| Previous changeset 9:f924a1728291 (2019-08-22) Next changeset 11:49d21d05f77c (2020-03-25) |
|
Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty" |
|
modified:
change_title_to_metadata_value.py change_title_to_metadata_value.xml ob_filter.py |
|
added:
__pycache__/cheminfolib.cpython-36.pyc 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 |
| b |
| diff -r f924a1728291 -r eed751918a20 __pycache__/cheminfolib.cpython-36.pyc |
| b |
| Binary file __pycache__/cheminfolib.cpython-36.pyc has changed |
| b |
| diff -r f924a1728291 -r eed751918a20 change_title_to_metadata_value.py --- 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() |
| b |
| diff -r f924a1728291 -r eed751918a20 change_title_to_metadata_value.xml --- 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[ |
| b |
| diff -r f924a1728291 -r eed751918a20 ob_filter.py --- a/ob_filter.py Thu Aug 22 10:28:24 2019 -0400 +++ b/ob_filter.py Sat Mar 21 10:26:59 2020 -0400 |
| b |
| @@ -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. |
| b |
| diff -r f924a1728291 -r eed751918a20 test-data/filterd_by_name.sdf --- /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 + 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 + +$$$$ |
| b |
| diff -r f924a1728291 -r eed751918a20 test-data/ligands_with_title.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligands_with_title.sdf Sat Mar 21 10:26:59 2020 -0400 |
| [ |
| b'@@ -0,0 +1,759 @@\n+abc_one\r\n+\r\n+\r\n+ 26 30 0 0 0 0 999 V2000\r\n+ -8.6396 0.9568 0.0000 O 0 0\r\n+ -7.6023 1.5602 0.0000 C 0 0\r\n+ -7.6071 3.0602 0.0000 C 0 0\r\n+ -6.3104 3.8143 0.0000 C 0 0\r\n+ -5.0090 3.0685 0.0000 C 0 0\r\n+ -5.0040 1.5682 0.0000 C 0 0\r\n+ -6.3008 0.8143 0.0000 C 0 0\r\n+ -3.7006 0.8244 0.0000 C 0 0\r\n+ -3.7006 -0.6045 0.0000 N 0 0\r\n+ -2.4915 -1.3190 0.0000 C 0 0\r\n+ -2.5059 -2.8197 0.0000 N 0 0\r\n+ -1.2156 -3.5847 0.0000 C 0 0\r\n+ -1.2329 -5.0846 0.0000 C 0 0\r\n+ -2.5404 -5.8196 0.0000 O 0 0\r\n+ -3.8308 -5.0547 0.0000 C 0 0\r\n+ -3.8135 -3.5548 0.0000 C 0 0\r\n+ -1.2274 -0.6045 0.0000 C 0 0\r\n+ 0.0000 -1.3190 0.0000 O 0 0\r\n+ 1.2274 -0.6045 0.0000 C 0 0\r\n+ 2.4732 -1.3190 0.0000 N 0 0\r\n+ 3.7372 -0.6045 0.0000 C 0 0\r\n+ 3.7372 0.8244 0.0000 C 0 0\r\n+ 2.4732 1.5389 0.0000 C 0 0\r\n+ 1.2274 0.8244 0.0000 C 0 0\r\n+ -1.2274 0.8244 0.0000 C 0 0\r\n+ -2.4915 1.5389 0.0000 N 0 0\r\n+ 1 2 1 0\r\n+ 2 3 1 0\r\n+ 3 4 2 0\r\n+ 4 5 1 0\r\n+ 5 6 2 0\r\n+ 6 7 1 0\r\n+ 2 7 2 0\r\n+ 6 8 1 0\r\n+ 8 9 1 0\r\n+ 9 10 2 0\r\n+ 10 11 1 0\r\n+ 11 12 1 0\r\n+ 12 13 1 0\r\n+ 13 14 1 0\r\n+ 14 15 1 0\r\n+ 15 16 1 0\r\n+ 11 16 1 0\r\n+ 10 17 1 0\r\n+ 17 18 1 0\r\n+ 18 19 1 0\r\n+ 19 20 2 0\r\n+ 20 21 1 0\r\n+ 21 22 2 0\r\n+ 22 23 1 0\r\n+ 23 24 2 0\r\n+ 19 24 1 0\r\n+ 24 25 1 0\r\n+ 17 25 2 0\r\n+ 25 26 1 0\r\n+ 8 26 2 0\r\n+M END\r\n+> <mr_id>\r\n+4358263\r\n+\r\n+> <SMI>\r\n+Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2\r\n+\r\n+$$$$\r\n+abc_two\r\n+\r\n+\r\n+ 43 51 0 0 1 0 999 V2000\r\n+ -4.7204 3.3431 0.0000 C 0 0\r\n+ -4.1471 2.2890 0.0000 O 0 0\r\n+ -2.6500 2.2500 0.0000 C 0 0 2 0 0 0\r\n+ -1.8100 3.5000 0.0000 C 0 0 1 0 0 0\r\n+ -0.2400 3.5200 0.0000 C 0 0\r\n+ 0.5000 2.1800 0.0000 C 0 0 1 0 0 0\r\n+ -1.0600 2.1800 0.0000 O 0 0\r\n+ -1.8300 0.9300 0.0000 C 0 0 1 0 0 0\r\n+ -3.0300 0.9300 0.0000 C 0 0\r\n+ -0.9800 -0.7800 0.0000 N 0 0\r\n+ -2.1300 -1.4600 0.0000 C 0 0\r\n+ -3.3200 -0.7600 0.0000 C 0 0\r\n+ -4.5500 -1.4800 0.0000 C 0 0\r\n+ -4.5800 -2.7700 0.0000 C 0 0\r\n+ -3.3400 -3.4700 0.0000 C 0 0\r\n+ -2.1300 -2.7900 0.0000 C 0 0\r\n+ 0.2400 -2.7700 0.0000 C 0 0\r\n+ 1.4300 -3.4700 0.0000 C 0 0\r\n+ 1.7600 -4.9700 0.0000 C 0 0\r\n+ 3.2600 -5.0800 0.0000 N 0 0\r\n+ 3.8500 -3.6300 0.0000 C 0 0\r\n+ 4.9971 -3.2777 0.0000 O 0 0\r\n+ 2.6600 -2.7500 0.0000 C 0 0\r\n+ 2.6800 -1.4600 0.0000 C 0 0\r\n+ 3.7900 0.5600 0.0000 C 0 0\r\n+ 4.9600 1.2800 0.0000 C 0 0\r\n+ 4.9600 2.6300 0.0000 C 0 0\r\n+ 3.8100 3.2900 0.0000 C 0 0\r\n+ 2.6400 2.5900 0.0000 C 0 0\r\n+ 2.6400 1.2400 0.0000 C 0 0\r\n+ 1.4900 0.5400 0.0000 N 0 0\r\n+ 1.4500 -0.7600 0.0000 C 0 0\r\n+ 0.2400 -1.4400 0.0000 C 0 0\r\n+ -2.5511 4.8030 0.0000 N 0 0\r\n+ -1.9442 5.8382 0.0000 C 0 0\r\n+ -4.0519 4.8135 0.0000 C 0 0\r\n+ -4.6588 3.7783 0.0000 O 0 0\r\n+ -4.7941 6.1180 0.0000 C 0 0\r\n+ -6.2940 6.1306 0.0000 C 0 0\r\n+ -7.0331 7.4359 0.0000 C 0 0\r\n+ -6.2722 8.7286 0.0000 C 0 0\r\n+ -4.7723 8.7160 0.0000 C 0 0\r\n+ -4.0332 7.4108 0.0000 C 0 0\r\n+ 1 2 1 0\r\n+ 3 2 1 6\r\n+ 3 4 1 0\r\n+ 4 5 1 0\r\n+ 6 5 1 6\r\n+ 6 7 1 0\r\n+ 7 8 1 0\r\n+ 3 8 1 0\r\n+ 8 9 1 1\r\n+ 8 10 1 0\r\n+ 10 11 1 0\r\n+ 11 12 1 0\r\n+ 12 13 2 0\r\n+ 13 14 1 0\r\n+ 14 15 2 0\r\n+ 15 16 1 0\r\n+ 11 16 2 0\r\n+ 16 17 1 0\r\n+ 17 18 1 0\r\n+ 18 19 1 0\r\n+ 19 20 1 0\r\n+ 20 21 1 0\r\n+ 21 22 2 0\r\n+ 21 23 1 0\r\n+ 18 23 2 '..b' 0.9300 0.0000 C 0 0\r\n+ -2.6500 2.2500 0.0000 C 0 0 2 0 0 0\r\n+ -4.1471 2.2892 0.0000 O 0 0\r\n+ -4.7748 1.2665 0.0000 C 0 0\r\n+ -0.9800 -0.7800 0.0000 N 0 0\r\n+ -2.1300 -1.4600 0.0000 C 0 0\r\n+ -3.3200 -0.7600 0.0000 C 0 0\r\n+ -4.5500 -1.4800 0.0000 C 0 0\r\n+ -4.5800 -2.7700 0.0000 C 0 0\r\n+ -3.3400 -3.4700 0.0000 C 0 0\r\n+ -2.1300 -2.7900 0.0000 C 0 0\r\n+ 0.2400 -2.7700 0.0000 C 0 0\r\n+ 1.4300 -3.4700 0.0000 C 0 0\r\n+ 1.7600 -4.9700 0.0000 C 0 0\r\n+ 3.2600 -5.0800 0.0000 N 0 0\r\n+ 3.8500 -3.6300 0.0000 C 0 0\r\n+ 4.9971 -3.2777 0.0000 O 0 0\r\n+ 2.6600 -2.7500 0.0000 C 0 0\r\n+ 2.6800 -1.4600 0.0000 C 0 0\r\n+ 3.7900 0.5600 0.0000 C 0 0\r\n+ 4.9600 1.2800 0.0000 C 0 0\r\n+ 4.9600 2.6300 0.0000 C 0 0\r\n+ 3.8100 3.2900 0.0000 C 0 0\r\n+ 2.6400 2.5900 0.0000 C 0 0\r\n+ 2.6400 1.2400 0.0000 C 0 0\r\n+ 1.4900 0.5400 0.0000 N 0 0\r\n+ 1.4500 -0.7600 0.0000 C 0 0\r\n+ 0.2400 -1.4400 0.0000 C 0 0\r\n+ 1 2 1 0\r\n+ 3 2 1 6\r\n+ 3 4 1 0\r\n+ 5 4 1 6\r\n+ 5 6 1 0\r\n+ 6 7 1 0\r\n+ 7 8 1 1\r\n+ 7 9 1 0\r\n+ 3 9 1 0\r\n+ 9 10 1 6\r\n+ 10 11 1 0\r\n+ 7 12 1 0\r\n+ 12 13 1 0\r\n+ 13 14 1 0\r\n+ 14 15 2 0\r\n+ 15 16 1 0\r\n+ 16 17 2 0\r\n+ 17 18 1 0\r\n+ 13 18 2 0\r\n+ 18 19 1 0\r\n+ 19 20 1 0\r\n+ 20 21 1 0\r\n+ 21 22 1 0\r\n+ 22 23 1 0\r\n+ 23 24 2 0\r\n+ 23 25 1 0\r\n+ 20 25 2 0\r\n+ 25 26 1 0\r\n+ 26 27 1 0\r\n+ 27 28 1 0\r\n+ 28 29 2 0\r\n+ 29 30 1 0\r\n+ 30 31 2 0\r\n+ 31 32 1 0\r\n+ 27 32 2 0\r\n+ 32 33 1 0\r\n+ 5 33 1 0\r\n+ 33 34 1 0\r\n+ 26 34 2 0\r\n+ 34 35 1 0\r\n+ 12 35 1 0\r\n+ 19 35 2 0\r\n+M END\r\n+> <mr_id>\r\n+66\r\n+\r\n+> <SMI>\r\n+CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35\r\n+\r\n+$$$$\r\n+abc_eleven\r\n+\r\n+\r\n+ 32 35 0 0 1 0 999 V2000\r\n+ 7.1381 -2.1568 0.0000 C 0 0\r\n+ 6.0456 -2.6531 0.0000 C 0 0\r\n+ 4.7409 -1.9129 0.0000 N 0 0\r\n+ 3.6552 -2.9294 0.0000 C 0 0\r\n+ 2.1855 -2.6254 0.0000 C 0 0\r\n+ 1.7138 -1.2033 0.0000 C 0 0\r\n+ 2.5889 0.0182 0.0000 C 0 0\r\n+ 3.7889 0.0269 0.0000 O 0 0\r\n+ 1.7138 1.2033 0.0000 N 0 0\r\n+ 0.2917 0.7475 0.0000 C 0 0\r\n+ -1.0028 1.5132 0.0000 C 0 0\r\n+ -2.3155 0.7475 0.0000 C 0 0\r\n+ -2.3155 -0.7475 0.0000 C 0 0\r\n+ -3.3560 -1.3452 0.0000 F 0 0\r\n+ -1.0028 -1.5132 0.0000 C 0 0\r\n+ 0.2917 -0.7475 0.0000 C 0 0\r\n+ 4.2542 -4.2907 0.0000 C 0 0\r\n+ 3.6559 -5.3308 0.0000 C 0 0\r\n+ 5.7448 -4.1226 0.0000 C 0 0\r\n+ 6.7580 -5.2264 0.0000 C 0 0\r\n+ 6.3978 -6.3710 0.0000 O 0 0\r\n+ 8.2231 -4.9012 0.0000 N 0 0\r\n+ 9.2380 -6.0068 0.0000 C 0 0\r\n+ 10.7032 -5.6816 0.0000 C 0 0 2 0 0 0\r\n+ 11.0634 -4.5369 0.0000 O 0 0\r\n+ 11.7181 -6.7872 0.0000 C 0 0\r\n+ 13.1833 -6.4620 0.0000 N 0 0\r\n+ 14.1993 -7.5656 0.0000 C 0 0\r\n+ 15.6630 -7.2376 0.0000 C 0 0\r\n+ 16.1108 -5.8060 0.0000 O 0 0\r\n+ 15.0949 -4.7024 0.0000 C 0 0\r\n+ 13.6312 -5.0304 0.0000 C 0 0\r\n+ 1 2 1 0\r\n+ 2 3 1 0\r\n+ 3 4 1 0\r\n+ 4 5 1 0\r\n+ 5 6 2 0\r\n+ 6 7 1 0\r\n+ 7 8 2 0\r\n+ 7 9 1 0\r\n+ 9 10 1 0\r\n+ 10 11 1 0\r\n+ 11 12 2 0\r\n+ 12 13 1 0\r\n+ 13 14 1 0\r\n+ 13 15 2 0\r\n+ 15 16 1 0\r\n+ 6 16 1 0\r\n+ 10 16 2 0\r\n+ 4 17 2 0\r\n+ 17 18 1 0\r\n+ 17 19 1 0\r\n+ 2 19 2 0\r\n+ 19 20 1 0\r\n+ 20 21 2 0\r\n+ 20 22 1 0\r\n+ 22 23 1 0\r\n+ 23 24 1 0\r\n+ 24 25 1 6\r\n+ 24 26 1 0\r\n+ 26 27 1 0\r\n+ 27 28 1 0\r\n+ 28 29 1 0\r\n+ 29 30 1 0\r\n+ 30 31 1 0\r\n+ 31 32 1 0\r\n+ 27 32 1 0\r\n+M END\r\n+> <mr_id>\r\n+4362206\r\n+\r\n+> <SMI>\r\n+Cc1[nH]c(/C=C/2\\C(=O)Nc3ccc(F)cc23)c(C)c1C(=O)NC[C@H](O)CN4CCOCC4\r\n+\r\n+$$$$\r\n' |
| b |
| diff -r f924a1728291 -r eed751918a20 test-data/name_file.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/name_file.txt Sat Mar 21 10:26:59 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +abc_one +abc_eleven |
| b |
| diff -r f924a1728291 -r eed751918a20 test-data/transfs.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transfs.sdf Sat Mar 21 10:26:59 2020 -0400 |
| b |
| @@ -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 + +$$$$ |
| b |
| diff -r f924a1728291 -r eed751918a20 test-data/transfs_changed_name.sdf --- /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 |
| b |
| @@ -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 + +$$$$ |