changeset 10:eed751918a20 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
author bgruening
date Sat, 21 Mar 2020 10:26:59 -0400
parents f924a1728291
children 49d21d05f77c
files __pycache__/cheminfolib.cpython-36.pyc change_title_to_metadata_value.py change_title_to_metadata_value.xml ob_filter.py test-data/filterd_by_name.sdf test-data/ligands_with_title.sdf test-data/name_file.txt test-data/transfs.sdf test-data/transfs_changed_name.sdf
diffstat 9 files changed, 1317 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
Binary file __pycache__/cheminfolib.cpython-36.pyc has changed
--- a/change_title_to_metadata_value.py	Thu Aug 22 10:28:24 2019 -0400
+++ b/change_title_to_metadata_value.py	Sat Mar 21 10:26:59 2020 -0400
@@ -12,6 +12,8 @@
 import openbabel
 openbabel.obErrorLog.StopLogging()
 import pybel
+import random
+import string
 
 
 def main():
@@ -25,14 +27,18 @@
         required=True, help="path to the output file")
     parser.add_argument('--key', '-k',
         required=True, help="the metadata key from the sdf file which should inlcude the new title")
+    parser.add_argument('--random', '-r',
+        action="store_true", help="Add random suffix to the title.")
 
     args = parser.parse_args()
 
     output = pybel.Outputfile("sdf", args.outfile, overwrite=True)
-
     for mol in pybel.readfile("sdf", args.infile):
         if args.key in mol.data:
             mol.title = mol.data[args.key]
+            if args.random:
+                suffix = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(13))
+                mol.title += '__%s' % suffix
         output.write( mol )
 
     output.close()
--- a/change_title_to_metadata_value.xml	Thu Aug 22 10:28:24 2019 -0400
+++ b/change_title_to_metadata_value.xml	Sat Mar 21 10:26:59 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="openbabel_change_title" name="Change title" version="@VERSION@.0">
+<tool id="openbabel_change_title" name="Change title" version="@VERSION@.1">
     <description>to metadata value.</description>
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
@@ -11,11 +11,14 @@
             --infile '${infile}'
             --key '${key}'
             --outfile '${outfile}'
+            $random
 ]]>
     </command>
     <inputs>
         <param name="infile" type="data" format="sdf,mol2" label="Compound file" help="Specify a compound file in SDF or MOL2 format."/>
         <param name="key" type="text" format="text" label="Compound identifier encoded in the SD-file." help="Specify the key name of the SDF metadata which contains the molecule identifier (e.g. 'PUBCHEM_SHAPE_VOLUME')"/>
+        <param name="random" type="boolean" truevalue="--random" falsevalue="" label="Add a random suffix to the title"
+            help="The title will be named like TITLE__xbrsjqssafh2t"/>
     </inputs>
     <outputs>
         <expand macro="output_like_input"/>
@@ -26,6 +29,16 @@
             <param name="key" value="PUBCHEM_SHAPE_VOLUME"/>
             <output name="outfile" ftype="sdf" file="change_title_on_CID_3033.sdf" lines_diff="2"/>
         </test>
+        <test>
+            <param name="infile" ftype="sdf" value="transfs.sdf"/>
+            <param name="key" value="Name"/>
+            <param name="random" value="true"/>
+            <output name="outfile" ftype="sdf">
+                <assert_contents>
+                    <has_text_matching expression="NC\(=NO\)NCCc1ccc\(S\(N\)\(=O\)=O\)cc1__(.*){13}" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
--- a/ob_filter.py	Thu Aug 22 10:28:24 2019 -0400
+++ b/ob_filter.py	Sat Mar 21 10:26:59 2020 -0400
@@ -29,6 +29,10 @@
         help="Specify the filters to apply",
         required=True,
         )
+    parser.add_argument('--list_of_names', 
+        help="A file with list of molecule names to extract. Every name is in one line.",
+        required=False,
+        )
     return parser.parse_args()
 
 def filter_precalculated_compounds(args, filters):
@@ -83,12 +87,24 @@
         sys.stdout.write(stdout.decode('utf-8'))
         sys.stdout.write(stderr.decode('utf-8'))
 
+def filter_by_name(args):
+    outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
+    for mol in pybel.readfile('sdf', args.input):
+        for name in open(args.list_of_names):
+            if mol.title.strip() == name.strip():
+                outfile.write(mol)
+    outfile.close()
 
 def __main__():
     """
         Select compounds with certain properties from a small library
     """
     args = parse_command_line()
+    
+    if args.filters == '__filter_by_name__':
+        filter_by_name(args)
+        return
+    
     # Its a small trick to get the parameters in an easy way from the xml file.
     # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed.
     # Also the last loop creates a ',{' that is not an valid jason expression.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filterd_by_name.sdf	Sat Mar 21 10:26:59 2020 -0400
@@ -0,0 +1,147 @@
+abc_one
+ OpenBabel03212013422D
+
+ 26 30  0  0  0  0  0  0  0  0999 V2000
+   -8.6396    0.9568    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.6023    1.5602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.6071    3.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.3104    3.8143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.0090    3.0685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.0040    1.5682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.3008    0.8143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.7006    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.7006   -0.6045    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4915   -1.3190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5059   -2.8197    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2156   -3.5847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2329   -5.0846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5404   -5.8196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.8308   -5.0547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.8135   -3.5548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2274   -0.6045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -1.3190    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2274   -0.6045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4732   -1.3190    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7372   -0.6045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7372    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4732    1.5389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2274    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2274    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4915    1.5389    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  2  7  2  0  0  0  0
+  3  4  2  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  2  0  0  0  0
+  6  7  1  0  0  0  0
+  6  8  1  0  0  0  0
+  8  9  1  0  0  0  0
+  8 26  2  0  0  0  0
+  9 10  2  0  0  0  0
+ 10 11  1  0  0  0  0
+ 10 17  1  0  0  0  0
+ 11 12  1  0  0  0  0
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+ 12 13  1  0  0  0  0
+ 13 14  1  0  0  0  0
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+ 15 16  1  0  0  0  0
+ 17 18  1  0  0  0  0
+ 17 25  2  0  0  0  0
+ 18 19  1  0  0  0  0
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+ 20 21  1  0  0  0  0
+ 21 22  2  0  0  0  0
+ 22 23  1  0  0  0  0
+ 23 24  2  0  0  0  0
+ 24 25  1  0  0  0  0
+ 25 26  1  0  0  0  0
+M  END
+>  <mr_id>
+4358263
+
+>  <SMI>
+Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2
+
+$$$$
+abc_eleven
+ OpenBabel03212013422D
+
+ 32 35  0  0  1  0  0  0  0  0999 V2000
+    7.1381   -2.1568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.0456   -2.6531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.7409   -1.9129    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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+   -2.3155   -0.7475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.3560   -1.3452    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
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+    9.2380   -6.0068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.7032   -5.6816    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
+   11.0634   -4.5369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   11.7181   -6.7872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   14.1993   -7.5656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+ 27 32  1  0  0  0  0
+ 28 29  1  0  0  0  0
+ 29 30  1  0  0  0  0
+ 30 31  1  0  0  0  0
+ 31 32  1  0  0  0  0
+M  END
+>  <mr_id>
+4362206
+
+>  <SMI>
+Cc1[nH]c(/C=C/2\C(=O)Nc3ccc(F)cc23)c(C)c1C(=O)NC[C@H](O)CN4CCOCC4
+
+$$$$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ligands_with_title.sdf	Sat Mar 21 10:26:59 2020 -0400
@@ -0,0 +1,759 @@
+abc_one
+
+
+ 26 30  0  0  0  0            999 V2000
+   -8.6396    0.9568    0.0000 O   0  0
+   -7.6023    1.5602    0.0000 C   0  0
+   -7.6071    3.0602    0.0000 C   0  0
+   -6.3104    3.8143    0.0000 C   0  0
+   -5.0090    3.0685    0.0000 C   0  0
+   -5.0040    1.5682    0.0000 C   0  0
+   -6.3008    0.8143    0.0000 C   0  0
+   -3.7006    0.8244    0.0000 C   0  0
+   -3.7006   -0.6045    0.0000 N   0  0
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+   -1.2156   -3.5847    0.0000 C   0  0
+   -1.2329   -5.0846    0.0000 C   0  0
+   -2.5404   -5.8196    0.0000 O   0  0
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+   -3.8135   -3.5548    0.0000 C   0  0
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+    2.4732    1.5389    0.0000 C   0  0
+    1.2274    0.8244    0.0000 C   0  0
+   -1.2274    0.8244    0.0000 C   0  0
+   -2.4915    1.5389    0.0000 N   0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  2  0
+  4  5  1  0
+  5  6  2  0
+  6  7  1  0
+  2  7  2  0
+  6  8  1  0
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+  9 10  2  0
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+ 23 24  2  0
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+ 17 25  2  0
+ 25 26  1  0
+  8 26  2  0
+M  END
+> <mr_id>
+4358263
+
+> <SMI>
+Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2
+
+$$$$
+abc_two
+
+
+ 43 51  0  0  1  0            999 V2000
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+ 40 41  1  0
+ 41 42  2  0
+ 42 43  1  0
+ 38 43  2  0
+M  END
+> <mr_id>
+8573
+
+> <SMI>
+CO[C@@H]1[C@@H](C[C@H]2O[C@]1(C)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35)N(C)C(=O)c9ccccc9
+
+$$$$
+abc_three
+
+
+ 25 28  0  0  0  0            999 V2000
+   -6.2193    5.8633    0.0000 Cl  0  0
+   -5.1815    5.2608    0.0000 C   0  0
+   -3.8807    6.0076    0.0000 C   0  0
+   -2.5835    5.2544    0.0000 C   0  0
+   -2.5870    3.7544    0.0000 C   0  0
+   -1.2907    2.9981    0.0000 N   0  0
+   -1.2964    1.4973    0.0000 C   0  0
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+   -1.2907   -2.9981    0.0000 C   0  0
+   -2.5870   -3.7544    0.0000 C   0  0
+   -2.5835   -5.2544    0.0000 C   0  0
+   -3.8807   -6.0076    0.0000 C   0  0
+   -5.1815   -5.2608    0.0000 N   0  0
+   -5.1852   -3.7608    0.0000 C   0  0
+   -3.8880   -3.0076    0.0000 C   0  0
+    0.0000   -0.7486    0.0000 C   0  0
+    1.2964   -1.4973    0.0000 C   0  0
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+    1.2964    1.4973    0.0000 C   0  0
+    0.0000    0.7486    0.0000 C   0  0
+   -3.8880    3.0076    0.0000 C   0  0
+   -5.1852    3.7608    0.0000 C   0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  2  0
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+ 22 23  1  0
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+ 18 23  1  0
+  5 24  2  0
+ 24 25  1  0
+  2 25  2  0
+M  END
+> <mr_id>
+4027
+
+> <SMI>
+Clc1ccc(Nc2nnc(Cc3ccncc3)c4ccccc24)cc1
+
+$$$$
+abc_four
+
+
+ 26 28  0  0  1  0            999 V2000
+   -1.2878    3.1508    0.0000 C   0  0
+   -2.3292    3.7470    0.0000 C   0  0
+   -3.6267    2.9927    0.0000 C   0  0  2  0  0  0
+   -4.9300    3.7369    0.0000 C   0  0
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+   -3.6187    1.4919    0.0000 N   0  0
+   -2.3155    0.7475    0.0000 C   0  0
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+   -1.0028   -1.5132    0.0000 C   0  0
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+   -2.2935   -3.7700    0.0000 C   0  0
+   -2.2878   -5.2708    0.0000 C   0  0
+   -3.5824   -6.0284    0.0000 C   0  0
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+   -2.2702   -8.2708    0.0000 C   0  0
+   -0.9756   -7.5132    0.0000 C   0  0
+   -0.9844   -6.0132    0.0000 C   0  0
+    0.2917   -0.7475    0.0000 C   0  0
+    1.7138   -1.2033    0.0000 N   0  0
+    2.5889    0.0182    0.0000 C   0  0
+    1.7138    1.2033    0.0000 N   0  0
+    2.1812    2.6271    0.0000 C   0  0
+    3.3556    2.8737    0.0000 C   0  0
+    1.3808    3.5211    0.0000 C   0  0
+    0.2917    0.7475    0.0000 C   0  0
+   -1.0028    1.5132    0.0000 N   0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  1  0
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+  6  7  1  0
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+ 22 23  1  0
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+ 21 25  1  0
+ 18 25  2  0
+ 25 26  1  0
+  7 26  2  0
+M  END
+> <mr_id>
+600
+
+> <SMI>
+CC[C@H](CO)Nc1nc(NCc2ccccc2)c3ncn(C(C)C)c3n1
+
+$$$$
+abc_five
+
+
+ 25 28  0  0  0  0            999 V2000
+    2.3383   -1.3500    0.0000 O   0  0
+    1.2990   -0.7500    0.0000 C   0  0
+    1.2990    0.7500    0.0000 C   0  0
+    0.0000    1.5000    0.0000 C   0  0
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+    0.0000   -1.5000    0.0000 C   0  0
+   -2.5987    1.5004    0.0000 C   0  0
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+   -4.2067    3.2905    0.0000 C   0  0
+   -4.9546    1.9903    0.0000 C   0  0
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+   -6.4469    1.8311    0.0000 C   0  0
+   -7.4153    2.9701    0.0000 C   0  0
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+   -6.8192    8.3502    0.0000 F   0  0
+   -7.0341    6.0170    0.0000 C   0  0
+   -6.3205    4.6976    0.0000 C   0  0
+  1  2  1  0
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+ 22 24  2  0
+ 24 25  1  0
+ 19 25  2  0
+M  END
+> <mr_id>
+8393
+
+> <SMI>
+Oc1ccc(cc1)c2nc(c([nH]2)c3ccncc3)c4ccc(F)cc4
+
+$$$$
+abc_six
+
+
+ 27 30  0  0  0  0            999 V2000
+    3.6375   -0.9049    0.0000 C   0  0
+    2.5973   -1.5031    0.0000 S   0  0
+    2.5956   -2.7031    0.0000 O   0  0
+    1.2990   -0.7500    0.0000 C   0  0
+    1.2990    0.7500    0.0000 C   0  0
+    0.0000    1.5000    0.0000 C   0  0
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+    0.0000   -1.5000    0.0000 C   0  0
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+   -4.9546    1.9903    0.0000 C   0  0
+   -3.9492    0.8772    0.0000 N   0  0
+   -6.4469    1.8311    0.0000 C   0  0
+   -7.4153    2.9701    0.0000 C   0  0
+   -8.8906    2.6991    0.0000 C   0  0
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+   -7.0341    6.0170    0.0000 C   0  0
+   -6.3205    4.6976    0.0000 C   0  0
+  1  2  1  0
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+ 26 27  1  0
+ 21 27  2  0
+M  END
+> <mr_id>
+3250
+
+> <SMI>
+CS(=O)c1ccc(cc1)c2nc(c([nH]2)c3ccncc3)c4ccc(F)cc4
+
+$$$$
+abc_seven
+
+
+ 29 33  0  0  0  0            999 V2000
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+   -1.0028   -1.5132    0.0000 C   0  0
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+  1  2  1  0
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+ 24 28  2  0
+ 28 29  1  0
+ 21 29  2  0
+M  END
+> <mr_id>
+4347423
+
+> <SMI>
+NC(=O)c1ccc(cc1)c2nc(c([nH]2)c3ccccn3)c4ccc5OCOc5c4
+
+$$$$
+abc_nine
+
+
+ 32 34  0  0  0  0            999 V2000
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+   -1.2990    0.7500    0.0000 C   0  0
+   -1.2990   -0.7500    0.0000 C   0  0
+    0.0000   -1.5000    0.0000 N   0  0
+  1  2  1  0
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+ 30 31  2  0
+ 31 32  1  0
+  5 32  2  0
+M  END
+> <mr_id>
+4255941
+
+> <SMI>
+CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3ccc(Cl)c(c3)C(F)(F)F)cc2)ccn1
+
+$$$$
+abc_ten
+
+
+ 35 42  0  0  1  0            999 V2000
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+   -2.5513    4.8029    0.0000 N   0  0
+   -1.8100    3.5000    0.0000 C   0  0  2  0  0  0
+   -0.2400    3.5200    0.0000 C   0  0
+    0.5000    2.1800    0.0000 C   0  0  1  0  0  0
+   -1.0600    2.1800    0.0000 O   0  0
+   -1.8300    0.9300    0.0000 C   0  0  1  0  0  0
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+   -0.9800   -0.7800    0.0000 N   0  0
+   -2.1300   -1.4600    0.0000 C   0  0
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+    1.4500   -0.7600    0.0000 C   0  0
+    0.2400   -1.4400    0.0000 C   0  0
+  1  2  1  0
+  3  2  1  6
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+  5  4  1  6
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+ 33 34  1  0
+ 26 34  2  0
+ 34 35  1  0
+ 12 35  1  0
+ 19 35  2  0
+M  END
+> <mr_id>
+66
+
+> <SMI>
+CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35
+
+$$$$
+abc_eleven
+
+
+ 32 35  0  0  1  0            999 V2000
+    7.1381   -2.1568    0.0000 C   0  0
+    6.0456   -2.6531    0.0000 C   0  0
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+    3.6552   -2.9294    0.0000 C   0  0
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+   -1.0028   -1.5132    0.0000 C   0  0
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+    4.2542   -4.2907    0.0000 C   0  0
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+    5.7448   -4.1226    0.0000 C   0  0
+    6.7580   -5.2264    0.0000 C   0  0
+    6.3978   -6.3710    0.0000 O   0  0
+    8.2231   -4.9012    0.0000 N   0  0
+    9.2380   -6.0068    0.0000 C   0  0
+   10.7032   -5.6816    0.0000 C   0  0  2  0  0  0
+   11.0634   -4.5369    0.0000 O   0  0
+   11.7181   -6.7872    0.0000 C   0  0
+   13.1833   -6.4620    0.0000 N   0  0
+   14.1993   -7.5656    0.0000 C   0  0
+   15.6630   -7.2376    0.0000 C   0  0
+   16.1108   -5.8060    0.0000 O   0  0
+   15.0949   -4.7024    0.0000 C   0  0
+   13.6312   -5.0304    0.0000 C   0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  1  0
+  4  5  1  0
+  5  6  2  0
+  6  7  1  0
+  7  8  2  0
+  7  9  1  0
+  9 10  1  0
+ 10 11  1  0
+ 11 12  2  0
+ 12 13  1  0
+ 13 14  1  0
+ 13 15  2  0
+ 15 16  1  0
+  6 16  1  0
+ 10 16  2  0
+  4 17  2  0
+ 17 18  1  0
+ 17 19  1  0
+  2 19  2  0
+ 19 20  1  0
+ 20 21  2  0
+ 20 22  1  0
+ 22 23  1  0
+ 23 24  1  0
+ 24 25  1  6
+ 24 26  1  0
+ 26 27  1  0
+ 27 28  1  0
+ 28 29  1  0
+ 29 30  1  0
+ 30 31  1  0
+ 31 32  1  0
+ 27 32  1  0
+M  END
+> <mr_id>
+4362206
+
+> <SMI>
+Cc1[nH]c(/C=C/2\C(=O)Nc3ccc(F)cc23)c(C)c1C(=O)NC[C@H](O)CN4CCOCC4
+
+$$$$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/name_file.txt	Sat Mar 21 10:26:59 2020 -0400
@@ -0,0 +1,2 @@
+abc_one
+abc_eleven
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/transfs.sdf	Sat Mar 21 10:26:59 2020 -0400
@@ -0,0 +1,186 @@
+NC(=NO)NCCc1ccc(S(N)(=O)=O)cc1
+     RDKit          3D
+
+ 17 17  0  0  0  0  0  0  0  0999 V2000
+   13.9302   -2.3261   22.5538 N   0  0  0  0  0  0  0  0  0  0  0  0
+   13.7238   -1.7706   23.7651 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.9709   -0.6511   23.8871 N   0  0  0  0  0  0  0  0  0  0  0  0
+   12.3387    0.0187   22.7430 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.9859    0.6425   23.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.9117    0.4770   22.0521 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.6451   -0.7505   21.4256 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.6682   -0.8525   20.4388 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.9346    0.2745   20.0745 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.7444    0.1313   18.7757 S   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4465    0.9786   19.4142 N   0  0  0  0  0  0  0  0  0  0  0  0
+    7.2019    0.8863   17.6332 O   0  0  0  0  0  0  0  0  0  0  0  0
+    6.3224   -1.2458   18.6840 O   0  0  0  0  0  0  0  0  0  0  0  0
+    8.1747    1.5057   20.6849 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.1574    1.6019   21.6751 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.2946   -2.3692   24.8521 N   0  0  0  0  0  0  0  0  0  0  0  0
+   14.1962   -1.9686   26.1940 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  1  0
+  2 16  2  0
+  3  4  1  0
+  4  5  1  0
+  5  6  1  0
+  6  7  2  0
+  6 15  1  0
+  7  8  1  0
+  8  9  2  0
+  9 10  1  0
+  9 14  1  0
+ 10 11  1  0
+ 10 12  2  0
+ 10 13  2  0
+ 14 15  2  0
+ 16 17  1  0
+M  CHG  1  16   1
+M  END
+>  <CHROM.0>  (1) 
+65.93051459,169.99861208,-59.68475000
+
+>  <CHROM.1>  (1) 
+145.66221290,-139.37796603,47.03157881,136.25602749,64.42425104,102.07311975
+9.88696665,-0.33137891,21.45559055,-0.16902134,0.67278808,-2.52516849
+
+>  <Name>  (1) 
+NC(=NO)NCCc1ccc(S(N)(=O)=O)cc1
+
+>  <RI>  (1) 
+1.41352e+07
+
+>  <Rbt.Current_Directory>  (1) 
+/data/dnb02/galaxy_db/job_working_directory/007/399/7399639/working
+
+>  <Rbt.Executable>  (1) 
+rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $)
+
+>  <Rbt.Library>  (1) 
+libRbt.so (2013.1, Build901 2013/11/27)
+
+>  <Rbt.Parameter_File>  (1) 
+/usr/local/tools/_conda/envs/__rdock@2013.1-0/share/rdock-2013.1-1/data/scripts/dock.prm
+
+>  <Rbt.Receptor>  (1) 
+receptor.prm
+
+>  <SCORE>  (1) 
+-30.3434
+
+>  <SCORE.INTER>  (1) 
+-15.8664
+
+>  <SCORE.INTER.CONST>  (1) 
+1
+
+>  <SCORE.INTER.POLAR>  (1) 
+-1.12178
+
+>  <SCORE.INTER.REPUL>  (1) 
+0
+
+>  <SCORE.INTER.ROT>  (1) 
+5
+
+>  <SCORE.INTER.VDW>  (1) 
+-22.4523
+
+>  <SCORE.INTER.norm>  (1) 
+-0.933318
+
+>  <SCORE.INTRA>  (1) 
+-2.33416
+
+>  <SCORE.INTRA.DIHEDRAL>  (1) 
+-1.88099
+
+>  <SCORE.INTRA.DIHEDRAL.0>  (1) 
+10.7462
+
+>  <SCORE.INTRA.POLAR>  (1) 
+0
+
+>  <SCORE.INTRA.POLAR.0>  (1) 
+0
+
+>  <SCORE.INTRA.REPUL>  (1) 
+0
+
+>  <SCORE.INTRA.REPUL.0>  (1) 
+0
+
+>  <SCORE.INTRA.VDW>  (1) 
+-1.39366
+
+>  <SCORE.INTRA.VDW.0>  (1) 
+0.160377
+
+>  <SCORE.INTRA.norm>  (1) 
+-0.137303
+
+>  <SCORE.RESTR>  (1) 
+
+
+>  <SCORE.RESTR.norm>  (1) 
+0
+
+>  <SCORE.SYSTEM>  (1) 
+-12.1428
+
+>  <SCORE.SYSTEM.CONST>  (1) 
+0
+
+>  <SCORE.SYSTEM.DIHEDRAL>  (1) 
+0.706521
+
+>  <SCORE.SYSTEM.POLAR>  (1) 
+-3.2443
+
+>  <SCORE.SYSTEM.REPUL>  (1) 
+0.676691
+
+>  <SCORE.SYSTEM.VDW>  (1) 
+-4.8489
+
+>  <SCORE.SYSTEM.norm>  (1) 
+-0.714283
+
+>  <SCORE.heavy>  (1) 
+17
+
+>  <SCORE.norm>  (1) 
+-1.7849
+
+>  <TransFSReceptor>  (1) 
+receptor
+
+>  <TransFSScore>  (1) 
+0.999997
+
+>  <Max_SuCOS_Score>  (1) 
+0.44454780182058773
+
+>  <Max_SuCOS_FeatureMap_Score>  (1) 
+0.19084575451625094
+
+>  <Max_SuCOS_Protrude_Score>  (1) 
+0.69824984912492449
+
+>  <Max_SuCOS_Cluster>  (1) 
+dataset_14281034.dat
+
+>  <Max_SuCOS_Index>  (1) 
+11
+
+>  <Cum_SuCOS_Score>  (1) 
+3.7946511319966216
+
+>  <Cum_SuCOS_FeatureMap_Score>  (1) 
+0.9189792141377946
+
+>  <Cum_SuCOS_Protrude_Score>  (1) 
+6.6703230498554467
+
+$$$$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/transfs_changed_name.sdf	Sat Mar 21 10:26:59 2020 -0400
@@ -0,0 +1,186 @@
+NC(=NO)NCCc1ccc(S(N)(=O)=O)cc1__xbrsjqssafh2t
+ OpenBabel03212010583D
+
+ 17 17  0  0  0  0  0  0  0  0999 V2000
+   13.9302   -2.3261   22.5538 N   0  0  0  0  0  0  0  0  0  0  0  0
+   13.7238   -1.7706   23.7651 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.9709   -0.6511   23.8871 N   0  0  0  0  0  0  0  0  0  0  0  0
+   12.3387    0.0187   22.7430 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.9859    0.6425   23.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.9117    0.4770   22.0521 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.6451   -0.7505   21.4256 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.6682   -0.8525   20.4388 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.9346    0.2745   20.0745 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.7444    0.1313   18.7757 S   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4465    0.9786   19.4142 N   0  0  0  0  0  0  0  0  0  0  0  0
+    7.2019    0.8863   17.6332 O   0  0  0  0  0  0  0  0  0  0  0  0
+    6.3224   -1.2458   18.6840 O   0  0  0  0  0  0  0  0  0  0  0  0
+    8.1747    1.5057   20.6849 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.1574    1.6019   21.6751 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.2946   -2.3692   24.8521 N   0  3  0  0  0  0  0  0  0  0  0  0
+   14.1962   -1.9686   26.1940 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  2 16  2  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6  7  2  0  0  0  0
+  6 15  1  0  0  0  0
+  7  8  1  0  0  0  0
+  8  9  2  0  0  0  0
+  9 10  1  0  0  0  0
+  9 14  1  0  0  0  0
+ 10 11  1  0  0  0  0
+ 10 12  2  0  0  0  0
+ 10 13  2  0  0  0  0
+ 14 15  2  0  0  0  0
+ 16 17  1  0  0  0  0
+M  CHG  1  16   1
+M  END
+>  <CHROM.0>
+65.93051459,169.99861208,-59.68475000
+
+>  <CHROM.1>
+145.66221290,-139.37796603,47.03157881,136.25602749,64.42425104,102.07311975
+9.88696665,-0.33137891,21.45559055,-0.16902134,0.67278808,-2.52516849
+
+>  <Name>
+NC(=NO)NCCc1ccc(S(N)(=O)=O)cc1
+
+>  <RI>
+1.41352e+07
+
+>  <Rbt.Current_Directory>
+/data/dnb02/galaxy_db/job_working_directory/007/399/7399639/working
+
+>  <Rbt.Executable>
+rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $)
+
+>  <Rbt.Library>
+libRbt.so (2013.1, Build901 2013/11/27)
+
+>  <Rbt.Parameter_File>
+/usr/local/tools/_conda/envs/__rdock@2013.1-0/share/rdock-2013.1-1/data/scripts/dock.prm
+
+>  <Rbt.Receptor>
+receptor.prm
+
+>  <SCORE>
+-30.3434
+
+>  <SCORE.INTER>
+-15.8664
+
+>  <SCORE.INTER.CONST>
+1
+
+>  <SCORE.INTER.POLAR>
+-1.12178
+
+>  <SCORE.INTER.REPUL>
+0
+
+>  <SCORE.INTER.ROT>
+5
+
+>  <SCORE.INTER.VDW>
+-22.4523
+
+>  <SCORE.INTER.norm>
+-0.933318
+
+>  <SCORE.INTRA>
+-2.33416
+
+>  <SCORE.INTRA.DIHEDRAL>
+-1.88099
+
+>  <SCORE.INTRA.DIHEDRAL.0>
+10.7462
+
+>  <SCORE.INTRA.POLAR>
+0
+
+>  <SCORE.INTRA.POLAR.0>
+0
+
+>  <SCORE.INTRA.REPUL>
+0
+
+>  <SCORE.INTRA.REPUL.0>
+0
+
+>  <SCORE.INTRA.VDW>
+-1.39366
+
+>  <SCORE.INTRA.VDW.0>
+0.160377
+
+>  <SCORE.INTRA.norm>
+-0.137303
+
+>  <SCORE.RESTR>
+
+
+>  <SCORE.RESTR.norm>
+0
+
+>  <SCORE.SYSTEM>
+-12.1428
+
+>  <SCORE.SYSTEM.CONST>
+0
+
+>  <SCORE.SYSTEM.DIHEDRAL>
+0.706521
+
+>  <SCORE.SYSTEM.POLAR>
+-3.2443
+
+>  <SCORE.SYSTEM.REPUL>
+0.676691
+
+>  <SCORE.SYSTEM.VDW>
+-4.8489
+
+>  <SCORE.SYSTEM.norm>
+-0.714283
+
+>  <SCORE.heavy>
+17
+
+>  <SCORE.norm>
+-1.7849
+
+>  <TransFSReceptor>
+receptor
+
+>  <TransFSScore>
+0.999997
+
+>  <Max_SuCOS_Score>
+0.44454780182058773
+
+>  <Max_SuCOS_FeatureMap_Score>
+0.19084575451625094
+
+>  <Max_SuCOS_Protrude_Score>
+0.69824984912492449
+
+>  <Max_SuCOS_Cluster>
+dataset_14281034.dat
+
+>  <Max_SuCOS_Index>
+11
+
+>  <Cum_SuCOS_Score>
+3.7946511319966216
+
+>  <Cum_SuCOS_FeatureMap_Score>
+0.9189792141377946
+
+>  <Cum_SuCOS_Protrude_Score>
+6.6703230498554467
+
+$$$$