Révision fd33bfdb modules/isolated.py
| b/modules/isolated.py | ||
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new mol object and the energies of its conformers. |
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run_isolated: directs the execution of functions to achieve the goal |
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""" |
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import os |
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import logging |
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import numpy as np |
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return np.array([res[1] for res in results]) |
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def prep_run(inp_file, mol: Chem.rdchem.Mol, exemplars): |
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from shutil import copy |
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# Checking if 'isolated' directory already exists and if so backing it up. |
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dir_name = 'isolated' |
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bak_num = 0 |
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while dir_name in os.listdir("."):
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bak_num += 1 |
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dir_name = dir_name.split(".")[0]+f".bak{bak_num}"
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if bak_num > 0: |
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os.rename('isolated', dir_name)
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logger.warning("'isolated' directory already present. Moved former "
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f"directory to {dir_name}")
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os.mkdir('isolated')
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# Creating |
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for i, conf in enumerate(exemplars): |
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os.mkdir(f'isolated/conf_{i}')
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copy(inp_file, f'isolated/conf_{i}/')
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Chem.MolToXYZFile(mol, f'isolated/conf_{i}/coord.xyz', confId=conf)
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def run_isolated(inp_vars): |
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"""Directs the execution of functions to obtain the conformers to adsorb |
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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']) |
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if inp_vars['min_confs']: |
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confs, confs_ener = mmff_opt_confs(confs) |
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rmsd_mtx = get_rmsd(confs) |
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confs = clustering(rmsd_mtx) |
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exemplars = clustering(rmsd_mtx) |
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prep_run(inp_vars['isol_inp_file'], confs, exemplars) |
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# run dft |
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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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if 'energy' in inp_vars['cluster_magns']: |
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if inp_vars['min_confs']: |
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confs, confs_eners = mmff_opt_confs(confs) |
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else: |
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confs_eners = mmff_opt_confs(confs, max_iters=0) |
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# clustering2() |
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# if 'energy' in inp_vars['cluster_magns']: |
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