Révision f3004731 modules/isolated.py
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logger = logging.getLogger('DockOnSurf')
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def confs_to_mol_list(mol: Chem.rdchem.Mol): |
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"""Converts the conformers inside a rdkit mol object to a list of |
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separate mol objects. |
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@param mol: rdkit mol object containing at least one conformer. |
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@return: list of separate mol objects. |
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""" |
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return [Chem.MolFromMolBlock(Chem.MolToMolBlock(mol, confId=conf.GetId())) |
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for conf in mol.GetConformers()] |
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def remove_C_linked_Hs(mol: Chem.rdchem.Mol): |
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"""Removes hydrogen atoms bonded to a carbon atom from a rdkit mol object. |
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@param inp_vars: Calculation parameters from input file. |
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@return: |
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""" |
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from modules.formats import adapt_format |
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from modules.formats import adapt_format, confs_to_mol_list, \ |
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rdkit_mol_to_ase_atoms |
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from modules.clustering import clustering |
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from modules.calculation import run_calc |
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rmsd_mtx = get_rmsd(confs) |
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confs_moi = get_moments_of_inertia(confs) |
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exemplars = clustering(rmsd_mtx) |
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run_calc('isolated', inp_vars, confs=confs, exemplars=exemplars)
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mol_list = confs_to_mol_list(confs, exemplars) |
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ase_atms_list = [rdkit_mol_to_ase_atoms(mol) for mol in mol_list] |
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run_calc('isolated', inp_vars, ase_atms_list)
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if 'moi' in inp_vars['cluster_magns']: |
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confs_moi = get_moments_of_inertia(confs) |
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