Mercurial > repos > bgruening > openbabel_filter
changeset 10:9cc9947c84a1 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
| author | bgruening |
|---|---|
| date | Sat, 21 Mar 2020 12:54:40 +0000 |
| parents | da4413d9308f |
| children | 24b5d5f8a5ff |
| files | __pycache__/cheminfolib.cpython-36.pyc change_title_to_metadata_value.py ob_filter.py ob_filter.xml 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, 1350 insertions(+), 32 deletions(-) [+] |
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--- a/change_title_to_metadata_value.py Thu Aug 22 10:19:43 2019 -0400 +++ b/change_title_to_metadata_value.py Sat Mar 21 12:54:40 2020 +0000 @@ -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/ob_filter.py Thu Aug 22 10:19:43 2019 -0400 +++ b/ob_filter.py Sat Mar 21 12:54:40 2020 +0000 @@ -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.
--- a/ob_filter.xml Thu Aug 22 10:19:43 2019 -0400 +++ b/ob_filter.xml Sat Mar 21 12:54:40 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="openbabel_filter" name="Filter" version="@VERSION@.0"> +<tool id="openbabel_filter" name="Filter" version="@VERSION@.1"> <description> a set of molecules from a file</description> <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> <macros> @@ -10,37 +10,42 @@ python '$__tool_directory__/ob_filter.py' -i '${infile}' -o '${outfile}' - -iformat "${infile.ext}" - -oformat "${infile.ext}" - --filters '{ - #if $filter_methods.filter_methods_opts == "ruleof5": - "hbd" : [0, 5], - "hba" : [0, 10], - "molwt" : [0, 500], - "logp" : [-5, 5], - #elif $filter_methods.filter_methods_opts == "LeadLike": - "rotbonds" : [0, 7], - "molwt" : [0, 350], - "logp" : [-5, 3.5], - #elif $filter_methods.filter_methods_opts == "DrugLike": - "hba" : [0, 10], - "rotbonds" : [0, 8], - "molwt" : [150, 500], - "logp" : [-5, 5], - "psa" : [0, 150], - #elif $filter_methods.filter_methods_opts == "FragmentLike": - "rotbonds" : [0, 5], - "molwt" : [0, 250], - "logp" : [-5, 2.5], - #else: - #for $filter in $filter_methods.filter_set: - #set $filter_selected = $filter.filter_sel.filter_sel_opts - #set $filter_min = $filter_selected + "_min" - #set $filter_max = $filter_selected + "_max" - "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ], - #end for + -iformat '${infile.ext}' + -oformat '${infile.ext}' + #if $filter_methods.filter_methods_opts == "__filter_by_name__": + --list_of_names '$name_file' + --filters '__filter_by_name__' + #else + --filters '{ + #if $filter_methods.filter_methods_opts == "ruleof5": + "hbd" : [0, 5], + "hba" : [0, 10], + "molwt" : [0, 500], + "logp" : [-5, 5], + #elif $filter_methods.filter_methods_opts == "LeadLike": + "rotbonds" : [0, 7], + "molwt" : [0, 350], + "logp" : [-5, 3.5], + #elif $filter_methods.filter_methods_opts == "DrugLike": + "hba" : [0, 10], + "rotbonds" : [0, 8], + "molwt" : [150, 500], + "logp" : [-5, 5], + "psa" : [0, 150], + #elif $filter_methods.filter_methods_opts == "FragmentLike": + "rotbonds" : [0, 5], + "molwt" : [0, 250], + "logp" : [-5, 2.5], + #else: + #for $filter in $filter_methods.filter_set: + #set $filter_selected = $filter.filter_sel.filter_sel_opts + #set $filter_min = $filter_selected + "_min" + #set $filter_max = $filter_selected + "_max" + "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ], + #end for + #end if + }' #end if - }' ]]> </command> <inputs> @@ -53,7 +58,12 @@ <option value="LeadLike">Lead-like properties</option> <option value="DrugLike">Drug-like properties</option> <option value="FragmentLike">Fragment-like properties</option> + <option value="__filter_by_name__">Filter by molecule name</option> </param> + <when value="__filter_by_name__"> + <param name="name_file" type="data" format="txt,tabular" + label="File with molecule names that match the names in the SDF file" help="Every name one line."/> + </when> <when value="ruleof5" /> <when value="LeadLike" /> <when value="DrugLike" /> @@ -121,6 +131,12 @@ </outputs> <tests> <test> + <param name="infile" value="ligands_with_title.sdf" ftype="sdf" /> + <param name="filter_methods_opts" value="__filter_by_name__" /> + <param name="name_file" value="name_file.txt" /> + <output name="outfile" file="filterd_by_name.sdf" ftype="sdf" lines_diff="4" /> + </test> + <test> <param name="infile" ftype="smi" value="CID_2244.smi"/> <param name="filter_methods_opts" value="ruleof5" /> <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filterd_by_name.sdf Sat Mar 21 12:54:40 2020 +0000 @@ -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 + 11 16 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 14 15 1 0 0 0 0 + 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 + 19 20 2 0 0 0 0 + 19 24 1 0 0 0 0 + 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 + 3.6552 -2.9294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1855 -2.6254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7138 -1.2033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5889 0.0182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7889 0.0269 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.7138 1.2033 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2917 0.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0028 1.5132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3155 0.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -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 + -1.0028 -1.5132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2917 -0.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.2542 -4.2907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6559 -5.3308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7448 -4.1226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7580 -5.2264 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3978 -6.3710 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.2231 -4.9012 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 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 + 13.1833 -6.4620 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 14.1993 -7.5656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.6630 -7.2376 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.1108 -5.8060 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 15.0949 -4.7024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.6312 -5.0304 0.0000 C 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 19 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 4 17 2 0 0 0 0 + 5 6 2 0 0 0 0 + 6 7 1 0 0 0 0 + 6 16 1 0 0 0 0 + 7 8 2 0 0 0 0 + 7 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 1 0 0 0 0 + 10 16 2 0 0 0 0 + 11 12 2 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 1 0 0 0 0 + 13 15 2 0 0 0 0 + 15 16 1 0 0 0 0 + 17 18 1 0 0 0 0 + 17 19 1 0 0 0 0 + 19 20 1 0 0 0 0 + 20 21 2 0 0 0 0 + 20 22 1 0 0 0 0 + 22 23 1 0 0 0 0 + 23 24 1 0 0 0 0 + 24 25 1 6 0 0 0 + 24 26 1 0 0 0 0 + 26 27 1 0 0 0 0 + 27 28 1 0 0 0 0 + 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 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligands_with_title.sdf Sat Mar 21 12:54:40 2020 +0000 @@ -0,0 +1,759 @@ +abc_one + + + 26 30 0 0 0 0 999 V2000 + -8.6396 0.9568 0.0000 O 0 0 + -7.6023 1.5602 0.0000 C 0 0 + -7.6071 3.0602 0.0000 C 0 0 + -6.3104 3.8143 0.0000 C 0 0 + -5.0090 3.0685 0.0000 C 0 0 + -5.0040 1.5682 0.0000 C 0 0 + -6.3008 0.8143 0.0000 C 0 0 + -3.7006 0.8244 0.0000 C 0 0 + -3.7006 -0.6045 0.0000 N 0 0 + -2.4915 -1.3190 0.0000 C 0 0 + -2.5059 -2.8197 0.0000 N 0 0 + -1.2156 -3.5847 0.0000 C 0 0 + -1.2329 -5.0846 0.0000 C 0 0 + -2.5404 -5.8196 0.0000 O 0 0 + -3.8308 -5.0547 0.0000 C 0 0 + -3.8135 -3.5548 0.0000 C 0 0 + -1.2274 -0.6045 0.0000 C 0 0 + 0.0000 -1.3190 0.0000 O 0 0 + 1.2274 -0.6045 0.0000 C 0 0 + 2.4732 -1.3190 0.0000 N 0 0 + 3.7372 -0.6045 0.0000 C 0 0 + 3.7372 0.8244 0.0000 C 0 0 + 2.4732 1.5389 0.0000 C 0 0 + 1.2274 0.8244 0.0000 C 0 0 + -1.2274 0.8244 0.0000 C 0 0 + -2.4915 1.5389 0.0000 N 0 0 + 1 2 1 0 + 2 3 1 0 + 3 4 2 0 + 4 5 1 0 + 5 6 2 0 + 6 7 1 0 + 2 7 2 0 + 6 8 1 0 + 8 9 1 0 + 9 10 2 0 + 10 11 1 0 + 11 12 1 0 + 12 13 1 0 + 13 14 1 0 + 14 15 1 0 + 15 16 1 0 + 11 16 1 0 + 10 17 1 0 + 17 18 1 0 + 18 19 1 0 + 19 20 2 0 + 20 21 1 0 + 21 22 2 0 + 22 23 1 0 + 23 24 2 0 + 19 24 1 0 + 24 25 1 0 + 17 25 2 0 + 25 26 1 0 + 8 26 2 0 +M END +> <mr_id> +4358263 + +> <SMI> +Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2 + +$$$$ +abc_two + + + 43 51 0 0 1 0 999 V2000 + -4.7204 3.3431 0.0000 C 0 0 + -4.1471 2.2890 0.0000 O 0 0 + -2.6500 2.2500 0.0000 C 0 0 2 0 0 0 + -1.8100 3.5000 0.0000 C 0 0 1 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 + -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 + -2.5511 4.8030 0.0000 N 0 0 + -1.9442 5.8382 0.0000 C 0 0 + -4.0519 4.8135 0.0000 C 0 0 + -4.6588 3.7783 0.0000 O 0 0 + -4.7941 6.1180 0.0000 C 0 0 + -6.2940 6.1306 0.0000 C 0 0 + -7.0331 7.4359 0.0000 C 0 0 + -6.2722 8.7286 0.0000 C 0 0 + -4.7723 8.7160 0.0000 C 0 0 + -4.0332 7.4108 0.0000 C 0 0 + 1 2 1 0 + 3 2 1 6 + 3 4 1 0 + 4 5 1 0 + 6 5 1 6 + 6 7 1 0 + 7 8 1 0 + 3 8 1 0 + 8 9 1 1 + 8 10 1 0 + 10 11 1 0 + 11 12 1 0 + 12 13 2 0 + 13 14 1 0 + 14 15 2 0 + 15 16 1 0 + 11 16 2 0 + 16 17 1 0 + 17 18 1 0 + 18 19 1 0 + 19 20 1 0 + 20 21 1 0 + 21 22 2 0 + 21 23 1 0 + 18 23 2 0 + 23 24 1 0 + 24 25 1 0 + 25 26 1 0 + 26 27 2 0 + 27 28 1 0 + 28 29 2 0 + 29 30 1 0 + 25 30 2 0 + 30 31 1 0 + 6 31 1 0 + 31 32 1 0 + 24 32 2 0 + 32 33 1 0 + 10 33 1 0 + 17 33 2 0 + 4 34 1 6 + 34 35 1 0 + 34 36 1 0 + 36 37 2 0 + 36 38 1 0 + 38 39 1 0 + 39 40 2 0 + 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 + +$$$$ +abc_three + + + 25 28 0 0 0 0 999 V2000 + -6.2193 5.8633 0.0000 Cl 0 0 + -5.1815 5.2608 0.0000 C 0 0 + -3.8807 6.0076 0.0000 C 0 0 + -2.5835 5.2544 0.0000 C 0 0 + -2.5870 3.7544 0.0000 C 0 0 + -1.2907 2.9981 0.0000 N 0 0 + -1.2964 1.4973 0.0000 C 0 0 + -2.6111 0.7486 0.0000 N 0 0 + -2.6111 -0.7486 0.0000 N 0 0 + -1.2964 -1.4973 0.0000 C 0 0 + -1.2907 -2.9981 0.0000 C 0 0 + -2.5870 -3.7544 0.0000 C 0 0 + -2.5835 -5.2544 0.0000 C 0 0 + -3.8807 -6.0076 0.0000 C 0 0 + -5.1815 -5.2608 0.0000 N 0 0 + -5.1852 -3.7608 0.0000 C 0 0 + -3.8880 -3.0076 0.0000 C 0 0 + 0.0000 -0.7486 0.0000 C 0 0 + 1.2964 -1.4973 0.0000 C 0 0 + 2.5929 -0.7486 0.0000 C 0 0 + 2.5929 0.7486 0.0000 C 0 0 + 1.2964 1.4973 0.0000 C 0 0 + 0.0000 0.7486 0.0000 C 0 0 + -3.8880 3.0076 0.0000 C 0 0 + -5.1852 3.7608 0.0000 C 0 0 + 1 2 1 0 + 2 3 1 0 + 3 4 2 0 + 4 5 1 0 + 5 6 1 0 + 6 7 1 0 + 7 8 1 0 + 8 9 2 0 + 9 10 1 0 + 10 11 1 0 + 11 12 1 0 + 12 13 1 0 + 13 14 2 0 + 14 15 1 0 + 15 16 2 0 + 16 17 1 0 + 12 17 2 0 + 10 18 2 0 + 18 19 1 0 + 19 20 2 0 + 20 21 1 0 + 21 22 2 0 + 22 23 1 0 + 7 23 2 0 + 18 23 1 0 + 5 24 2 0 + 24 25 1 0 + 2 25 2 0 +M END +> <mr_id> +4027 + +> <SMI> +Clc1ccc(Nc2nnc(Cc3ccncc3)c4ccccc24)cc1 + +$$$$ +abc_four + + + 26 28 0 0 1 0 999 V2000 + -1.2878 3.1508 0.0000 C 0 0 + -2.3292 3.7470 0.0000 C 0 0 + -3.6267 2.9927 0.0000 C 0 0 2 0 0 0 + -4.9300 3.7369 0.0000 C 0 0 + -4.9364 4.9369 0.0000 O 0 0 + -3.6187 1.4919 0.0000 N 0 0 + -2.3155 0.7475 0.0000 C 0 0 + -2.3155 -0.7475 0.0000 N 0 0 + -1.0028 -1.5132 0.0000 C 0 0 + -0.9971 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C 0 0 + 1.2990 0.7500 0.0000 C 0 0 + 0.0000 1.5000 0.0000 C 0 0 + -1.2990 0.7500 0.0000 C 0 0 + -1.2990 -0.7500 0.0000 C 0 0 + 0.0000 -1.5000 0.0000 C 0 0 + -2.5987 1.5004 0.0000 C 0 0 + -2.7390 2.9810 0.0000 N 0 0 + -4.2067 3.2905 0.0000 C 0 0 + -4.9546 1.9903 0.0000 C 0 0 + -3.9492 0.8772 0.0000 N 0 0 + -6.4469 1.8311 0.0000 C 0 0 + -7.4153 2.9701 0.0000 C 0 0 + -8.8906 2.6991 0.0000 C 0 0 + -9.3937 1.2860 0.0000 N 0 0 + -8.4213 0.1438 0.0000 C 0 0 + -6.9460 0.4147 0.0000 C 0 0 + -4.8193 4.6606 0.0000 C 0 0 + -4.0353 5.9336 0.0000 C 0 0 + -4.7489 7.2530 0.0000 C 0 0 + -6.2483 7.2947 0.0000 C 0 0 + -6.8192 8.3502 0.0000 F 0 0 + -7.0341 6.0170 0.0000 C 0 0 + -6.3205 4.6976 0.0000 C 0 0 + 1 2 1 0 + 2 3 1 0 + 3 4 2 0 + 4 5 1 0 + 5 6 2 0 + 6 7 1 0 + 2 7 2 0 + 5 8 1 0 + 8 9 2 0 + 9 10 1 0 + 10 11 2 0 + 11 12 1 0 + 8 12 1 0 + 11 13 1 0 + 13 14 1 0 + 14 15 2 0 + 15 16 1 0 + 16 17 2 0 + 17 18 1 0 + 13 18 2 0 + 10 19 1 0 + 19 20 1 0 + 20 21 2 0 + 21 22 1 0 + 22 23 1 0 + 22 24 2 0 + 24 25 1 0 + 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0 + 20 22 2 0 + 22 23 1 0 + 17 23 2 0 + 22 24 1 0 + 24 25 1 0 + 24 26 1 0 + 24 27 1 0 + 12 28 2 0 + 28 29 1 0 + 9 29 2 0 + 7 30 1 0 + 30 31 2 0 + 31 32 1 0 + 5 32 2 0 +M END +> <mr_id> +4255941 + +> <SMI> +CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3ccc(Cl)c(c3)C(F)(F)F)cc2)ccn1 + +$$$$ +abc_ten + + + 35 42 0 0 1 0 999 V2000 + -1.9455 5.8387 0.0000 C 0 0 + -2.5513 4.8029 0.0000 N 0 0 + -1.8100 3.5000 0.0000 C 0 0 2 0 0 0 + -0.2400 3.5200 0.0000 C 0 0 + 0.5000 2.1800 0.0000 C 0 0 1 0 0 0 + -1.0600 2.1800 0.0000 O 0 0 + -1.8300 0.9300 0.0000 C 0 0 1 0 0 0 + -3.0300 0.9300 0.0000 C 0 0 + -2.6500 2.2500 0.0000 C 0 0 2 0 0 0 + -4.1471 2.2892 0.0000 O 0 0 + -4.7748 1.2665 0.0000 C 0 0 + -0.9800 -0.7800 0.0000 N 0 0 + -2.1300 -1.4600 0.0000 C 0 0 + -3.3200 -0.7600 0.0000 C 0 0 + -4.5500 -1.4800 0.0000 C 0 0 + -4.5800 -2.7700 0.0000 C 0 0 + -3.3400 -3.4700 0.0000 C 0 0 + -2.1300 -2.7900 0.0000 C 0 0 + 0.2400 -2.7700 0.0000 C 0 0 + 1.4300 -3.4700 0.0000 C 0 0 + 1.7600 -4.9700 0.0000 C 0 0 + 3.2600 -5.0800 0.0000 N 0 0 + 3.8500 -3.6300 0.0000 C 0 0 + 4.9971 -3.2777 0.0000 O 0 0 + 2.6600 -2.7500 0.0000 C 0 0 + 2.6800 -1.4600 0.0000 C 0 0 + 3.7900 0.5600 0.0000 C 0 0 + 4.9600 1.2800 0.0000 C 0 0 + 4.9600 2.6300 0.0000 C 0 0 + 3.8100 3.2900 0.0000 C 0 0 + 2.6400 2.5900 0.0000 C 0 0 + 2.6400 1.2400 0.0000 C 0 0 + 1.4900 0.5400 0.0000 N 0 0 + 1.4500 -0.7600 0.0000 C 0 0 + 0.2400 -1.4400 0.0000 C 0 0 + 1 2 1 0 + 3 2 1 6 + 3 4 1 0 + 5 4 1 6 + 5 6 1 0 + 6 7 1 0 + 7 8 1 1 + 7 9 1 0 + 3 9 1 0 + 9 10 1 6 + 10 11 1 0 + 7 12 1 0 + 12 13 1 0 + 13 14 1 0 + 14 15 2 0 + 15 16 1 0 + 16 17 2 0 + 17 18 1 0 + 13 18 2 0 + 18 19 1 0 + 19 20 1 0 + 20 21 1 0 + 21 22 1 0 + 22 23 1 0 + 23 24 2 0 + 23 25 1 0 + 20 25 2 0 + 25 26 1 0 + 26 27 1 0 + 27 28 1 0 + 28 29 2 0 + 29 30 1 0 + 30 31 2 0 + 31 32 1 0 + 27 32 2 0 + 32 33 1 0 + 5 33 1 0 + 33 34 1 0 + 26 34 2 0 + 34 35 1 0 + 12 35 1 0 + 19 35 2 0 +M END +> <mr_id> +66 + +> <SMI> +CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35 + +$$$$ +abc_eleven + + + 32 35 0 0 1 0 999 V2000 + 7.1381 -2.1568 0.0000 C 0 0 + 6.0456 -2.6531 0.0000 C 0 0 + 4.7409 -1.9129 0.0000 N 0 0 + 3.6552 -2.9294 0.0000 C 0 0 + 2.1855 -2.6254 0.0000 C 0 0 + 1.7138 -1.2033 0.0000 C 0 0 + 2.5889 0.0182 0.0000 C 0 0 + 3.7889 0.0269 0.0000 O 0 0 + 1.7138 1.2033 0.0000 N 0 0 + 0.2917 0.7475 0.0000 C 0 0 + -1.0028 1.5132 0.0000 C 0 0 + -2.3155 0.7475 0.0000 C 0 0 + -2.3155 -0.7475 0.0000 C 0 0 + -3.3560 -1.3452 0.0000 F 0 0 + -1.0028 -1.5132 0.0000 C 0 0 + 0.2917 -0.7475 0.0000 C 0 0 + 4.2542 -4.2907 0.0000 C 0 0 + 3.6559 -5.3308 0.0000 C 0 0 + 5.7448 -4.1226 0.0000 C 0 0 + 6.7580 -5.2264 0.0000 C 0 0 + 6.3978 -6.3710 0.0000 O 0 0 + 8.2231 -4.9012 0.0000 N 0 0 + 9.2380 -6.0068 0.0000 C 0 0 + 10.7032 -5.6816 0.0000 C 0 0 2 0 0 0 + 11.0634 -4.5369 0.0000 O 0 0 + 11.7181 -6.7872 0.0000 C 0 0 + 13.1833 -6.4620 0.0000 N 0 0 + 14.1993 -7.5656 0.0000 C 0 0 + 15.6630 -7.2376 0.0000 C 0 0 + 16.1108 -5.8060 0.0000 O 0 0 + 15.0949 -4.7024 0.0000 C 0 0 + 13.6312 -5.0304 0.0000 C 0 0 + 1 2 1 0 + 2 3 1 0 + 3 4 1 0 + 4 5 1 0 + 5 6 2 0 + 6 7 1 0 + 7 8 2 0 + 7 9 1 0 + 9 10 1 0 + 10 11 1 0 + 11 12 2 0 + 12 13 1 0 + 13 14 1 0 + 13 15 2 0 + 15 16 1 0 + 6 16 1 0 + 10 16 2 0 + 4 17 2 0 + 17 18 1 0 + 17 19 1 0 + 2 19 2 0 + 19 20 1 0 + 20 21 2 0 + 20 22 1 0 + 22 23 1 0 + 23 24 1 0 + 24 25 1 6 + 24 26 1 0 + 26 27 1 0 + 27 28 1 0 + 28 29 1 0 + 29 30 1 0 + 30 31 1 0 + 31 32 1 0 + 27 32 1 0 +M END +> <mr_id> +4362206 + +> <SMI> +Cc1[nH]c(/C=C/2\C(=O)Nc3ccc(F)cc23)c(C)c1C(=O)NC[C@H](O)CN4CCOCC4 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/name_file.txt Sat Mar 21 12:54:40 2020 +0000 @@ -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 12:54:40 2020 +0000 @@ -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 12:54:40 2020 +0000 @@ -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 + +$$$$