Added conformer generator example workflow #71
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| @<TRIPOS>MOLECULE | ||
| A:6JWL | ||
| 72 75 1 0 1 | ||
| SMALL | ||
| NO_CHARGES | ||
| **** | ||
| Generated from the CSD | ||
|
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| @<TRIPOS>ATOM | ||
| 1 C13 -47.0936 -3.8091 -13.4034 C.3 1 YY31101 0.0000 | ||
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| 3 C12 -45.9115 -3.0021 -15.2755 C.3 1 YY31101 0.0000 | ||
| 4 C11 -46.7746 -1.4560 -13.7005 C.3 1 YY31101 0.0000 | ||
| 5 C10 -47.4726 -0.3070 -14.4355 C.3 1 YY31101 0.0000 | ||
| 6 N1 -48.9046 -0.5000 -14.3475 N.pl3 1 YY31101 0.0000 | ||
| 7 C28 -49.4387 -1.1750 -13.1824 C.3 1 YY31101 0.0000 | ||
| 8 C3 -50.4137 1.1840 -15.2065 C.ar 1 YY31101 0.0000 | ||
| 9 C4 -51.2787 1.6321 -16.1655 C.ar 1 YY31101 0.0000 | ||
| 10 O1 -51.9027 2.8521 -16.0285 O.3 1 YY31101 0.0000 | ||
| 11 C14 -51.6957 3.4241 -14.7895 C.3 1 YY31101 0.0000 | ||
| 12 C2 -49.8087 -0.0340 -15.3855 C.ar 1 YY31101 0.0000 | ||
| 13 C1 -50.0827 -0.7970 -16.5066 C.ar 1 YY31101 0.0000 | ||
| 14 N -49.4027 -2.0741 -16.6096 N.am 1 YY31101 0.0000 | ||
| 15 C7 -49.6557 -3.0691 -17.6256 C.2 1 YY31101 0.0000 | ||
| 16 O -50.4457 -2.8851 -18.4616 O.2 1 YY31101 0.0000 | ||
| 17 C8 -48.8456 -4.3581 -17.5956 C.3 1 YY31101 0.0000 | ||
| 18 C9 -49.6517 -5.6372 -17.7846 C.3 1 YY31101 0.0000 | ||
| 19 C6 -50.9617 -0.3360 -17.4786 C.ar 1 YY31101 0.0000 | ||
| 20 C5 -51.5537 0.9000 -17.2826 C.ar 1 YY31101 0.0000 | ||
| 21 N3 -52.4998 1.5241 -18.1876 N.pl3 1 YY31101 0.0000 | ||
| 22 C15 -52.4578 1.3800 -19.6177 C.ar 1 YY31101 0.0000 | ||
| 23 N5 -51.5097 0.6790 -20.1647 N.ar 1 YY31101 0.0000 | ||
| 24 N4 -53.3928 1.9621 -20.3097 N.ar 1 YY31101 0.0000 | ||
| 25 C16 -53.4318 1.8691 -21.6127 C.ar 1 YY31101 0.0000 | ||
| 26 C17 -52.4518 1.1400 -22.2417 C.ar 1 YY31101 0.0000 | ||
| 27 C18 -51.4837 0.5540 -21.4637 C.ar 1 YY31101 0.0000 | ||
| 28 C19 -50.3887 -0.2730 -22.1187 C.2 1 YY31101 0.0000 | ||
| 29 C26 -49.1556 -0.6420 -21.5447 C.ar 1 YY31101 0.0000 | ||
| 30 C25 -48.5396 -0.3950 -20.3087 C.ar 1 YY31101 0.0000 | ||
| 31 C24 -47.2806 -0.9140 -20.0517 C.ar 1 YY31101 0.0000 | ||
| 32 C23 -46.6356 -1.6751 -21.0187 C.ar 1 YY31101 0.0000 | ||
| 33 C22 -47.2446 -1.9131 -22.2327 C.ar 1 YY31101 0.0000 | ||
| 34 C21 -48.5256 -1.3830 -22.4878 C.ar 1 YY31101 0.0000 | ||
| 35 N6 -49.3076 -1.4780 -23.5728 N.pl3 1 YY31101 0.0000 | ||
| 36 C27 -48.9656 -2.1931 -24.7758 C.3 1 YY31101 0.0000 | ||
| 37 C20 -50.4267 -0.8280 -23.3788 C.2 1 YY31101 0.0000 | ||
| 38 H1282 -51.2463 -0.7410 -24.0905 H 1 YY31101 0.0000 | ||
| 39 H1286 -48.6942 -2.2848 -15.9139 H 1 YY31101 0.0000 | ||
| 40 H1287 -48.3421 -4.4169 -16.6318 H 1 YY31101 0.0000 | ||
| 41 H1288 -48.1031 -4.3077 -18.3906 H 1 YY31101 0.0000 | ||
| 42 H1291 -52.4429 1.0302 -23.3252 H 1 YY31101 0.0000 | ||
| 43 H1294 -45.7035 -1.2610 -13.6727 H 1 YY31101 0.0000 | ||
| 44 H1295 -47.1597 -1.5128 -12.6834 H 1 YY31101 0.0000 | ||
| 45 H1306 -47.2682 -4.7498 -13.9236 H 1 YY31101 0.0000 | ||
| 46 H1307 -47.9158 -3.6164 -12.7159 H 1 YY31101 0.0000 | ||
| 47 H1308 -46.1605 -3.8708 -12.8453 H 1 YY31101 0.0000 | ||
| 48 H1309 -48.6222 -1.4507 -12.5166 H 1 YY31101 0.0000 | ||
| 49 H1310 -49.9709 -2.0722 -13.4949 H 1 YY31101 0.0000 | ||
| 50 H1311 -50.1243 -0.5097 -12.6599 H 1 YY31101 0.0000 | ||
| 51 H1316 -46.0900 -3.9453 -15.7897 H 1 YY31101 0.0000 | ||
| 52 H1317 -44.9823 -3.0664 -14.7114 H 1 YY31101 0.0000 | ||
| 53 H1318 -45.8375 -2.1984 -16.0066 H 1 YY31101 0.0000 | ||
| 54 H1319 -50.2092 1.7814 -14.3192 H 1 YY31101 0.0000 | ||
| 55 H1321 -50.1543 -5.6101 -18.7503 H 1 YY31101 0.0000 | ||
| 56 H1322 -48.9834 -6.4962 -17.7471 H 1 YY31101 0.0000 | ||
| 57 H1323 -50.3934 -5.7194 -16.9915 H 1 YY31101 0.0000 | ||
| 58 H1324 -52.0840 2.7638 -14.0154 H 1 YY31101 0.0000 | ||
| 59 H1325 -52.2111 4.3823 -14.7413 H 1 YY31101 0.0000 | ||
| 60 H1326 -50.6288 3.5776 -14.6342 H 1 YY31101 0.0000 | ||
| 61 H1327 -53.2358 2.0970 -17.7874 H 1 YY31101 0.0000 | ||
| 62 H1331 -49.0489 0.2024 -19.5539 H 1 YY31101 0.0000 | ||
| 63 H1332 -45.6467 -2.0845 -20.8174 H 1 YY31101 0.0000 | ||
| 64 H1335 -46.7380 -2.5080 -22.9913 H 1 YY31101 0.0000 | ||
| 65 H1336 -48.8006 -3.2432 -24.5395 H 1 YY31101 0.0000 | ||
| 66 H1337 -49.7799 -2.1062 -25.4937 H 1 YY31101 0.0000 | ||
| 67 H1338 -48.0579 -1.7703 -25.2037 H 1 YY31101 0.0000 | ||
| 68 H1342 -46.7979 -0.7258 -19.0938 H 1 YY31101 0.0000 | ||
| 69 H1343 -47.1673 -0.3019 -15.4808 H 1 YY31101 0.0000 | ||
| 70 H1344 -47.2018 0.6413 -13.9736 H 1 YY31101 0.0000 | ||
| 71 H1345 -51.1782 -0.9281 -18.3665 H 1 YY31101 0.0000 | ||
| 72 H1347 -54.2200 2.3564 -22.1846 H 1 YY31101 0.0000 | ||
| @<TRIPOS>BOND | ||
| 1 1 2 1 | ||
| 2 2 3 1 | ||
| 3 2 4 1 | ||
| 4 4 5 1 | ||
| 5 5 6 1 | ||
| 6 6 7 1 | ||
| 7 8 9 ar | ||
| 8 9 10 1 | ||
| 9 10 11 1 | ||
| 10 6 12 1 | ||
| 11 8 12 ar | ||
| 12 12 13 ar | ||
| 13 13 14 1 | ||
| 14 14 15 am | ||
| 15 15 16 2 | ||
| 16 15 17 1 | ||
| 17 17 18 1 | ||
| 18 13 19 ar | ||
| 19 9 20 ar | ||
| 20 19 20 ar | ||
| 21 20 21 1 | ||
| 22 21 22 1 | ||
| 23 22 23 ar | ||
| 24 22 24 ar | ||
| 25 24 25 ar | ||
| 26 25 26 ar | ||
| 27 23 27 ar | ||
| 28 26 27 ar | ||
| 29 27 28 1 | ||
| 30 28 29 1 | ||
| 31 29 30 ar | ||
| 32 30 31 ar | ||
| 33 31 32 ar | ||
| 34 32 33 ar | ||
| 35 29 34 ar | ||
| 36 33 34 ar | ||
| 37 34 35 1 | ||
| 38 35 36 1 | ||
| 39 28 37 2 | ||
| 40 35 37 1 | ||
| 41 37 38 1 | ||
| 42 14 39 1 | ||
| 43 17 40 1 | ||
| 44 17 41 1 | ||
| 45 26 42 1 | ||
| 46 4 43 1 | ||
| 47 4 44 1 | ||
| 48 1 45 1 | ||
| 49 1 46 1 | ||
| 50 1 47 1 | ||
| 51 7 48 1 | ||
| 52 7 49 1 | ||
| 53 7 50 1 | ||
| 54 3 51 1 | ||
| 55 3 52 1 | ||
| 56 3 53 1 | ||
| 57 8 54 1 | ||
| 58 18 55 1 | ||
| 59 18 56 1 | ||
| 60 18 57 1 | ||
| 61 11 58 1 | ||
| 62 11 59 1 | ||
| 63 11 60 1 | ||
| 64 21 61 1 | ||
| 65 30 62 1 | ||
| 66 32 63 1 | ||
| 67 33 64 1 | ||
| 68 36 65 1 | ||
| 69 36 66 1 | ||
| 70 36 67 1 | ||
| 71 31 68 1 | ||
| 72 5 69 1 | ||
| 73 5 70 1 | ||
| 74 19 71 1 | ||
| 75 25 72 1 | ||
| @<TRIPOS>SUBSTRUCTURE | ||
| 1 YY31101 1 GROUP 0 A YY3 0 | ||
| @<TRIPOS>SET | ||
| CCDC_LIGAND STATIC ATOMS | ||
| 72 1 2 3 4 5 6 7 8 9 \ | ||
| 10 11 12 13 14 15 16 17 18 19 \ | ||
| 20 21 22 23 24 25 26 27 28 29 \ | ||
| 30 31 32 33 34 35 36 37 38 39 \ | ||
| 40 41 42 43 44 45 46 47 48 49 \ | ||
| 50 51 52 53 54 55 56 57 58 59 \ | ||
| 60 61 62 63 64 65 66 67 68 69 \ | ||
| 70 71 72 |
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| #! /usr/bin/env python | ||
| ######################################################################################################################## | ||
| # | ||
| # This script can be used for any purpose without limitation subject to the | ||
| # conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx | ||
| # | ||
| # This permission notice and the following statement of attribution must be | ||
| # included in all copies or substantial portions of this script. | ||
| # | ||
| # 2024-11-22: created by the Cambridge Crystallographic Data Centre | ||
| # | ||
| ######################################################################################################################## | ||
|
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| from ccdc import conformer, descriptors, io, molecule | ||
| from ccdc.search import SubstructureSearch, SMARTSSubstructure | ||
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| def read(molecule_file: str) -> molecule: | ||
| print(f'Reading file: {molecule_file} ... ', end='') | ||
| mol_reader = io.MoleculeReader(molecule_file) | ||
| mol = mol_reader[0] | ||
| print('done.') | ||
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| return mol | ||
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| def generate_conformers(molecule: molecule, max_conformers: int = 50) -> conformer.ConformerHitList: | ||
| """ | ||
| Generate conformers for a molecule. | ||
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| :param molecule: The Molecule (ccdc Molecule object) to generate conformers for. | ||
| :param max_conformers: The maximum number of conformers to generate. | ||
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| :returns: ccdc.conformer.ConformerHitList | ||
| """ | ||
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| # Set up the ConformerGenerator | ||
| confgen = conformer.ConformerGenerator() | ||
| confgen.settings.max_conformers = max_conformers | ||
| # confgen.settings.superimpose_conformers_onto_reference = True | ||
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| # Generate conformers and assign identifiers to them before returning | ||
| conformers = confgen.generate(molecule) | ||
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| print(f'Generating conformers, maximum of {max_conformers} ... ', end='') | ||
| for i, conf in enumerate(conformers): | ||
| conf.molecule.identifier = '{}_{:04}'.format(conf.molecule.identifier, i + 1) | ||
| print(f'done, generated {len(conformers)} conformers.') | ||
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| return conformers | ||
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| def analyse(conformers: conformer.ConformerHitList) -> molecule: | ||
| """ | ||
| Perform some basic analysis of the conformers generated. | ||
| :param conformers: Conformers generated from ConfGen | ||
| :return: The best molecule of all the conformers generated. | ||
| """ | ||
| print(f'Sampling limit reached? {"Yes." if conformers.sampling_limit_reached else "No."}') | ||
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| print(f'How many rotamers had no observations? {conformers.n_rotamers_with_no_observations}.') | ||
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| most_probable_conformer = conformers[0] | ||
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| print(f'Normalised score of most probable conformer: {round(most_probable_conformer.normalised_score, 5)}.') | ||
| print(f'Most probable conformer RMSD wrt input: {round(most_probable_conformer.rmsd(), 3)}; ' | ||
| f'wrt minimised: {round(most_probable_conformer.rmsd(wrt="minimised"), 3)}.') | ||
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| print('Scores of top 10 conformers: ', end='') | ||
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| top_ten = conformers[:10] | ||
| for i in range(len(top_ten)): | ||
| if i < len(top_ten) - 1: | ||
| print(f'{round(top_ten[i].normalised_score, 3):.3f}, ', end='') | ||
| else: | ||
| print(f'{round(top_ten[i].normalised_score, 3):.3f}.') | ||
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| return most_probable_conformer.molecule | ||
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| def overlay(conformers, query: str, output_filename: str) -> None: | ||
| """ | ||
| Overlay conformers based on a SMARTS substructure pattern | ||
| :param conformers: Conformers generated from ConfGen | ||
| :param query: SMARTS pattern which the conformers will overlay on top of. | ||
| Should be consistent across all conformers, e.g. benzene ring. | ||
| """ | ||
| print('Overlaying conformers ... ', end='') | ||
| conformers_mols = [c.molecule for c in conformers] | ||
| ss_search = SubstructureSearch() | ||
| substructure = SMARTSSubstructure(query) | ||
| ss_search.add_substructure(substructure) | ||
| hits = ss_search.search(conformers_mols, max_hits_per_structure=1) | ||
| ref_ats = hits[0].match_atoms() | ||
| print('done.') | ||
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| print('Writing file superimposed ... ', end='') | ||
| with io.MoleculeWriter(output_filename) as writer: | ||
| for hit in hits: | ||
| hit_ats = hit.match_atoms() | ||
| atoms = zip(ref_ats, hit_ats) | ||
| ov = descriptors.MolecularDescriptors.Overlay(hits[0].molecule, hit.molecule, atoms) | ||
| superimposed_hit = ov.molecule | ||
| writer.write(superimposed_hit) | ||
| print('done.') | ||
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| def write_conformers_to_file(conformers: conformer.ConformerHitList, filename: str) -> None: | ||
| """ | ||
| Write conformers to a file without any addition overlaying. | ||
| :param conformers: Conformer generated from ConfGen. | ||
| :param filename: The name of the output file. | ||
| """ | ||
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| with io.MoleculeWriter(filename) as writer: | ||
| for conf in conformers: | ||
| writer.write(conf.molecule) | ||
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| if __name__ == '__main__': | ||
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| input_filename = 'AZD9291.mol2' | ||
| # Read example molecule | ||
| mol = read(input_filename) | ||
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| # Generate conformers | ||
| confs = generate_conformers(mol, 20) | ||
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| # Provide summary of analysis | ||
| analyse(confs) | ||
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| # Overlay structures based on common substructure | ||
| query = 'c1cncnc1' | ||
| output_filename = f'superimposed_{input_filename}' | ||
| overlay(confs, query, output_filename) |
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| # Conformer Demo | ||||||
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| This is a short script to generate conformers with some rudimentary analysis for a single molecule. | ||||||
| There are also options to overlay the results to view in Hermes. | ||||||
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| ### Example output showing what the user can expect to see: | ||||||
|
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| ``` | ||||||
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| Reading file: AZD9291.mol2 ... done. | ||||||
| Generating conformers, maximum of 20 ... done, generated 20 conformers. | ||||||
| Sampling limit reached? No. | ||||||
| How many rotamers had no observations? 0. | ||||||
| Normalised score of most probable conformer: 0.0. | ||||||
| Most probable conformer RMSD wrt input: 3.276; wrt minimised: 3.202. | ||||||
| Scores of top 10 conformers: 0.000, 0.000, 0.000, 0.027, 0.027, 0.027, 0.027, 0.027, 0.029, 0.029. | ||||||
| Overlaying conformers ... done. | ||||||
| Writing file superimposed ... done. | ||||||
| ``` | ||||||
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| CCDC Python API Licence required, minimum version: 3.0.15 | ||||||
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| There is an accompanying mol2 file with this script, but users may use any small molecule provided in a file format readable by our API (e.g. mol, mol2, sdf, etc) | ||||||
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| Author: Chris Ringrose - 22/11/24 | ||||||
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| For feedback or to report any issues please contact [email protected] | ||||||
|
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[markdownlint] reported by reviewdog 🐶
MD001/heading-increment Heading levels should only increment by one level at a time [Expected: h2; Actual: h3]