Mercurial > repos > bgruening > openbabel_change_title
changeset 11:8ce2e38376b5 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"
| author | bgruening |
|---|---|
| date | Wed, 25 Mar 2020 20:38:32 +0000 |
| parents | 304324b4865d |
| children | d90097da216a |
| files | __pycache__/cheminfolib.cpython-36.pyc distance_finder.py test-data/ligands.sdf |
| diffstat | 3 files changed, 457 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/distance_finder.py Wed Mar 25 20:38:32 2020 +0000 @@ -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()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligands.sdf Wed Mar 25 20:38:32 2020 +0000 @@ -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 +$$$$ +C[C@@H](NS(C)(=O)=O)c1ccccn1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 13 13 0 0 0 0 0 0 0 0999 V2000 + 6.8559 1.7506 21.3142 C 0 0 0 0 0 0 + 7.4019 0.6872 20.3547 C 0 0 0 0 0 0 + 7.4689 1.2291 18.9518 N 0 0 0 0 0 0 + 6.4062 0.5634 17.8113 S 0 0 0 0 0 0 + 4.8453 0.8765 18.6009 C 0 0 0 0 0 0 + 6.4632 1.4005 16.6345 O 0 0 0 0 0 0 + 6.5887 -0.8668 17.7602 O 0 0 0 0 0 0 + 8.6586 -0.0013 20.8698 C 0 0 0 0 0 0 + 9.8290 0.7331 21.0631 C 0 0 0 0 0 0 + 10.9643 0.0817 21.5388 C 0 0 0 0 0 0 + 10.9072 -1.2804 21.8047 C 0 0 0 0 0 0 + 9.7156 -1.9413 21.5709 C 0 0 0 0 0 0 + 8.6053 -1.3390 21.0982 N 0 0 0 0 0 0 + 2 1 1 0 0 0 + 2 3 1 0 0 0 + 2 8 1 0 0 0 + 3 4 1 0 0 0 + 4 5 1 0 0 0 + 4 6 2 0 0 0 + 4 7 2 0 0 0 + 8 9 2 0 0 0 + 8 13 1 0 0 0 + 9 10 1 0 0 0 + 10 11 2 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 +M END +$$$$ +FC(F)(F)c1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 10 10 0 0 0 0 0 0 0 0999 V2000 + 9.6749 1.3998 21.0525 F 0 0 0 0 0 0 + 10.4122 1.5718 22.1856 C 0 0 0 0 0 0 + 10.7385 2.8940 22.2189 F 0 0 0 0 0 0 + 9.5494 1.3747 23.2216 F 0 0 0 0 0 0 + 11.6206 0.6719 22.2638 C 0 0 0 0 0 0 + 12.7782 1.0724 22.9480 C 0 0 0 0 0 0 + 13.8994 0.2427 22.9901 C 0 0 0 0 0 0 + 13.8750 -0.9970 22.3527 C 0 0 0 0 0 0 + 12.7278 -1.4119 21.6796 C 0 0 0 0 0 0 + 11.6049 -0.5838 21.6354 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 2 4 1 0 0 0 + 2 5 1 0 0 0 + 5 6 2 0 0 0 + 5 10 1 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 + 8 9 1 0 0 0 + 9 10 2 0 0 0 +M END +$$$$ +O=[SH](=O)c1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 9 9 0 0 0 0 0 0 0 0999 V2000 + 13.5834 1.0389 23.2971 O 0 0 0 0 0 0 + 12.4089 1.7539 22.8402 S 0 0 0 0 0 0 + 11.1134 1.5953 23.4682 O 0 0 0 0 0 0 + 12.7957 3.4745 22.8588 C 0 0 0 0 0 0 + 13.0347 4.1328 21.6517 C 0 0 0 0 0 0 + 13.3512 5.4908 21.6741 C 0 0 0 0 0 0 + 13.4284 6.1723 22.8914 C 0 0 0 0 0 0 + 13.1905 5.5006 24.0928 C 0 0 0 0 0 0 + 12.8736 4.1434 24.0815 C 0 0 0 0 0 0 + 1 2 2 0 0 0 + 2 3 2 0 0 0 + 2 4 1 0 0 0 + 4 5 2 0 0 0 + 4 9 1 0 0 0 + 5 6 1 0 0 0 + 6 7 2 0 0 0 + 7 8 1 0 0 0 + 8 9 2 0 0 0 +M END +$$$$ +CSCCNC(=O)c1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 13 13 0 0 0 0 0 0 0 0999 V2000 + 5.5458 -1.4150 18.8612 C 0 0 0 0 0 0 + 5.7667 0.2529 18.1959 S 0 0 0 0 0 0 + 7.4715 0.5847 18.7876 C 0 0 0 0 0 0 + 7.5534 0.7884 20.3036 C 0 0 0 0 0 0 + 8.9454 1.0042 20.7146 N 0 0 0 0 0 0 + 9.6402 -0.1322 20.8514 C 0 0 0 0 0 0 + 9.3233 -1.2490 20.4452 O 0 0 0 0 0 0 + 10.9406 -0.0002 21.5911 C 0 0 0 0 0 0 + 11.2868 1.2512 22.1206 C 0 0 0 0 0 0 + 12.4999 1.4280 22.7900 C 0 0 0 0 0 0 + 13.3773 0.3543 22.9381 C 0 0 0 0 0 0 + 13.0426 -0.8964 22.4196 C 0 0 0 0 0 0 + 11.8294 -1.0724 21.7499 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 1 0 0 0 + 4 5 1 0 0 0 + 5 6 1 0 0 0 + 6 7 2 0 0 0 + 6 8 1 0 0 0 + 8 9 2 0 0 0 + 8 13 1 0 0 0 + 9 10 1 0 0 0 + 10 11 2 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 +M END +$$$$ +CCNS(=O)(=O)Cc1cccnc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 13 13 0 0 0 0 0 0 0 0999 V2000 + 13.3598 -1.5609 21.7877 C 0 0 0 0 0 0 + 13.7113 -0.3498 22.6305 C 0 0 0 0 0 0 + 12.7714 0.7692 22.3361 N 0 0 0 0 0 0 + 11.8062 1.1577 23.6906 S 0 0 0 0 0 0 + 10.8599 0.0665 23.8065 O 0 0 0 0 0 0 + 12.7113 1.5035 24.7620 O 0 0 0 0 0 0 + 10.9309 2.6284 23.1295 C 0 0 0 0 0 0 + 11.9375 3.7368 22.9987 C 0 0 0 0 0 0 + 12.7555 3.8614 21.8705 C 0 0 0 0 0 0 + 13.6216 4.9464 21.7613 C 0 0 0 0 0 0 + 13.6489 5.8696 22.7918 C 0 0 0 0 0 0 + 12.8858 5.7762 23.9008 N 0 0 0 0 0 0 + 12.0407 4.7242 23.9742 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 1 0 0 0 + 4 5 2 0 0 0 + 4 6 2 0 0 0 + 4 7 1 0 0 0 + 7 8 1 0 0 0 + 8 9 2 0 0 0 + 8 13 1 0 0 0 + 9 10 1 0 0 0 + 10 11 2 0 0 0 + 11 12 1 0 0 0 + 12 13 2 0 0 0 +M END +$$$$ +CCc1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 8 8 0 0 0 0 0 0 0 0999 V2000 + 9.3165 -1.3968 21.4474 C 0 0 0 0 0 0 + 10.1701 -1.9537 22.5759 C 0 0 0 0 0 0 + 11.4727 -1.2108 22.7284 C 0 0 0 0 0 0 + 11.5710 -0.1198 23.6025 C 0 0 0 0 0 0 + 12.7795 0.5633 23.7497 C 0 0 0 0 0 0 + 13.8989 0.1675 23.0199 C 0 0 0 0 0 0 + 13.8083 -0.9074 22.1374 C 0 0 0 0 0 0 + 12.6006 -1.5917 21.9895 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 2 0 0 0 + 3 8 1 0 0 0 + 4 5 1 0 0 0 + 5 6 2 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 +M END +$$$$ +CS(=O)(=O)NCCN1CCCC1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 12 12 0 0 0 0 0 0 0 0999 V2000 + 6.8490 0.5139 18.2625 C 0 0 0 0 0 0 + 7.3129 0.1623 19.9428 S 0 0 0 0 0 0 + 7.4343 1.3973 20.6804 O 0 0 0 0 0 0 + 6.5548 -0.9612 20.4458 O 0 0 0 0 0 0 + 8.9263 -0.3881 19.7641 N 0 0 0 0 0 0 + 9.5060 -0.7657 21.0831 C 0 0 0 0 0 0 + 10.8140 -0.0093 21.3638 C 0 0 0 0 0 0 + 11.5742 -0.6154 22.5359 N 0 0 0 0 0 0 + 11.4738 0.2167 23.7970 C 0 0 0 0 0 0 + 12.6714 1.1335 23.7058 C 0 0 0 0 0 0 + 13.7645 0.2387 23.1560 C 0 0 0 0 0 0 + 13.0648 -0.8014 22.2945 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 2 0 0 0 + 2 4 2 0 0 0 + 2 5 1 0 0 0 + 5 6 1 0 0 0 + 6 7 1 0 0 0 + 7 8 1 0 0 0 + 8 9 1 0 0 0 + 8 12 1 0 0 0 + 9 10 1 0 0 0 + 10 11 1 0 0 0 + 11 12 1 0 0 0 +M END +$$$$ +C=Cc1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 8 8 0 0 0 0 0 0 0 0999 V2000 + 3.0012 2.5994 19.2746 C 0 0 0 0 0 0 + 3.4784 1.3846 19.5760 C 0 0 0 0 0 0 + 4.7459 0.8376 19.0724 C 0 0 0 0 0 0 + 5.0977 -0.4790 19.4008 C 0 0 0 0 0 0 + 6.2949 -1.0353 18.9390 C 0 0 0 0 0 0 + 7.1469 -0.2825 18.1324 C 0 0 0 0 0 0 + 6.7985 1.0178 17.7793 C 0 0 0 0 0 0 + 5.6004 1.5702 18.2385 C 0 0 0 0 0 0 + 1 2 2 0 0 0 + 2 3 1 0 0 0 + 3 4 2 0 0 0 + 3 8 1 0 0 0 + 4 5 1 0 0 0 + 5 6 2 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 +M END +$$$$ +CC(C)(C)c1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 10 10 0 0 0 0 0 0 0 0999 V2000 + 13.4848 4.7599 24.0453 C 0 0 0 0 0 0 + 12.5126 4.3820 22.9047 C 0 0 0 0 0 0 + 11.1564 5.0474 23.2199 C 0 0 0 0 0 0 + 13.0811 4.9891 21.6031 C 0 0 0 0 0 0 + 12.3310 2.8640 22.7263 C 0 0 0 0 0 0 + 13.0824 1.9208 23.4483 C 0 0 0 0 0 0 + 12.9272 0.5461 23.2348 C 0 0 0 0 0 0 + 12.0121 0.0832 22.2967 C 0 0 0 0 0 0 + 11.2426 0.9922 21.5790 C 0 0 0 0 0 0 + 11.3986 2.3657 21.7948 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 2 4 1 0 0 0 + 2 5 1 0 0 0 + 5 6 2 0 0 0 + 5 10 1 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 + 8 9 1 0 0 0 + 9 10 2 0 0 0 +M END +$$$$ +CCN(C)C(=O)c1ccccc1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 12 12 0 0 0 0 0 0 0 0999 V2000 + 10.6306 -0.4318 24.2468 C 0 0 0 0 0 0 + 11.2738 -0.2591 22.8777 C 0 0 0 0 0 0 + 11.5027 1.1477 22.5523 N 0 0 0 0 0 0 + 10.6408 1.7231 21.5282 C 0 0 0 0 0 0 + 12.6021 1.7847 23.1411 C 0 0 0 0 0 0 + 13.4087 1.1762 23.8483 O 0 0 0 0 0 0 + 12.8518 3.2389 22.9240 C 0 0 0 0 0 0 + 12.7404 3.8481 21.6696 C 0 0 0 0 0 0 + 12.9990 5.2139 21.5196 C 0 0 0 0 0 0 + 13.3123 5.9914 22.6330 C 0 0 0 0 0 0 + 13.3606 5.4074 23.8976 C 0 0 0 0 0 0 + 13.1331 4.0370 24.0436 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 1 0 0 0 + 3 5 1 0 0 0 + 5 6 2 0 0 0 + 5 7 1 0 0 0 + 7 8 2 0 0 0 + 7 12 1 0 0 0 + 8 9 1 0 0 0 + 9 10 2 0 0 0 + 10 11 1 0 0 0 + 11 12 2 0 0 0 +M END +$$$$ +CNC(=O)c1cccc(CCNS(C)(=O)=O)c1 + rDOCK(R) 3D +libRbt.so/2013.1/901 2013/11/27 + 17 17 0 0 0 0 0 0 0 0999 V2000 + 10.0019 1.6672 21.8593 C 0 0 0 0 0 0 + 8.7487 1.5971 21.1244 N 0 0 0 0 0 0 + 8.6290 0.5212 20.3389 C 0 0 0 0 0 0 + 9.4567 -0.3639 20.1329 O 0 0 0 0 0 0 + 7.3235 0.4378 19.6088 C 0 0 0 0 0 0 + 7.1514 -0.5242 18.6092 C 0 0 0 0 0 0 + 5.9627 -0.5677 17.8790 C 0 0 0 0 0 0 + 4.9453 0.3559 18.1379 C 0 0 0 0 0 0 + 5.0962 1.3237 19.1419 C 0 0 0 0 0 0 + 3.9963 2.3284 19.4060 C 0 0 0 0 0 0 + 3.7241 2.6438 20.8872 C 0 0 0 0 0 0 + 2.6087 3.6063 21.0810 N 0 0 0 0 0 0 + 1.3263 3.1043 22.0447 S 0 0 0 0 0 0 + 0.5403 1.9194 20.9788 C 0 0 0 0 0 0 + 1.8577 2.3935 23.1858 O 0 0 0 0 0 0 + 0.4357 4.2308 22.2210 O 0 0 0 0 0 0 + 6.2789 1.3264 19.8924 C 0 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 2 0 0 0 + 3 5 1 0 0 0 + 5 6 2 0 0 0 + 5 17 1 0 0 0 + 6 7 1 0 0 0 + 7 8 2 0 0 0 + 8 9 1 0 0 0 + 9 10 1 0 0 0 + 9 17 2 0 0 0 + 10 11 1 0 0 0 + 11 12 1 0 0 0 + 12 13 1 0 0 0 + 13 14 1 0 0 0 + 13 15 2 0 0 0 + 13 16 2 0 0 0 +M END +$$$$