Révision 695dcff8 modules/isolated.py
| b/modules/isolated.py | ||
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are required to be local minima, ie. setting the 'local_min' value to |
| 56 | 56 |
True, a geometry optimisation using UFF is performed. |
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""" |
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logger.debug('Generating Conformers')
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logger.debug('Generating Conformers.')
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mol = Chem.AddHs(mol) |
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Chem.EmbedMultipleConfs(mol, numConfs=num_confs, numThreads=0) |
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Chem.AlignMolConformers(mol) |
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logger.info(f'Generated {len(mol.GetConformers())} conformers')
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logger.info(f'Generated {len(mol.GetConformers())} conformers.')
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return mol |
| 65 | 65 |
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| ... | ... | |
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if mol.GetNumConformers() < init_num_confs: |
| 115 | 115 |
logger.warning(f'MMFF Geometry optimization did not comverge for at' |
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f'least one conformer. Continuing with ' |
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f'{mol.GetNumConformers()} converged conformers')
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f'{mol.GetNumConformers()} converged conformers.')
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logger.info(f'Pre-optimized conformers with MMFF.') |
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return mol, np.array([res[1] for res in results if res[0] == 0]) |
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else: |
| ... | ... | |
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from modules.clustering import clustering, get_rmsd |
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from modules.calculation import run_calc |
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logger.info('Carrying out procedures for the isolated molecule')
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logger.info('Carrying out procedures for the isolated molecule.')
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rd_mol = adapt_format('rdkit', inp_vars['molec_file'])
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confs = gen_confs(rd_mol, inp_vars['num_conformers']) |
| 139 | 139 |
if inp_vars['min_confs']: |
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