# HG changeset patch # User bgruening # Date 1584800819 14400 # Node ID eed751918a20a172d72242995435a10bd7c22701 # Parent f924a172829113a33d43724e62bfa8ac26d27040 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty" diff -r f924a1728291 -r eed751918a20 __pycache__/cheminfolib.cpython-36.pyc Binary file __pycache__/cheminfolib.cpython-36.pyc has changed 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() 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 @@ - + to metadata value. @@ -11,11 +11,14 @@ --infile '${infile}' --key '${key}' --outfile '${outfile}' + $random ]]> + @@ -26,6 +29,16 @@ + + + + + + + + + + +4358263 + +> +Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2 + +$$$$ +abc_eleven + OpenBabel03212013422D + + 32 35 0 0 1 0 0 0 0 0999 V2000 + 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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 +> (1) +65.93051459,169.99861208,-59.68475000 + +> (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 + +> (1) +NC(=NO)NCCc1ccc(S(N)(=O)=O)cc1 + +> (1) +1.41352e+07 + +> (1) +/data/dnb02/galaxy_db/job_working_directory/007/399/7399639/working + +> (1) +rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $) + +> (1) +libRbt.so (2013.1, Build901 2013/11/27) + +> (1) +/usr/local/tools/_conda/envs/__rdock@2013.1-0/share/rdock-2013.1-1/data/scripts/dock.prm + +> (1) +receptor.prm + +> (1) +-30.3434 + +> (1) +-15.8664 + +> (1) +1 + +> (1) 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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 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