Mercurial > repos > bgruening > openbabel_remsmall
changeset 10:0c95b0f51114 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"
| author | bgruening |
|---|---|
| date | Wed, 25 Mar 2020 16:46:28 -0400 |
| parents | ac9567d307a2 |
| children | e38d865baa37 |
| files | change_title_to_metadata_value.py distance_finder.py ob_filter.py test-data/filterd_by_name.sdf test-data/ligands.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, 1760 insertions(+), 1 deletions(-) [+] |
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--- a/change_title_to_metadata_value.py Thu Aug 22 10:27:02 2019 -0400 +++ b/change_title_to_metadata_value.py Wed Mar 25 16:46:28 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()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/distance_finder.py Wed Mar 25 16:46:28 2020 -0400 @@ -0,0 +1,109 @@ +# Reports distances of ligands to reference points. An example input for the points is: +# +# 5.655 1.497 18.223 +# 1.494 -8.367 18.574 +# 13.034 6.306 25.232 +# +# Data can be space or tab separated but must contain 3 and only 3 numbers for the x, y and z coordinates +# +# That would encode 3 points. +# Each record in the SDF input is read and the closest heavy atom to each of the reference points is recorded as +# a property named distance1 where the numeric part is the index (starting from 1) of the points (in that example +# there would be properties for distance1, distance2 and distance3. + +import argparse, os, sys, math +from openbabel import pybel + + + +def log(*args, **kwargs): + """Log output to STDERR + """ + print(*args, file=sys.stderr, ** kwargs) + + +def execute(ligands_sdf, points_file, outfile): + """ + :param ligands_sdf: A SDF with the 3D molecules to test + :param points_file: A file with the points to consider. + :param outfile: The name of the file for the SDF output + :return: + """ + + + points = [] + + # read the points + with open(points_file, 'r') as f: + for line in f.readlines(): + line.strip() + if line: + p = line.split() + if len(p) == 3: + points.append((float(p[0]), float(p[1]), float(p[2]))) + log("Read points",p) + continue + log("Failed to read line:", line) + log('Found', len(points), 'atom points') + + sdf_writer = pybel.Outputfile("sdf", outfile, overwrite=True) + + count = 0 + for mol in pybel.readfile("sdf", ligands_sdf): + count += 1 + if count % 50000 == 0: + log('Processed', count) + + try: + # print("Processing mol", mol.title) + + clone = pybel.Molecule(mol) + clone.removeh() + + coords = [] + for atom in clone.atoms: + coords.append(atom.coords) + + p = 0 + for point in points: + p += 1 + distances = [] + for i in coords: + # calculates distance based on cartesian coordinates + distance = math.sqrt((point[0] - i[0])**2 + (point[1] - i[1])**2 + (point[2] - i[2])**2) + distances.append(distance) + # log("distance:", distance) + min_distance = min(distances) + # log('Min:', min_distance) + # log(count, p, min_distance) + + mol.data['distance' + str(p)] = min_distance + + sdf_writer.write(mol) + + except Exception as e: + log('Failed to handle molecule: '+ str(e)) + continue + + sdf_writer.close() + log('Wrote', count, 'molecules') + + +def main(): + global work_dir + + parser = argparse.ArgumentParser(description='XChem distances - measure distances to particular points') + + parser.add_argument('-i', '--input', help="SDF containing the 3D molecules to score)") + parser.add_argument('-p', '--points', help="PDB format file with atoms") + parser.add_argument('-o', '--outfile', default='output.sdf', help="File name for results") + + + args = parser.parse_args() + log("XChem distances args: ", args) + + execute(args.input, args.points, args.outfile) + + +if __name__ == "__main__": + main()
--- a/ob_filter.py Thu Aug 22 10:27:02 2019 -0400 +++ b/ob_filter.py Wed Mar 25 16:46:28 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 Wed Mar 25 16:46:28 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 + +$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligands.sdf Wed Mar 25 16:46:28 2020 -0400 @@ -0,0 +1,348 @@ +C[C@H](NS(C)(=O)=O)c1ccccn1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 13 13 0 0 0 0 0 0 0 0999 V2000 + 13.1106 0.7550 23.2143 C 0 0 0 0 0 0 + 12.0087 1.7547 22.8361 C 0 0 0 0 0 0 + 11.4071 1.4261 21.5334 N 0 0 0 0 0 0 + 9.9388 0.8337 21.6338 S 0 0 0 0 0 0 + 9.0411 2.3499 21.9038 C 0 0 0 0 0 0 + 9.3678 0.3273 20.3892 O 0 0 0 0 0 0 + 9.6367 0.0497 22.8298 O 0 0 0 0 0 0 + 12.5588 3.1798 22.7273 C 0 0 0 0 0 0 + 12.8091 3.9103 23.8920 C 0 0 0 0 0 0 + 13.2507 5.2279 23.7909 C 0 0 0 0 0 0 + 13.4398 5.7854 22.5337 C 0 0 0 0 0 0 + 13.1881 4.9943 21.4282 C 0 0 0 0 0 0 + 12.7627 3.7170 21.4945 N 0 0 0 0 0 0 + 2 8 1 0 0 0 + 2 3 1 0 0 0 + 2 1 1 0 0 0 + 3 4 1 0 0 0 + 4 5 1 0 0 0 + 4 6 2 0 0 0 + 4 7 2 0 0 0 + 8 9 2 0 0 0 + 8 13 1 0 0 0 + 9 10 1 0 0 0 + 10 11 2 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 +M END +$$$$ +C[C@@H](NS(C)(=O)=O)c1ccccn1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 13 13 0 0 0 0 0 0 0 0999 V2000 + 6.8559 1.7506 21.3142 C 0 0 0 0 0 0 + 7.4019 0.6872 20.3547 C 0 0 0 0 0 0 + 7.4689 1.2291 18.9518 N 0 0 0 0 0 0 + 6.4062 0.5634 17.8113 S 0 0 0 0 0 0 + 4.8453 0.8765 18.6009 C 0 0 0 0 0 0 + 6.4632 1.4005 16.6345 O 0 0 0 0 0 0 + 6.5887 -0.8668 17.7602 O 0 0 0 0 0 0 + 8.6586 -0.0013 20.8698 C 0 0 0 0 0 0 + 9.8290 0.7331 21.0631 C 0 0 0 0 0 0 + 10.9643 0.0817 21.5388 C 0 0 0 0 0 0 + 10.9072 -1.2804 21.8047 C 0 0 0 0 0 0 + 9.7156 -1.9413 21.5709 C 0 0 0 0 0 0 + 8.6053 -1.3390 21.0982 N 0 0 0 0 0 0 + 2 1 1 0 0 0 + 2 3 1 0 0 0 + 2 8 1 0 0 0 + 3 4 1 0 0 0 + 4 5 1 0 0 0 + 4 6 2 0 0 0 + 4 7 2 0 0 0 + 8 9 2 0 0 0 + 8 13 1 0 0 0 + 9 10 1 0 0 0 + 10 11 2 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 +M END +$$$$ +FC(F)(F)c1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 10 10 0 0 0 0 0 0 0 0999 V2000 + 9.6749 1.3998 21.0525 F 0 0 0 0 0 0 + 10.4122 1.5718 22.1856 C 0 0 0 0 0 0 + 10.7385 2.8940 22.2189 F 0 0 0 0 0 0 + 9.5494 1.3747 23.2216 F 0 0 0 0 0 0 + 11.6206 0.6719 22.2638 C 0 0 0 0 0 0 + 12.7782 1.0724 22.9480 C 0 0 0 0 0 0 + 13.8994 0.2427 22.9901 C 0 0 0 0 0 0 + 13.8750 -0.9970 22.3527 C 0 0 0 0 0 0 + 12.7278 -1.4119 21.6796 C 0 0 0 0 0 0 + 11.6049 -0.5838 21.6354 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 2 4 1 0 0 0 + 2 5 1 0 0 0 + 5 6 2 0 0 0 + 5 10 1 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 + 8 9 1 0 0 0 + 9 10 2 0 0 0 +M END +$$$$ +O=[SH](=O)c1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 9 9 0 0 0 0 0 0 0 0999 V2000 + 13.5834 1.0389 23.2971 O 0 0 0 0 0 0 + 12.4089 1.7539 22.8402 S 0 0 0 0 0 0 + 11.1134 1.5953 23.4682 O 0 0 0 0 0 0 + 12.7957 3.4745 22.8588 C 0 0 0 0 0 0 + 13.0347 4.1328 21.6517 C 0 0 0 0 0 0 + 13.3512 5.4908 21.6741 C 0 0 0 0 0 0 + 13.4284 6.1723 22.8914 C 0 0 0 0 0 0 + 13.1905 5.5006 24.0928 C 0 0 0 0 0 0 + 12.8736 4.1434 24.0815 C 0 0 0 0 0 0 + 1 2 2 0 0 0 + 2 3 2 0 0 0 + 2 4 1 0 0 0 + 4 5 2 0 0 0 + 4 9 1 0 0 0 + 5 6 1 0 0 0 + 6 7 2 0 0 0 + 7 8 1 0 0 0 + 8 9 2 0 0 0 +M END +$$$$ +CSCCNC(=O)c1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 13 13 0 0 0 0 0 0 0 0999 V2000 + 5.5458 -1.4150 18.8612 C 0 0 0 0 0 0 + 5.7667 0.2529 18.1959 S 0 0 0 0 0 0 + 7.4715 0.5847 18.7876 C 0 0 0 0 0 0 + 7.5534 0.7884 20.3036 C 0 0 0 0 0 0 + 8.9454 1.0042 20.7146 N 0 0 0 0 0 0 + 9.6402 -0.1322 20.8514 C 0 0 0 0 0 0 + 9.3233 -1.2490 20.4452 O 0 0 0 0 0 0 + 10.9406 -0.0002 21.5911 C 0 0 0 0 0 0 + 11.2868 1.2512 22.1206 C 0 0 0 0 0 0 + 12.4999 1.4280 22.7900 C 0 0 0 0 0 0 + 13.3773 0.3543 22.9381 C 0 0 0 0 0 0 + 13.0426 -0.8964 22.4196 C 0 0 0 0 0 0 + 11.8294 -1.0724 21.7499 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 1 0 0 0 + 4 5 1 0 0 0 + 5 6 1 0 0 0 + 6 7 2 0 0 0 + 6 8 1 0 0 0 + 8 9 2 0 0 0 + 8 13 1 0 0 0 + 9 10 1 0 0 0 + 10 11 2 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 +M END +$$$$ +CCNS(=O)(=O)Cc1cccnc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 13 13 0 0 0 0 0 0 0 0999 V2000 + 13.3598 -1.5609 21.7877 C 0 0 0 0 0 0 + 13.7113 -0.3498 22.6305 C 0 0 0 0 0 0 + 12.7714 0.7692 22.3361 N 0 0 0 0 0 0 + 11.8062 1.1577 23.6906 S 0 0 0 0 0 0 + 10.8599 0.0665 23.8065 O 0 0 0 0 0 0 + 12.7113 1.5035 24.7620 O 0 0 0 0 0 0 + 10.9309 2.6284 23.1295 C 0 0 0 0 0 0 + 11.9375 3.7368 22.9987 C 0 0 0 0 0 0 + 12.7555 3.8614 21.8705 C 0 0 0 0 0 0 + 13.6216 4.9464 21.7613 C 0 0 0 0 0 0 + 13.6489 5.8696 22.7918 C 0 0 0 0 0 0 + 12.8858 5.7762 23.9008 N 0 0 0 0 0 0 + 12.0407 4.7242 23.9742 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 1 0 0 0 + 4 5 2 0 0 0 + 4 6 2 0 0 0 + 4 7 1 0 0 0 + 7 8 1 0 0 0 + 8 9 2 0 0 0 + 8 13 1 0 0 0 + 9 10 1 0 0 0 + 10 11 2 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 +M END +$$$$ +CCc1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 8 8 0 0 0 0 0 0 0 0999 V2000 + 9.3165 -1.3968 21.4474 C 0 0 0 0 0 0 + 10.1701 -1.9537 22.5759 C 0 0 0 0 0 0 + 11.4727 -1.2108 22.7284 C 0 0 0 0 0 0 + 11.5710 -0.1198 23.6025 C 0 0 0 0 0 0 + 12.7795 0.5633 23.7497 C 0 0 0 0 0 0 + 13.8989 0.1675 23.0199 C 0 0 0 0 0 0 + 13.8083 -0.9074 22.1374 C 0 0 0 0 0 0 + 12.6006 -1.5917 21.9895 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 2 0 0 0 + 3 8 1 0 0 0 + 4 5 1 0 0 0 + 5 6 2 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 +M END +$$$$ +CS(=O)(=O)NCCN1CCCC1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 12 12 0 0 0 0 0 0 0 0999 V2000 + 6.8490 0.5139 18.2625 C 0 0 0 0 0 0 + 7.3129 0.1623 19.9428 S 0 0 0 0 0 0 + 7.4343 1.3973 20.6804 O 0 0 0 0 0 0 + 6.5548 -0.9612 20.4458 O 0 0 0 0 0 0 + 8.9263 -0.3881 19.7641 N 0 0 0 0 0 0 + 9.5060 -0.7657 21.0831 C 0 0 0 0 0 0 + 10.8140 -0.0093 21.3638 C 0 0 0 0 0 0 + 11.5742 -0.6154 22.5359 N 0 0 0 0 0 0 + 11.4738 0.2167 23.7970 C 0 0 0 0 0 0 + 12.6714 1.1335 23.7058 C 0 0 0 0 0 0 + 13.7645 0.2387 23.1560 C 0 0 0 0 0 0 + 13.0648 -0.8014 22.2945 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 2 0 0 0 + 2 4 2 0 0 0 + 2 5 1 0 0 0 + 5 6 1 0 0 0 + 6 7 1 0 0 0 + 7 8 1 0 0 0 + 8 9 1 0 0 0 + 8 12 1 0 0 0 + 9 10 1 0 0 0 + 10 11 1 0 0 0 + 11 12 1 0 0 0 +M END +$$$$ +C=Cc1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 8 8 0 0 0 0 0 0 0 0999 V2000 + 3.0012 2.5994 19.2746 C 0 0 0 0 0 0 + 3.4784 1.3846 19.5760 C 0 0 0 0 0 0 + 4.7459 0.8376 19.0724 C 0 0 0 0 0 0 + 5.0977 -0.4790 19.4008 C 0 0 0 0 0 0 + 6.2949 -1.0353 18.9390 C 0 0 0 0 0 0 + 7.1469 -0.2825 18.1324 C 0 0 0 0 0 0 + 6.7985 1.0178 17.7793 C 0 0 0 0 0 0 + 5.6004 1.5702 18.2385 C 0 0 0 0 0 0 + 1 2 2 0 0 0 + 2 3 1 0 0 0 + 3 4 2 0 0 0 + 3 8 1 0 0 0 + 4 5 1 0 0 0 + 5 6 2 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 +M END +$$$$ +CC(C)(C)c1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 10 10 0 0 0 0 0 0 0 0999 V2000 + 13.4848 4.7599 24.0453 C 0 0 0 0 0 0 + 12.5126 4.3820 22.9047 C 0 0 0 0 0 0 + 11.1564 5.0474 23.2199 C 0 0 0 0 0 0 + 13.0811 4.9891 21.6031 C 0 0 0 0 0 0 + 12.3310 2.8640 22.7263 C 0 0 0 0 0 0 + 13.0824 1.9208 23.4483 C 0 0 0 0 0 0 + 12.9272 0.5461 23.2348 C 0 0 0 0 0 0 + 12.0121 0.0832 22.2967 C 0 0 0 0 0 0 + 11.2426 0.9922 21.5790 C 0 0 0 0 0 0 + 11.3986 2.3657 21.7948 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 2 4 1 0 0 0 + 2 5 1 0 0 0 + 5 6 2 0 0 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligands_with_title.sdf Wed Mar 25 16:46:28 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 + -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 + 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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 Wed Mar 25 16:46:28 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 Wed Mar 25 16:46:28 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 Wed Mar 25 16:46:28 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 + +$$$$