changeset 8:a84187d7bda6 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
author bgruening
date Fri, 10 May 2019 08:04:18 -0400
parents 9c15e92bed39
children f924a1728291
files test-data/ob_prepare_ligands.sdf test-data/ob_prepare_ligands1.mol2 test-data/ob_prepare_ligands1.pdbqt test-data/ob_prepare_ligands2.mol2 test-data/ob_prepare_ligands2.pdbqt
diffstat 5 files changed, 1122 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ob_prepare_ligands.sdf	Fri May 10 08:04:18 2019 -0400
@@ -0,0 +1,759 @@
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+   -1.3039    3.7494    0.0000 C   0  0
+   -1.3092    5.2494    0.0000 C   0  0
+   -2.6108    5.9949    0.0000 C   0  0
+   -3.9073    5.2404    0.0000 C   0  0
+   -5.2112    5.9836    0.0000 N   0  0
+   -6.5072    5.2269    0.0000 C   0  0
+   -6.5010    4.0269    0.0000 O   0  0
+   -7.8111    5.9701    0.0000 N   0  0
+   -9.1072    5.2134    0.0000 C   0  0
+  -10.4114    5.9543    0.0000 C   0  0
+  -11.7053    5.1953    0.0000 C   0  0
+  -11.6949    3.6953    0.0000 C   0  0
+  -12.7299    3.0882    0.0000 Cl  0  0
+  -10.3907    2.9543    0.0000 C   0  0
+   -9.0969    3.7133    0.0000 C   0  0
+  -10.3803    1.4536    0.0000 C   0  0
+  -11.4150    0.8457    0.0000 F   0  0
+   -9.3367    0.8611    0.0000 F   0  0
+  -10.3714    0.2536    0.0000 F   0  0
+   -3.9021    3.7404    0.0000 C   0  0
+   -2.6005    2.9949    0.0000 C   0  0
+   -1.2990    0.7500    0.0000 C   0  0
+   -1.2990   -0.7500    0.0000 C   0  0
+    0.0000   -1.5000    0.0000 N   0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  2  0
+  3  5  1  0
+  5  6  1  0
+  6  7  2  0
+  7  8  1  0
+  8  9  1  0
+  9 10  1  0
+ 10 11  2  0
+ 11 12  1  0
+ 12 13  1  0
+ 13 14  1  0
+ 14 15  2  0
+ 14 16  1  0
+ 16 17  1  0
+ 17 18  1  0
+ 18 19  2  0
+ 19 20  1  0
+ 20 21  1  0
+ 20 22  2  0
+ 22 23  1  0
+ 17 23  2  0
+ 22 24  1  0
+ 24 25  1  0
+ 24 26  1  0
+ 24 27  1  0
+ 12 28  2  0
+ 28 29  1  0
+  9 29  2  0
+  7 30  1  0
+ 30 31  2  0
+ 31 32  1  0
+  5 32  2  0
+M  END
+> <mr_id>
+4255941
+
+> <SMI>
+CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3ccc(Cl)c(c3)C(F)(F)F)cc2)ccn1
+
+$$$$
+
+  SciTegic01171120562D
+
+ 35 42  0  0  1  0            999 V2000
+   -1.9455    5.8387    0.0000 C   0  0
+   -2.5513    4.8029    0.0000 N   0  0
+   -1.8100    3.5000    0.0000 C   0  0  2  0  0  0
+   -0.2400    3.5200    0.0000 C   0  0
+    0.5000    2.1800    0.0000 C   0  0  1  0  0  0
+   -1.0600    2.1800    0.0000 O   0  0
+   -1.8300    0.9300    0.0000 C   0  0  1  0  0  0
+   -3.0300    0.9300    0.0000 C   0  0
+   -2.6500    2.2500    0.0000 C   0  0  2  0  0  0
+   -4.1471    2.2892    0.0000 O   0  0
+   -4.7748    1.2665    0.0000 C   0  0
+   -0.9800   -0.7800    0.0000 N   0  0
+   -2.1300   -1.4600    0.0000 C   0  0
+   -3.3200   -0.7600    0.0000 C   0  0
+   -4.5500   -1.4800    0.0000 C   0  0
+   -4.5800   -2.7700    0.0000 C   0  0
+   -3.3400   -3.4700    0.0000 C   0  0
+   -2.1300   -2.7900    0.0000 C   0  0
+    0.2400   -2.7700    0.0000 C   0  0
+    1.4300   -3.4700    0.0000 C   0  0
+    1.7600   -4.9700    0.0000 C   0  0
+    3.2600   -5.0800    0.0000 N   0  0
+    3.8500   -3.6300    0.0000 C   0  0
+    4.9971   -3.2777    0.0000 O   0  0
+    2.6600   -2.7500    0.0000 C   0  0
+    2.6800   -1.4600    0.0000 C   0  0
+    3.7900    0.5600    0.0000 C   0  0
+    4.9600    1.2800    0.0000 C   0  0
+    4.9600    2.6300    0.0000 C   0  0
+    3.8100    3.2900    0.0000 C   0  0
+    2.6400    2.5900    0.0000 C   0  0
+    2.6400    1.2400    0.0000 C   0  0
+    1.4900    0.5400    0.0000 N   0  0
+    1.4500   -0.7600    0.0000 C   0  0
+    0.2400   -1.4400    0.0000 C   0  0
+  1  2  1  0
+  3  2  1  6
+  3  4  1  0
+  5  4  1  6
+  5  6  1  0
+  6  7  1  0
+  7  8  1  1
+  7  9  1  0
+  3  9  1  0
+  9 10  1  6
+ 10 11  1  0
+  7 12  1  0
+ 12 13  1  0
+ 13 14  1  0
+ 14 15  2  0
+ 15 16  1  0
+ 16 17  2  0
+ 17 18  1  0
+ 13 18  2  0
+ 18 19  1  0
+ 19 20  1  0
+ 20 21  1  0
+ 21 22  1  0
+ 22 23  1  0
+ 23 24  2  0
+ 23 25  1  0
+ 20 25  2  0
+ 25 26  1  0
+ 26 27  1  0
+ 27 28  1  0
+ 28 29  2  0
+ 29 30  1  0
+ 30 31  2  0
+ 31 32  1  0
+ 27 32  2  0
+ 32 33  1  0
+  5 33  1  0
+ 33 34  1  0
+ 26 34  2  0
+ 34 35  1  0
+ 12 35  1  0
+ 19 35  2  0
+M  END
+> <mr_id>
+66
+
+> <SMI>
+CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35
+
+$$$$
+
+  SciTegic01171120562D
+
+ 32 35  0  0  1  0            999 V2000
+    7.1381   -2.1568    0.0000 C   0  0
+    6.0456   -2.6531    0.0000 C   0  0
+    4.7409   -1.9129    0.0000 N   0  0
+    3.6552   -2.9294    0.0000 C   0  0
+    2.1855   -2.6254    0.0000 C   0  0
+    1.7138   -1.2033    0.0000 C   0  0
+    2.5889    0.0182    0.0000 C   0  0
+    3.7889    0.0269    0.0000 O   0  0
+    1.7138    1.2033    0.0000 N   0  0
+    0.2917    0.7475    0.0000 C   0  0
+   -1.0028    1.5132    0.0000 C   0  0
+   -2.3155    0.7475    0.0000 C   0  0
+   -2.3155   -0.7475    0.0000 C   0  0
+   -3.3560   -1.3452    0.0000 F   0  0
+   -1.0028   -1.5132    0.0000 C   0  0
+    0.2917   -0.7475    0.0000 C   0  0
+    4.2542   -4.2907    0.0000 C   0  0
+    3.6559   -5.3308    0.0000 C   0  0
+    5.7448   -4.1226    0.0000 C   0  0
+    6.7580   -5.2264    0.0000 C   0  0
+    6.3978   -6.3710    0.0000 O   0  0
+    8.2231   -4.9012    0.0000 N   0  0
+    9.2380   -6.0068    0.0000 C   0  0
+   10.7032   -5.6816    0.0000 C   0  0  2  0  0  0
+   11.0634   -4.5369    0.0000 O   0  0
+   11.7181   -6.7872    0.0000 C   0  0
+   13.1833   -6.4620    0.0000 N   0  0
+   14.1993   -7.5656    0.0000 C   0  0
+   15.6630   -7.2376    0.0000 C   0  0
+   16.1108   -5.8060    0.0000 O   0  0
+   15.0949   -4.7024    0.0000 C   0  0
+   13.6312   -5.0304    0.0000 C   0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  1  0
+  4  5  1  0
+  5  6  2  0
+  6  7  1  0
+  7  8  2  0
+  7  9  1  0
+  9 10  1  0
+ 10 11  1  0
+ 11 12  2  0
+ 12 13  1  0
+ 13 14  1  0
+ 13 15  2  0
+ 15 16  1  0
+  6 16  1  0
+ 10 16  2  0
+  4 17  2  0
+ 17 18  1  0
+ 17 19  1  0
+  2 19  2  0
+ 19 20  1  0
+ 20 21  2  0
+ 20 22  1  0
+ 22 23  1  0
+ 23 24  1  0
+ 24 25  1  6
+ 24 26  1  0
+ 26 27  1  0
+ 27 28  1  0
+ 28 29  1  0
+ 29 30  1  0
+ 30 31  1  0
+ 31 32  1  0
+ 27 32  1  0
+M  END
+> <mr_id>
+4362206
+
+> <SMI>
+Cc1[nH]c(/C=C/2\C(=O)Nc3ccc(F)cc23)c(C)c1C(=O)NC[C@H](O)CN4CCOCC4
+
+$$$$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ob_prepare_ligands1.mol2	Fri May 10 08:04:18 2019 -0400
@@ -0,0 +1,96 @@
+@<TRIPOS>MOLECULE
+*****
+ 42 46 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1 O          -8.6396    0.9568    0.0000 O.3     1  UNL1       -0.5067
+      2 C          -7.6023    1.5602    0.0000 C.ar    1  UNL1        0.1175
+      3 C          -7.6071    3.0602    0.0000 C.ar    1  UNL1       -0.0201
+      4 C          -6.3104    3.8143    0.0000 C.ar    1  UNL1       -0.0576
+      5 C          -5.0090    3.0685    0.0000 C.ar    1  UNL1       -0.0508
+      6 C          -5.0040    1.5682    0.0000 C.ar    1  UNL1        0.0226
+      7 C          -6.3008    0.8143    0.0000 C.ar    1  UNL1       -0.0095
+      8 C          -3.7006    0.8244    0.0000 C.ar    1  UNL1        0.1627
+      9 N          -3.7006   -0.6045    0.0000 N.ar    1  UNL1       -0.2088
+     10 C          -2.4915   -1.3190    0.0000 C.ar    1  UNL1        0.1687
+     11 N          -2.5059   -2.8197    0.0000 N.pl3   1  UNL1       -0.3078
+     12 C          -1.2156   -3.5847    0.0000 C.3     1  UNL1        0.0371
+     13 C          -1.2329   -5.0846    0.0000 C.3     1  UNL1        0.0634
+     14 O          -2.5404   -5.8196    0.0000 O.3     1  UNL1       -0.3767
+     15 C          -3.8308   -5.0547    0.0000 C.3     1  UNL1        0.0634
+     16 C          -3.8135   -3.5548    0.0000 C.3     1  UNL1        0.0371
+     17 C          -1.2274   -0.6045    0.0000 C.ar    1  UNL1        0.1961
+     18 O           0.0000   -1.3190    0.0000 O.2     1  UNL1       -0.4317
+     19 C           1.2274   -0.6045    0.0000 C.ar    1  UNL1        0.2301
+     20 N           2.4732   -1.3190    0.0000 N.ar    1  UNL1       -0.2204
+     21 C           3.7372   -0.6045    0.0000 C.ar    1  UNL1        0.0314
+     22 C           3.7372    0.8244    0.0000 C.ar    1  UNL1       -0.0427
+     23 C           2.4732    1.5389    0.0000 C.ar    1  UNL1       -0.0459
+     24 C           1.2274    0.8244    0.0000 C.ar    1  UNL1        0.0660
+     25 C          -1.2274    0.8244    0.0000 C.ar    1  UNL1        0.1241
+     26 N          -2.4915    1.5389    0.0000 N.ar    1  UNL1       -0.2233
+     27 H          -9.4526    1.4227    0.0000 H       1  UNL1        0.2921
+     28 H          -8.5025    3.5734    0.0000 H       1  UNL1        0.0654
+     29 H          -6.3137    4.8463    0.0000 H       1  UNL1        0.0619
+     30 H          -4.1170    3.5874    0.0000 H       1  UNL1        0.0625
+     31 H          -6.2976   -0.2177    0.0000 H       1  UNL1        0.0661
+     32 H          -0.2828   -3.0604    0.0000 H       1  UNL1        0.0487
+     33 H          -0.2952   -4.1304    0.0000 H       1  UNL1        0.0487
+     34 H          -0.3125   -5.6302    0.0000 H       1  UNL1        0.0575
+     35 H          -1.2452   -6.1545    0.0000 H       1  UNL1        0.0575
+     36 H          -4.7635   -5.5790    0.0000 H       1  UNL1        0.0575
+     37 H          -4.7512   -4.5091    0.0000 H       1  UNL1        0.0575
+     38 H          -4.7339   -3.0092    0.0000 H       1  UNL1        0.0487
+     39 H          -3.8012   -2.4849    0.0000 H       1  UNL1        0.0487
+     40 H           4.6286   -1.1246    0.0000 H       1  UNL1        0.0831
+     41 H           4.6286    1.3445    0.0000 H       1  UNL1        0.0633
+     42 H           2.4700    2.5709    0.0000 H       1  UNL1        0.0626
+@<TRIPOS>BOND
+     1     1     2    1
+     2     2     3   ar
+     3     3     4   ar
+     4     4     5   ar
+     5     5     6   ar
+     6     6     7   ar
+     7     2     7   ar
+     8     6     8    1
+     9     8     9   ar
+    10     9    10   ar
+    11    10    11    1
+    12    11    12    1
+    13    12    13    1
+    14    13    14    1
+    15    14    15    1
+    16    15    16    1
+    17    11    16    1
+    18    10    17   ar
+    19    17    18   ar
+    20    18    19   ar
+    21    19    20   ar
+    22    20    21   ar
+    23    21    22   ar
+    24    22    23   ar
+    25    23    24   ar
+    26    19    24   ar
+    27    24    25   ar
+    28    17    25   ar
+    29    25    26   ar
+    30     8    26   ar
+    31     1    27    1
+    32     3    28    1
+    33     4    29    1
+    34     5    30    1
+    35     7    31    1
+    36    12    32    1
+    37    12    33    1
+    38    13    34    1
+    39    13    35    1
+    40    15    36    1
+    41    15    37    1
+    42    16    38    1
+    43    16    39    1
+    44    21    40    1
+    45    22    41    1
+    46    23    42    1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ob_prepare_ligands1.pdbqt	Fri May 10 08:04:18 2019 -0400
@@ -0,0 +1,41 @@
+REMARK  Name = 
+REMARK  2 active torsions:
+REMARK  status: ('A' for Active; 'I' for Inactive)
+REMARK    1  A    between atoms: O_1  and  C_2
+REMARK    2  A    between atoms: C_6  and  C_8
+REMARK                            x       y       z     vdW  Elec       q    Type
+REMARK                         _______ _______ _______ _____ _____    ______ ____
+ROOT
+ATOM      1  C   UNL     1      -3.701   0.824   0.000  0.00  0.00    +0.163 A 
+ATOM      2  N   UNL     1      -2.491   1.539   0.000  0.00  0.00    -0.223 NA
+ATOM      3  C   UNL     1      -1.227   0.824   0.000  0.00  0.00    +0.124 A 
+ATOM      4  C   UNL     1      -1.227  -0.605   0.000  0.00  0.00    +0.196 A 
+ATOM      5  O   UNL     1       0.000  -1.319   0.000  0.00  0.00    -0.432 OA
+ATOM      6  C   UNL     1       1.227  -0.605   0.000  0.00  0.00    +0.230 A 
+ATOM      7  N   UNL     1       2.473  -1.319   0.000  0.00  0.00    -0.220 NA
+ATOM      8  C   UNL     1       3.737  -0.605   0.000  0.00  0.00    +0.114 A 
+ATOM      9  C   UNL     1       3.737   0.824   0.000  0.00  0.00    +0.021 A 
+ATOM     10  C   UNL     1       2.473   1.539   0.000  0.00  0.00    +0.017 A 
+ATOM     11  C   UNL     1      -2.491  -1.319   0.000  0.00  0.00    +0.169 A 
+ATOM     12  N   UNL     1      -2.506  -2.820   0.000  0.00  0.00    -0.308 N 
+ATOM     13  C   UNL     1      -3.813  -3.555   0.000  0.00  0.00    +0.134 C 
+ATOM     14  C   UNL     1      -3.831  -5.055   0.000  0.00  0.00    +0.178 C 
+ATOM     15  O   UNL     1      -2.540  -5.820   0.000  0.00  0.00    -0.377 OA
+ATOM     16  C   UNL     1      -1.233  -5.085   0.000  0.00  0.00    +0.178 C 
+ATOM     17  C   UNL     1      -1.216  -3.585   0.000  0.00  0.00    +0.134 C 
+ATOM     18  C   UNL     1       1.227   0.824   0.000  0.00  0.00    +0.066 A 
+ATOM     19  N   UNL     1      -3.701  -0.605   0.000  0.00  0.00    -0.209 NA
+ENDROOT
+BRANCH   1  22
+ATOM     20  C   UNL     1      -7.602   1.560   0.000  0.00  0.00    +0.118 A 
+ATOM     21  C   UNL     1      -6.301   0.814   0.000  0.00  0.00    +0.057 A 
+ATOM     22  C   UNL     1      -5.004   1.568   0.000  0.00  0.00    +0.023 A 
+ATOM     23  C   UNL     1      -5.009   3.068   0.000  0.00  0.00    +0.012 A 
+ATOM     24  C   UNL     1      -6.310   3.814   0.000  0.00  0.00    +0.004 A 
+ATOM     25  C   UNL     1      -7.607   3.060   0.000  0.00  0.00    +0.045 A 
+BRANCH  20  26
+ATOM     26  O   UNL     1      -8.640   0.957   0.000  0.00  0.00    -0.507 OA
+ATOM     27  H   UNL     1      -9.453   1.423   0.000  0.00  0.00    +0.292 HD
+ENDBRANCH  20  26
+ENDBRANCH   1  22
+TORSDOF 2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ob_prepare_ligands2.mol2	Fri May 10 08:04:18 2019 -0400
@@ -0,0 +1,162 @@
+@<TRIPOS>MOLECULE
+*****
+ 73 81 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1 C          -4.7204    3.3431    0.0000 C.3     1  UNL1        0.0371
+      2 O          -4.1471    2.2890    0.0000 O.3     1  UNL1       -0.3732
+      3 C          -2.6500    2.2500    0.0000 C.3     1  UNL1        0.1246
+      4 C          -1.8100    3.5000    0.0000 C.3     1  UNL1        0.0607
+      5 C          -0.2400    3.5200    0.0000 C.3     1  UNL1        0.0140
+      6 C           0.5000    2.1800    0.0000 C.3     1  UNL1        0.1404
+      7 O          -1.0600    2.1800    0.0000 O.3     1  UNL1       -0.3282
+      8 C          -1.8300    0.9300    0.0000 C.3     1  UNL1        0.1744
+      9 C          -3.0300    0.9300    0.0000 C.3     1  UNL1       -0.0136
+     10 N          -0.9800   -0.7800    0.0000 N.ar    1  UNL1       -0.3070
+     11 C          -2.1300   -1.4600    0.0000 C.ar    1  UNL1        0.0527
+     12 C          -3.3200   -0.7600    0.0000 C.ar    1  UNL1       -0.0375
+     13 C          -4.5500   -1.4800    0.0000 C.ar    1  UNL1       -0.0598
+     14 C          -4.5800   -2.7700    0.0000 C.ar    1  UNL1       -0.0611
+     15 C          -3.3400   -3.4700    0.0000 C.ar    1  UNL1       -0.0520
+     16 C          -2.1300   -2.7900    0.0000 C.ar    1  UNL1        0.0081
+     17 C           0.2400   -2.7700    0.0000 C.ar    1  UNL1        0.0151
+     18 C           1.4300   -3.4700    0.0000 C.ar    1  UNL1       -0.0078
+     19 C           1.7600   -4.9700    0.0000 C.3     1  UNL1        0.0385
+     20 N           3.2600   -5.0800    0.0000 N.am    1  UNL1       -0.3072
+     21 C           3.8500   -3.6300    0.0000 C.2     1  UNL1        0.2453
+     22 O           4.9971   -3.2777    0.0000 O.2     1  UNL1       -0.2702
+     23 C           2.6600   -2.7500    0.0000 C.ar    1  UNL1        0.0518
+     24 C           2.6800   -1.4600    0.0000 C.ar    1  UNL1        0.0221
+     25 C           3.7900    0.5600    0.0000 C.ar    1  UNL1        0.0085
+     26 C           4.9600    1.2800    0.0000 C.ar    1  UNL1       -0.0520
+     27 C           4.9600    2.6300    0.0000 C.ar    1  UNL1       -0.0611
+     28 C           3.8100    3.2900    0.0000 C.ar    1  UNL1       -0.0598
+     29 C           2.6400    2.5900    0.0000 C.ar    1  UNL1       -0.0375
+     30 C           2.6400    1.2400    0.0000 C.ar    1  UNL1        0.0524
+     31 N           1.4900    0.5400    0.0000 N.ar    1  UNL1       -0.3115
+     32 C           1.4500   -0.7600    0.0000 C.ar    1  UNL1        0.0774
+     33 C           0.2400   -1.4400    0.0000 C.ar    1  UNL1        0.0772
+     34 N          -2.5511    4.8030    0.0000 N.am    1  UNL1       -0.2947
+     35 C          -1.9442    5.8382    0.0000 C.3     1  UNL1        0.0039
+     36 C          -4.0519    4.8135    0.0000 C.2     1  UNL1        0.2467
+     37 O          -4.6588    3.7783    0.0000 O.2     1  UNL1       -0.2700
+     38 C          -4.7941    6.1180    0.0000 C.ar    1  UNL1        0.0369
+     39 C          -6.2940    6.1306    0.0000 C.ar    1  UNL1       -0.0496
+     40 C          -7.0331    7.4359    0.0000 C.ar    1  UNL1       -0.0610
+     41 C          -6.2722    8.7286    0.0000 C.ar    1  UNL1       -0.0617
+     42 C          -4.7723    8.7160    0.0000 C.ar    1  UNL1       -0.0610
+     43 C          -4.0332    7.4108    0.0000 C.ar    1  UNL1       -0.0496
+     44 H          -4.1620    4.2558    0.0000 H       1  UNL1        0.0524
+     45 H          -5.7901    3.3703    0.0000 H       1  UNL1        0.0524
+     46 H          -5.2316    4.2831    0.0000 H       1  UNL1        0.0524
+     47 H          -3.1408    3.2008    0.0000 H       1  UNL1        0.0663
+     48 H          -2.8793    3.5399    0.0000 H       1  UNL1        0.0529
+     49 H           0.2979    4.4450    0.0000 H       1  UNL1        0.0328
+     50 H           0.8299    3.5081    0.0000 H       1  UNL1        0.0328
+     51 H          -0.4215    2.7238    0.0000 H       1  UNL1        0.0839
+     52 H          -3.5650    1.8566    0.0000 H       1  UNL1        0.0277
+     53 H          -3.5650    0.0034    0.0000 H       1  UNL1        0.0277
+     54 H          -4.1000    0.9300    0.0000 H       1  UNL1        0.0277
+     55 H          -3.3189    0.2720    0.0000 H       1  UNL1        0.0638
+     56 H          -5.4393   -0.9563    0.0000 H       1  UNL1        0.0618
+     57 H          -5.4772   -3.2799    0.0000 H       1  UNL1        0.0618
+     58 H          -3.3410   -4.5020    0.0000 H       1  UNL1        0.0624
+     59 H           1.0595   -5.7788    0.0000 H       1  UNL1        0.0512
+     60 H           2.1687   -5.9589    0.0000 H       1  UNL1        0.0512
+     61 H           3.7793   -5.9164    0.0000 H       1  UNL1        0.1493
+     62 H           5.8609    0.7766    0.0000 H       1  UNL1        0.0624
+     63 H           5.8531    3.1472    0.0000 H       1  UNL1        0.0618
+     64 H           3.8006    4.3220    0.0000 H       1  UNL1        0.0618
+     65 H           1.7423    3.0990    0.0000 H       1  UNL1        0.0638
+     66 H          -0.8742    5.8311    0.0000 H       1  UNL1        0.0429
+     67 H          -2.4730    6.7684    0.0000 H       1  UNL1        0.0429
+     68 H          -1.4030    6.7613    0.0000 H       1  UNL1        0.0429
+     69 H          -6.8175    5.2412    0.0000 H       1  UNL1        0.0625
+     70 H          -8.0651    7.4446    0.0000 H       1  UNL1        0.0618
+     71 H          -6.7807    9.6266    0.0000 H       1  UNL1        0.0618
+     72 H          -4.2488    9.6054    0.0000 H       1  UNL1        0.0618
+     73 H          -3.0012    7.4022    0.0000 H       1  UNL1        0.0625
+@<TRIPOS>BOND
+     1     1     2    1
+     2     3     2    1
+     3     3     4    1
+     4     4     5    1
+     5     6     5    1
+     6     6     7    1
+     7     7     8    1
+     8     3     8    1
+     9     8     9    1
+    10     8    10    1
+    11    10    11   ar
+    12    11    12   ar
+    13    12    13   ar
+    14    13    14   ar
+    15    14    15   ar
+    16    15    16   ar
+    17    11    16   ar
+    18    16    17   ar
+    19    17    18   ar
+    20    18    19    1
+    21    19    20    1
+    22    20    21   am
+    23    21    22    2
+    24    21    23    1
+    25    18    23   ar
+    26    23    24   ar
+    27    24    25   ar
+    28    25    26   ar
+    29    26    27   ar
+    30    27    28   ar
+    31    28    29   ar
+    32    29    30   ar
+    33    25    30   ar
+    34    30    31   ar
+    35     6    31    1
+    36    31    32   ar
+    37    24    32   ar
+    38    32    33   ar
+    39    10    33   ar
+    40    17    33   ar
+    41     4    34    1
+    42    34    35    1
+    43    34    36   am
+    44    36    37    2
+    45    36    38    1
+    46    38    39   ar
+    47    39    40   ar
+    48    40    41   ar
+    49    41    42   ar
+    50    42    43   ar
+    51    38    43   ar
+    52     1    44    1
+    53     1    45    1
+    54     1    46    1
+    55     3    47    1
+    56     4    48    1
+    57     5    49    1
+    58     5    50    1
+    59     6    51    1
+    60     9    52    1
+    61     9    53    1
+    62     9    54    1
+    63    12    55    1
+    64    13    56    1
+    65    14    57    1
+    66    15    58    1
+    67    19    59    1
+    68    19    60    1
+    69    20    61    1
+    70    26    62    1
+    71    27    63    1
+    72    28    64    1
+    73    29    65    1
+    74    35    66    1
+    75    35    67    1
+    76    35    68    1
+    77    39    69    1
+    78    40    70    1
+    79    41    71    1
+    80    42    72    1
+    81    43    73    1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ob_prepare_ligands2.pdbqt	Fri May 10 08:04:18 2019 -0400
@@ -0,0 +1,64 @@
+REMARK  Name = 
+REMARK  6 active torsions:
+REMARK  status: ('A' for Active; 'I' for Inactive)
+REMARK    1  A    between atoms: C_1  and  O_2
+REMARK    2  A    between atoms: O_2  and  C_3
+REMARK    3  A    between atoms: C_4  and  N_34
+REMARK    4  A    between atoms: C_8  and  C_9
+REMARK    5  A    between atoms: N_34  and  C_35
+REMARK    6  A    between atoms: C_36  and  C_38
+REMARK                            x       y       z     vdW  Elec       q    Type
+REMARK                         _______ _______ _______ _____ _____    ______ ____
+ROOT
+ATOM      1  C   UNL     1      -2.650   2.250   0.000  0.00  0.00    +0.191 C 
+ATOM      2  C   UNL     1      -1.830   0.930   0.000  0.00  0.00    +0.174 C 
+ATOM      3  N   UNL     1      -0.980  -0.780   0.000  0.00  0.00    -0.307 N 
+ATOM      4  C   UNL     1       0.240  -1.440   0.000  0.00  0.00    +0.077 A 
+ATOM      5  C   UNL     1       0.240  -2.770   0.000  0.00  0.00    +0.015 A 
+ATOM      6  C   UNL     1       1.430  -3.470   0.000  0.00  0.00    -0.008 A 
+ATOM      7  C   UNL     1       2.660  -2.750   0.000  0.00  0.00    +0.052 A 
+ATOM      8  C   UNL     1       2.680  -1.460   0.000  0.00  0.00    +0.022 A 
+ATOM      9  C   UNL     1       3.790   0.560   0.000  0.00  0.00    +0.008 A 
+ATOM     10  C   UNL     1       2.640   1.240   0.000  0.00  0.00    +0.052 A 
+ATOM     11  N   UNL     1       1.490   0.540   0.000  0.00  0.00    -0.311 N 
+ATOM     12  C   UNL     1       0.500   2.180   0.000  0.00  0.00    +0.224 C 
+ATOM     13  C   UNL     1      -0.240   3.520   0.000  0.00  0.00    +0.080 C 
+ATOM     14  C   UNL     1       2.640   2.590   0.000  0.00  0.00    +0.026 A 
+ATOM     15  C   UNL     1       3.810   3.290   0.000  0.00  0.00    +0.002 A 
+ATOM     16  C   UNL     1       4.960   2.630   0.000  0.00  0.00    +0.001 A 
+ATOM     17  C   UNL     1       4.960   1.280   0.000  0.00  0.00    +0.010 A 
+ATOM     18  C   UNL     1       3.850  -3.630   0.000  0.00  0.00    +0.245 C 
+ATOM     19  O   UNL     1       4.997  -3.278   0.000  0.00  0.00    -0.270 OA
+ATOM     20  N   UNL     1       3.260  -5.080   0.000  0.00  0.00    -0.307 N 
+ATOM     21  H   UNL     1       3.779  -5.916   0.000  0.00  0.00    +0.149 HD
+ATOM     22  C   UNL     1       1.760  -4.970   0.000  0.00  0.00    +0.141 C 
+ATOM     23  C   UNL     1      -2.130  -2.790   0.000  0.00  0.00    +0.008 A 
+ATOM     24  C   UNL     1      -3.340  -3.470   0.000  0.00  0.00    +0.010 A 
+ATOM     25  C   UNL     1      -4.580  -2.770   0.000  0.00  0.00    +0.001 A 
+ATOM     26  C   UNL     1      -4.550  -1.480   0.000  0.00  0.00    +0.002 A 
+ATOM     27  C   UNL     1      -3.320  -0.760   0.000  0.00  0.00    +0.026 A 
+ATOM     28  C   UNL     1       1.450  -0.760   0.000  0.00  0.00    +0.077 A 
+ATOM     29  C   UNL     1      -2.130  -1.460   0.000  0.00  0.00    +0.053 A 
+ATOM     30  C   UNL     1      -3.030   0.930   0.000  0.00  0.00    +0.069 C 
+ATOM     31  O   UNL     1      -1.060   2.180   0.000  0.00  0.00    -0.328 OA
+ATOM     32  C   UNL     1      -1.810   3.500   0.000  0.00  0.00    +0.114 C 
+ENDROOT
+BRANCH  32  33
+ATOM     33  N   UNL     1      -2.551   4.803   0.000  0.00  0.00    -0.295 N 
+ATOM     34  C   UNL     1      -4.052   4.814   0.000  0.00  0.00    +0.247 C 
+ATOM     35  O   UNL     1      -4.659   3.778   0.000  0.00  0.00    -0.270 OA
+ATOM     36  C   UNL     1      -1.944   5.838   0.000  0.00  0.00    +0.132 C 
+BRANCH  34  37
+ATOM     37  C   UNL     1      -4.794   6.118   0.000  0.00  0.00    +0.037 A 
+ATOM     38  C   UNL     1      -4.033   7.411   0.000  0.00  0.00    +0.013 A 
+ATOM     39  C   UNL     1      -4.772   8.716   0.000  0.00  0.00    +0.001 A 
+ATOM     40  C   UNL     1      -6.272   8.729   0.000  0.00  0.00    +0.000 A 
+ATOM     41  C   UNL     1      -7.033   7.436   0.000  0.00  0.00    +0.001 A 
+ATOM     42  C   UNL     1      -6.294   6.131   0.000  0.00  0.00    +0.013 A 
+ENDBRANCH  34  37
+ENDBRANCH  32  33
+BRANCH   1  44
+ATOM     43  C   UNL     1      -4.720   3.343   0.000  0.00  0.00    +0.194 C 
+ATOM     44  O   UNL     1      -4.147   2.289   0.000  0.00  0.00    -0.373 OA
+ENDBRANCH   1  44
+TORSDOF 3