63                                                 
+CONECT   23   20   65   25   64                                                 
+CONECT   24   21   27   66   26                                                 
+CONECT   25   22   23   67   28                                                 
+CONECT   26   24   68   70   69                                                 
+CONECT   27   24   71   73   72                                                 
+CONECT   28   25   74                                                           
+CONECT   29    1                                                                
+CONECT   30    1                                                                
+CONECT   31    1                                                                
+CONECT   32    3                                                                
+CONECT   33    4                                                                
+CONECT   34    5                                                                
+CONECT   35    5                                                                
+CONECT   36    6                                                                
+CONECT   37    7                                                                
+CONECT   38    7                                                                
+CONECT   39    8                                                                
+CONECT   40    9                                                                
+CONECT   41    9                                                                
+CONECT   42   10                                                                
+CONECT   43   10                                                                
+CONECT   44   11                                                                
+CONECT   45   12                                                                
+CONECT   46   12                                                                
+CONECT   47   13                                                                
+CONECT   48   13                                                                
+CONECT   49   14                                                                
+CONECT   50   14                                                                
+CONECT   51   14                                                                
+CONECT   52   16                                                                
+CONECT   53   17                                                                
+CONECT   54   17                                                                
+CONECT   55   18                                                                
+CONECT   56   18                                                                
+CONECT   57   18                                                                
+CONECT   58   20                                                                
+CONECT   59   20                                                                
+CONECT   60   21                                                                
+CONECT   61   21                                                                
+CONECT   62   22                                                                
+CONECT   63   22                                                                
+CONECT   64   23                                                                
+CONECT   65   23                                                                
+CONECT   66   24                                                                
+CONECT   67   25                                                                
+CONECT   68   26                                                                
+CONECT   69   26                                                                
+CONECT   70   26                                                                
+CONECT   71   27                                                                
+CONECT   72   27                                                                
+CONECT   73   27                                                                
+CONECT   74   28                                                                
+END
Index: tests/regression/Atoms/Saturate/pre/water.pdb
===================================================================
--- tests/regression/Atoms/Saturate/pre/water.pdb	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
+++ tests/regression/Atoms/Saturate/pre/water.pdb	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
@@ -0,0 +1,8 @@
+REMARK created by molecuilder on Fri Feb  6 23:34:57 2015, time step 0
+ATOM      1 O01 0non 01          4.494   5.000   5.000  0.00  0.00           O 0
+ATOM      2 H01 0non 01          5.253   5.000   5.504  0.00  0.00           H 0
+ATOM      3 H02 0non 01          5.253   5.000   4.496  0.00  0.00           H 0
+CONECT    1    2    3                                                           
+CONECT    2    1                                                                
+CONECT    3    1                                                                
+END
Index: tests/regression/Atoms/Saturate/testsuite-atoms-saturate-atoms-bonded_atoms.at
===================================================================
--- tests/regression/Atoms/Saturate/testsuite-atoms-saturate-atoms-bonded_atoms.at	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
+++ tests/regression/Atoms/Saturate/testsuite-atoms-saturate-atoms-bonded_atoms.at	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
@@ -0,0 +1,52 @@
+#
+#    MoleCuilder - creates and alters molecular systems
+#    Copyright (C) 2016 Frederik Heber
+#
+#    This program 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 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+### saturate atoms with (partial) bonding
+
+AT_SETUP([Atoms - saturating water molecule])
+AT_KEYWORDS([atoms saturate-atoms])
+# this should not do anything as water is fully saturated
+
+file=saturated_water.pdb
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/Saturate/pre/water.pdb .], 0)
+AT_CHECK([chmod u+w water.pdb], 0)
+AT_CHECK([../../molecuilder -i water.pdb --select-atom-by-element 8 --saturate-atoms --output-as $file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/saturated_water.pdb], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+AT_SETUP([Atoms - saturating partial water molecule])
+AT_KEYWORDS([atoms saturate-atoms])
+
+file=saturated_water_H1.pdb
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/Saturate/pre/water.pdb .], 0)
+AT_CHECK([chmod u+w water.pdb], 0)
+AT_CHECK([../../molecuilder -i water.pdb --select-atom-by-id 2 --remove-atom --select-atom-by-element 8 --saturate-atoms --output-as $file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/saturated_water_H1.pdb], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+AT_SETUP([Atoms - saturating partial cholesterol molecule])
+AT_KEYWORDS([atoms saturate-atoms])
+
+file=saturated_cholesterol.pdb
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Atoms/Saturate/pre/cholesterol.pdb .], 0)
+AT_CHECK([chmod u+w cholesterol.pdb], 0)
+AT_CHECK([../../molecuilder -i cholesterol.pdb --select-atom-by-id 48 50 53 67 73 --remove-atom --select-all-atoms --correct-bonddegree --unselect-atom-by-element 1 --saturate-atoms --output-as $file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/saturated_cholesterol_H48_50_53_67_73.pdb], 0, [ignore], [ignore])
+
+AT_CLEANUP
Index: tests/regression/Atoms/Saturate/testsuite-atoms-saturate-atoms-carbon.at
===================================================================
--- tests/regression/Atoms/Saturate/testsuite-atoms-saturate-atoms-carbon.at	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
+++ tests/regression/Atoms/Saturate/testsuite-atoms-saturate-atoms-carbon.at	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
@@ -0,0 +1,45 @@
+#
+#    MoleCuilder - creates and alters molecular systems
+#    Copyright (C) 2015 Frederik Heber
+#
+#    This program 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 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+### add atom
+
+AT_SETUP([Atoms - saturating carbon])
+AT_KEYWORDS([atoms saturate-atoms])
+
+file=saturated_carbon.xyz
+AT_CHECK([../../molecuilder -a 6 --domain-position "10., 10., 10." --select-all-atoms --saturate-atoms --output-as $file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+AT_SETUP([Atoms - saturating carbon with Undo])
+AT_KEYWORDS([atoms saturate-atoms undo])
+
+file=carbon.xyz
+AT_CHECK([../../molecuilder -a 6 --domain-position "10., 10., 10." --select-all-atoms --saturate-atoms --undo --output-as $file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+AT_SETUP([Atoms - saturating carbon with Redo])
+AT_KEYWORDS([atoms saturate-atoms redo])
+
+file=saturated_carbon.xyz
+AT_CHECK([../../molecuilder -a 6 --domain-position "10., 10., 10." --select-all-atoms --saturate-atoms --undo --redo --output-as $file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/], 0, [ignore], [ignore])
+
+AT_CLEANUP
Index: tests/regression/Atoms/Saturate/testsuite-atoms-saturate-atoms-nitrogen.at
===================================================================
--- tests/regression/Atoms/Saturate/testsuite-atoms-saturate-atoms-nitrogen.at	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
+++ tests/regression/Atoms/Saturate/testsuite-atoms-saturate-atoms-nitrogen.at	(revision c6ddcb49851617a614ac989bfeae41c91886a779)
@@ -0,0 +1,45 @@
+#
+#    MoleCuilder - creates and alters molecular systems
+#    Copyright (C) 2015 Frederik Heber
+#
+#    This program 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 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+### add atom
+
+AT_SETUP([Atoms - saturating nitrogen])
+AT_KEYWORDS([atoms saturate-atoms])
+
+file=saturated_nitrogen.xyz
+AT_CHECK([../../molecuilder -a 7 --domain-position "10., 10., 10." --select-all-atoms --saturate-atoms --output-as $file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+AT_SETUP([Atoms - saturating nitrogen with Undo])
+AT_KEYWORDS([atoms saturate-atoms undo])
+
+file=nitrogen.xyz
+AT_CHECK([../../molecuilder -a 7 --domain-position "10., 10., 10." --select-all-atoms --saturate-atoms --undo --output-as $file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/], 0, [ignore], [ignore])
+
+AT_CLEANUP
+
+AT_SETUP([Atoms - saturating nitrogen with Redo])
+AT_KEYWORDS([atoms saturate-atoms redo])
+
+file=saturated_nitrogen.xyz
+AT_CHECK([../../molecuilder -a 7 --domain-position "10., 10., 10." --select-all-atoms --saturate-atoms --undo --redo --output-as $file], 0, [ignore], [ignore])
+AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/], 0, [ignore], [ignore])
+
+AT_CLEANUP
Index: tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at
===================================================================
--- tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at	(revision 3dadd5a84cf7d86e22653ada5a8baa486b85d081)
+++ 	(revision )
@@ -1,45 +1,0 @@
-#
-#    MoleCuilder - creates and alters molecular systems
-#    Copyright (C) 2015 Frederik Heber
-#
-#    This program 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 3 of the License, or
-#    (at your option) any later version.
-#
-#    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
-#
-### add atom
-
-AT_SETUP([Atoms - saturating carbon])
-AT_KEYWORDS([atoms saturate-atoms])
-
-file=saturated_carbon.xyz
-AT_CHECK([../../molecuilder -a 6 --domain-position "10., 10., 10." --select-all-atoms --saturate-atoms --output-as $file], 0, [ignore], [ignore])
-AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/], 0, [ignore], [ignore])
-
-AT_CLEANUP
-
-AT_SETUP([Atoms - saturating carbon with Undo])
-AT_KEYWORDS([atoms saturate-atoms undo])
-
-file=carbon.xyz
-AT_CHECK([../../molecuilder -a 6 --domain-position "10., 10., 10." --select-all-atoms --saturate-atoms --undo --output-as $file], 0, [ignore], [ignore])
-AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/], 0, [ignore], [ignore])
-
-AT_CLEANUP
-
-AT_SETUP([Atoms - saturating carbon with Redo])
-AT_KEYWORDS([atoms saturate-atoms redo])
-
-file=saturated_carbon.xyz
-AT_CHECK([../../molecuilder -a 6 --domain-position "10., 10., 10." --select-all-atoms --saturate-atoms --undo --redo --output-as $file], 0, [ignore], [ignore])
-AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/], 0, [ignore], [ignore])
-
-AT_CLEANUP
Index: tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at
===================================================================
--- tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at	(revision 3dadd5a84cf7d86e22653ada5a8baa486b85d081)
+++ 	(revision )
@@ -1,45 +1,0 @@
-#
-#    MoleCuilder - creates and alters molecular systems
-#    Copyright (C) 2015 Frederik Heber
-#
-#    This program 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 3 of the License, or
-#    (at your option) any later version.
-#
-#    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
-#
-### add atom
-
-AT_SETUP([Atoms - saturating nitrogen])
-AT_KEYWORDS([atoms saturate-atoms])
-
-file=saturated_nitrogen.xyz
-AT_CHECK([../../molecuilder -a 7 --domain-position "10., 10., 10." --select-all-atoms --saturate-atoms --output-as $file], 0, [ignore], [ignore])
-AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/], 0, [ignore], [ignore])
-
-AT_CLEANUP
-
-AT_SETUP([Atoms - saturating nitrogen with Undo])
-AT_KEYWORDS([atoms saturate-atoms undo])
-
-file=nitrogen.xyz
-AT_CHECK([../../molecuilder -a 7 --domain-position "10., 10., 10." --select-all-atoms --saturate-atoms --undo --output-as $file], 0, [ignore], [ignore])
-AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/], 0, [ignore], [ignore])
-
-AT_CLEANUP
-
-AT_SETUP([Atoms - saturating nitrogen with Redo])
-AT_KEYWORDS([atoms saturate-atoms redo])
-
-file=saturated_nitrogen.xyz
-AT_CHECK([../../molecuilder -a 7 --domain-position "10., 10., 10." --select-all-atoms --saturate-atoms --undo --redo --output-as $file], 0, [ignore], [ignore])
-AT_CHECK([diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/tests/regression/Atoms/Saturate/post/], 0, [ignore], [ignore])
-
-AT_CLEANUP
